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First version of the host model

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Files changed (45) hide show
  1. checkpoint-1000/config.json +33 -0
  2. checkpoint-1000/optimizer.pt +3 -0
  3. checkpoint-1000/pytorch_model.bin +3 -0
  4. checkpoint-1000/scheduler.pt +3 -0
  5. checkpoint-1000/trainer_state.json +28 -0
  6. checkpoint-1000/training_args.bin +3 -0
  7. checkpoint-2000/config.json +33 -0
  8. checkpoint-2000/optimizer.pt +3 -0
  9. checkpoint-2000/pytorch_model.bin +3 -0
  10. checkpoint-2000/scheduler.pt +3 -0
  11. checkpoint-2000/trainer_state.json +40 -0
  12. checkpoint-2000/training_args.bin +3 -0
  13. checkpoint-3000/config.json +33 -0
  14. checkpoint-3000/optimizer.pt +3 -0
  15. checkpoint-3000/pytorch_model.bin +3 -0
  16. checkpoint-3000/scheduler.pt +3 -0
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  18. checkpoint-3000/training_args.bin +3 -0
  19. checkpoint-4000/config.json +33 -0
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  21. checkpoint-4000/pytorch_model.bin +3 -0
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  23. checkpoint-4000/trainer_state.json +64 -0
  24. checkpoint-4000/training_args.bin +3 -0
  25. checkpoint-5000/config.json +33 -0
  26. checkpoint-5000/optimizer.pt +3 -0
  27. checkpoint-5000/pytorch_model.bin +3 -0
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  29. checkpoint-5000/trainer_state.json +76 -0
  30. checkpoint-5000/training_args.bin +3 -0
  31. checkpoint-6000/config.json +33 -0
  32. checkpoint-6000/optimizer.pt +3 -0
  33. checkpoint-6000/pytorch_model.bin +3 -0
  34. checkpoint-6000/scheduler.pt +3 -0
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  36. checkpoint-6000/training_args.bin +3 -0
  37. config.json +33 -0
  38. eval_results.txt +7 -0
  39. pytorch_model.bin +3 -0
  40. special_tokens_map.json +1 -0
  41. test_predictions.txt +10379 -0
  42. test_results.txt +6 -0
  43. tokenizer_config.json +1 -0
  44. training_args.bin +3 -0
  45. vocab.txt +0 -0
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38
+ with O
39
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40
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41
+ salinity O
42
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43
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44
+ / O
45
+ L O
46
+ ) O
47
+ and O
48
+ filtered O
49
+ autoclaved O
50
+ seawater O
51
+ medium O
52
+ ( O
53
+ FAS O
54
+ ) O
55
+ supplemented O
56
+ with O
57
+ 0 O
58
+ . O
59
+ 5 O
60
+ g O
61
+ / O
62
+ L O
63
+ of O
64
+ each O
65
+ of O
66
+ the O
67
+ following O
68
+ polymers O
69
+ : O
70
+ agarose O
71
+ , O
72
+ chitin O
73
+ , O
74
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75
+ starch O
76
+ ( O
77
+ FAS O
78
+ - O
79
+ POL O
80
+ ) O
81
+ . O
82
+
83
+ Genomic O
84
+ DNA O
85
+ was O
86
+ PCR O
87
+ amplified O
88
+ with O
89
+ primers O
90
+ 515F O
91
+ modified O
92
+ and O
93
+ 926R65 O
94
+ targeting O
95
+ the O
96
+ V4 O
97
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98
+ V5 O
99
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100
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101
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102
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103
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104
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105
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106
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107
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108
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109
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110
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111
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112
+ sequencing O
113
+ ( O
114
+ TAS O
115
+ ) O
116
+ protocol66 O
117
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118
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119
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120
+ on O
121
+ the O
122
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123
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124
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125
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126
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127
+ times O
128
+ over O
129
+ both O
130
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131
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132
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133
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134
+ 110 O
135
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136
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137
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138
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139
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140
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141
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142
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143
+ the O
144
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145
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146
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147
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148
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149
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150
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151
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152
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153
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154
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155
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156
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157
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158
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159
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160
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161
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162
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163
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164
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165
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166
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167
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168
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169
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170
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171
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172
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173
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174
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175
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176
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177
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178
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179
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180
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181
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182
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183
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184
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185
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186
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187
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188
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189
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190
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191
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192
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193
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194
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195
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196
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197
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198
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199
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200
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201
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202
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203
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204
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205
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206
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207
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208
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209
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210
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211
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212
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213
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214
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215
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216
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217
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218
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219
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220
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221
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222
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223
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224
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225
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226
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227
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228
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229
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230
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231
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232
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233
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234
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235
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236
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237
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238
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239
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240
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241
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242
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243
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244
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245
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246
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247
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248
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249
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250
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251
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252
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253
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254
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255
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256
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257
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258
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259
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260
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261
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262
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263
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264
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265
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266
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267
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268
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269
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270
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271
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272
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273
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274
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275
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276
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277
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278
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279
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280
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281
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282
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283
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284
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285
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286
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287
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288
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289
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290
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291
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292
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293
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294
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295
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296
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297
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298
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299
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300
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301
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302
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303
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304
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305
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306
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307
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308
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309
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310
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311
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312
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313
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314
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315
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316
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317
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318
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319
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320
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321
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322
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323
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324
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325
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326
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327
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328
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329
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330
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331
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332
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333
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334
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335
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336
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337
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338
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339
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340
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341
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342
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345
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346
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347
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348
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349
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350
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351
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352
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353
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354
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355
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356
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357
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359
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360
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361
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362
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363
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364
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365
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366
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368
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369
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370
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371
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374
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375
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376
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380
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381
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382
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383
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384
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385
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386
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387
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388
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389
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390
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391
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392
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393
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394
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395
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396
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397
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398
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399
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400
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401
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402
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403
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404
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405
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406
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407
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408
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409
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410
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411
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412
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413
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414
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415
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416
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417
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418
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419
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420
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421
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422
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423
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424
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425
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427
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428
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429
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430
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431
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432
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433
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434
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435
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436
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437
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438
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439
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440
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441
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442
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444
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445
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446
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447
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448
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449
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450
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452
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453
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454
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455
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458
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475
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481
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488
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489
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494
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495
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496
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497
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498
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499
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500
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501
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502
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503
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504
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506
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507
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508
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509
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510
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512
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515
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517
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527
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528
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529
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530
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531
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532
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541
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550
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551
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555
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556
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557
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558
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560
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564
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566
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590
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616
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619
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621
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623
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629
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631
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647
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651
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652
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653
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654
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655
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657
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1025
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1026
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1306
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1367
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1368
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1381
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1384
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1385
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1386
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1388
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1389
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1390
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1391
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1393
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1394
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1395
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1396
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1397
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1398
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1399
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1400
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1401
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1402
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1403
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1412
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1419
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1420
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1421
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1422
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1423
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1424
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1425
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1427
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1428
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1430
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1431
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1432
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1433
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1434
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1436
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1437
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1446
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1447
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1448
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1449
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1451
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1455
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1456
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1457
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1458
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1459
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1460
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1461
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1483
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1493
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1511
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1512
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1513
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1514
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1516
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1517
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1518
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1519
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1520
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1522
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1523
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1524
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1525
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1526
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1528
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1529
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1534
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1535
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1536
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1537
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1538
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1539
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1540
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1542
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1543
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1544
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1545
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1546
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1549
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1616
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1660
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1661
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1696
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1709
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1711
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1712
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1715
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1716
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1717
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1718
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1719
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1720
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1721
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1722
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1724
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1729
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1759
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1760
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1761
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1799
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1813
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1814
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1816
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1817
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1820
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1822
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1885
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1894
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1897
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1901
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1902
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1903
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1904
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1905
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1921
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1922
+ number O
1923
+ of O
1924
+ reads O
1925
+ , O
1926
+ read O
1927
+ length O
1928
+ , O
1929
+ dataset O
1930
+ size O
1931
+ ) O
1932
+ and O
1933
+ % O
1934
+ of O
1935
+ Chloroflexi O
1936
+ assigned O
1937
+ 16S O
1938
+ rRNA O
1939
+ reads O
1940
+ identified O
1941
+ in O
1942
+ all O
1943
+ metagenomes O
1944
+ used O
1945
+ for O
1946
+ assembly O
1947
+ are O
1948
+ provided O
1949
+ in O
1950
+ Supplementary O
1951
+ TableS1 O
1952
+ . O
1953
+
1954
+ Materials O
1955
+ and O
1956
+ methods O
1957
+ Reactors O
1958
+ operation O
1959
+ and O
1960
+ sampling O
1961
+ Anaerobic O
1962
+ sludge O
1963
+ was O
1964
+ obtained O
1965
+ from O
1966
+ a O
1967
+ well O
1968
+ - O
1969
+ performing O
1970
+ anaerobic O
1971
+ lab O
1972
+ - O
1973
+ scale O
1974
+ CSTR O
1975
+ reactor O
1976
+ that O
1977
+ had O
1978
+ not O
1979
+ been O
1980
+ exposed O
1981
+ to O
1982
+ any O
1983
+ antibiotics O
1984
+ . O
1985
+
1986
+ The O
1987
+ chimneys O
1988
+ are O
1989
+ porous O
1990
+ structures O
1991
+ , O
1992
+ mainly O
1993
+ composed O
1994
+ of O
1995
+ brucite O
1996
+ [ O
1997
+ Mg O
1998
+ ( O
1999
+ OH O
2000
+ ) O
2001
+ 2 O
2002
+ ] O
2003
+ , O
2004
+ aragonite O
2005
+ and O
2006
+ calcite O
2007
+ ( O
2008
+ CaCO3 O
2009
+ ) O
2010
+ and O
2011
+ magnesium O
2012
+ carbonates O
2013
+ ( O
2014
+ MgCO3 O
2015
+ ) O
2016
+ ( O
2017
+ Pisapia O
2018
+ et O
2019
+ al O
2020
+ . O
2021
+ , O
2022
+ 2017 O
2023
+ ) O
2024
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2025
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2026
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2027
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2028
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2029
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2030
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2031
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2032
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2033
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2034
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2035
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2036
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2037
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2038
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2039
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2040
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2041
+ primer O
2042
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2043
+ , O
2044
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2045
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2046
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2047
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2048
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2049
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2050
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2051
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2052
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2053
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2054
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2055
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2056
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2057
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2058
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2059
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2060
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2061
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2062
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2063
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2064
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2065
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2066
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2067
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2068
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2069
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2070
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2071
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2072
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2073
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2074
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2075
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2076
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2077
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2078
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2079
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2080
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2081
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2082
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2083
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2084
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2085
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2086
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2087
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2088
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2089
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2090
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2091
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2092
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2093
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2095
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2096
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2097
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2098
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2099
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2100
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2101
+ , O
2102
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2103
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2104
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2105
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2106
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2107
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2108
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2109
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2111
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2112
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2113
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2114
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2115
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2116
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2117
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2119
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2120
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2132
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2135
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2137
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2139
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2142
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2146
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2148
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2149
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2150
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2151
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2152
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2153
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2154
+
2155
+ Maltose O
2156
+ , O
2157
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2158
+ , O
2159
+ fructose O
2160
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2161
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2162
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2163
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2164
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2165
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2169
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2170
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2182
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2186
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2188
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2198
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2199
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2200
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2201
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2202
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2203
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2204
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2205
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2207
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2216
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2223
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2227
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2228
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2229
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2240
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2241
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2242
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2243
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2245
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2246
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2247
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2248
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2249
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2250
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2251
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2252
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2253
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2254
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2255
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2256
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2257
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2258
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2259
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2260
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2261
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2262
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2265
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2266
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2267
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2268
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2269
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2270
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2271
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2272
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2273
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2274
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2275
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2276
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2283
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2284
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2286
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2287
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2288
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2290
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2292
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2295
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2296
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2302
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2303
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2307
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2310
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2311
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2312
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2313
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2314
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2315
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2316
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2317
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2321
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2322
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2323
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2324
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2326
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2344
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2345
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2346
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2347
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2348
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2349
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2350
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2351
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2352
+ DNA O
2353
+ from O
2354
+ Geobacter O
2355
+ sulfurreducens O
2356
+ and O
2357
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2358
+ Methanosarcina O
2359
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2360
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2361
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2362
+ . O
2363
+
2364
+ Biogas O
2365
+ production O
2366
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2367
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2368
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2369
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2370
+ ( O
2371
+ CH4 O
2372
+ , O
2373
+ CO2 O
2374
+ , O
2375
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2376
+ , O
2377
+ H2 O
2378
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2379
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2380
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2381
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2382
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2383
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2384
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2385
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2386
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2387
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2388
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2389
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2390
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2391
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2392
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2393
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2394
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2395
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2396
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2397
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2398
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2399
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2400
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2401
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2402
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2403
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2404
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2405
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2406
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2407
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2409
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2410
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2411
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2412
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2413
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2414
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2415
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2416
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2417
+ Twelve O
2418
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2419
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2420
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2421
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2422
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2423
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2424
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2425
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2426
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2427
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2428
+ , O
2429
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2430
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2431
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2432
+ , O
2433
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2434
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2435
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2436
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2437
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2438
+ the O
2439
+ AnMBR O
2440
+ process O
2441
+ were O
2442
+ analyzed O
2443
+ . O
2444
+
2445
+ Subsurface O
2446
+ sediments O
2447
+ of O
2448
+ all O
2449
+ zones O
2450
+ ( O
2451
+ > O
2452
+ 2m O
2453
+ below O
2454
+ sea O
2455
+ floor O
2456
+ ) O
2457
+ were O
2458
+ obtained O
2459
+ by O
2460
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2461
+ corer O
2462
+ . O
2463
+
2464
+ In O
2465
+ order O
2466
+ to O
2467
+ quantify O
2468
+ neustonic O
2469
+ plastic O
2470
+ debris O
2471
+ , O
2472
+ a O
2473
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2474
+ trawl O
2475
+ ( O
2476
+ 91 O
2477
+ ) O
2478
+ provided O
2479
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2480
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2481
+ Algalita O
2482
+ Marine O
2483
+ Research O
2484
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2485
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2486
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2487
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2488
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2489
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2490
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2491
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2492
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2493
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2494
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2495
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2496
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2497
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2498
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2499
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2500
+ . O
2501
+ 5 O
2502
+ - O
2503
+ m O
2504
+ - O
2505
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2506
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2507
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2508
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2509
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2510
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2511
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2512
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2513
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2514
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2515
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2516
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2517
+ towed O
2518
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2519
+ the O
2520
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2521
+ for O
2522
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2523
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2524
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2525
+ a O
2526
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2527
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2528
+ 1 O
2529
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2530
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2531
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2532
+
2533
+ Briefly O
2534
+ , O
2535
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2536
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2537
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2538
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2539
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2540
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2541
+ set O
2542
+ : O
2543
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2544
+ forward O
2545
+ ( O
2546
+ 5 O
2547
+ TCGTCGGCAG O
2548
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2549
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2550
+ CAGCCTACGG O
2551
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2552
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2553
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2554
+ and O
2555
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2556
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2557
+ ( O
2558
+ 5 O
2559
+ GTCTCGTGGG O
2560
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2561
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2562
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2563
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2564
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2565
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2566
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2567
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2568
+ KAPA O
2569
+ HiFi O
2570
+ Hotstart O
2571
+ Readymix O
2572
+ ( O
2573
+ Kapa O
2574
+ Biosystems O
2575
+ , O
2576
+ Wilmington O
2577
+ , O
2578
+ MA O
2579
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2582
+ ) O
2583
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2584
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2585
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2586
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2591
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2592
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2593
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2595
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2598
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2599
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2600
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2601
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2602
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2603
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2604
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2605
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2606
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2607
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2608
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2609
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2610
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2611
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2612
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2613
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2614
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2615
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2616
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2617
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2618
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2619
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2620
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2621
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2622
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2623
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2624
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2625
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2626
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2627
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2628
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2629
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2630
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2631
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2632
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2633
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2634
+ Environmental O
2635
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2636
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2637
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2638
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2639
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2640
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2641
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2642
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2643
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2644
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2645
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2646
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2647
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2648
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2649
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2650
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2651
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2652
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2653
+ MoBio O
2654
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2655
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2656
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2657
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2658
+ The O
2659
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2660
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2661
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2662
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2664
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2670
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2673
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2675
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2676
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2677
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2678
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2679
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2680
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2681
+ of O
2682
+ length O
2683
+ 150bp O
2684
+ ) O
2685
+ . O
2686
+
2687
+ Microbiome O
2688
+ Sampling O
2689
+ and O
2690
+ DNA O
2691
+ Extraction O
2692
+ The O
2693
+ mouse B
2694
+ fecal O
2695
+ microbiome O
2696
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2697
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2698
+ by O
2699
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2700
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2701
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2702
+ pellets O
2703
+ upon O
2704
+ defecation O
2705
+ using O
2706
+ sterile O
2707
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2708
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2709
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2710
+ / O
2711
+ DNA O
2712
+ - O
2713
+ / O
2714
+ RNAse O
2715
+ - O
2716
+ / O
2717
+ DNAse O
2718
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2719
+ free O
2720
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2721
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2722
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2723
+
2724
+ Inoculation O
2725
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2726
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2727
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2728
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2729
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2730
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2731
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2732
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2733
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2734
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2735
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2736
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2737
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2738
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2739
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2740
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2741
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2742
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2743
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2744
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2745
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2746
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2747
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2748
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2749
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2750
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2751
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2752
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2753
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2754
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2755
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2756
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2757
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2758
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2759
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2760
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2761
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2762
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2763
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2764
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2765
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2766
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2768
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2769
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2770
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2771
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2772
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2773
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2775
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2779
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2781
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2782
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2783
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2784
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2785
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2786
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2787
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2788
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2789
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2790
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2792
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2793
+ FastDNA O
2794
+ SPIN O
2795
+ kit O
2796
+ for O
2797
+ soil O
2798
+ ( O
2799
+ MP O
2800
+ Biomedicals O
2801
+ , O
2802
+ Illkirch O
2803
+ , O
2804
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2805
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2806
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2807
+
2808
+ The O
2809
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2810
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2811
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2812
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2813
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2814
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2815
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2816
+ according O
2817
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2818
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2819
+ 16S O
2820
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2821
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2822
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2823
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2824
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2825
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2826
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2827
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2828
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2829
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2830
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2831
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2832
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2833
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2834
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2835
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2836
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2837
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2838
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2839
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2840
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2841
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2842
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2843
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2844
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2845
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2846
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2847
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2848
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2849
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2850
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2851
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2852
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2853
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2854
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2855
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2856
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2857
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2858
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2859
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2860
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2861
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2862
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2864
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2865
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2866
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2867
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2868
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2869
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2870
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2871
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2872
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2874
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2877
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2878
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2879
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2880
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2886
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2888
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2889
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2890
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2892
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2896
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2897
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2899
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2900
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2901
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2902
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2903
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2905
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2908
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2912
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2914
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2917
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2918
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2919
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2922
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2923
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2925
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2926
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2927
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2928
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2929
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2930
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2931
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2932
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2933
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2936
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2938
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2940
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2942
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2943
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2944
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2945
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2950
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2952
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2954
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2955
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2956
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2957
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2958
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2959
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2961
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2962
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2969
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2971
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2990
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2991
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2993
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3039
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3065
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3067
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3069
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3070
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3084
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3088
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3089
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3090
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3092
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3093
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3097
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3101
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3110
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3137
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3141
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3144
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3162
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3175
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3191
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3207
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3210
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3211
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3213
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3214
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3215
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3217
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3218
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3219
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3220
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3221
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3222
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3223
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3224
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3225
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3226
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3227
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3228
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3229
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3230
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3231
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3232
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3233
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3234
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3235
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3237
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3238
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3239
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3240
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3241
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3242
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3243
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3244
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3248
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3250
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3251
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3252
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3259
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3260
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3262
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3266
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3267
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3268
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3269
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3270
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3278
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3279
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3280
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3281
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3284
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3285
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3286
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3287
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3288
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3289
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3290
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3291
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3292
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3293
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3294
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3295
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3297
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3298
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3299
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3300
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3301
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3302
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3304
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3306
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3321
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3330
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3332
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3334
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3349
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3350
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3351
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3352
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3354
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3356
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3360
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3361
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3362
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3364
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3369
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3371
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3372
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3374
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3376
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3377
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3384
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3386
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3388
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3390
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3391
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3392
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3393
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3395
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3397
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3398
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3402
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3404
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3407
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3412
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3415
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3419
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3421
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3422
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3423
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3424
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3425
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3426
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3427
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3428
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3429
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3430
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3432
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3433
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3434
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3435
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3436
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3437
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3439
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3442
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3445
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3446
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3447
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3448
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3449
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3450
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3451
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3452
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3453
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3455
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3456
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3457
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3458
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3459
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3460
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3461
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3462
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3463
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3464
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3465
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3466
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3467
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3468
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3469
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3470
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3473
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3474
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3476
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3477
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3478
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3479
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3480
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3481
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3482
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3483
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3484
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3486
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3487
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3488
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3489
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3490
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3491
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3492
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3493
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3494
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3495
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3496
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3497
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3498
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3499
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3500
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3501
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3502
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3503
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3504
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3505
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3506
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3507
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3508
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3509
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3510
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3511
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3512
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3513
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3514
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3515
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3516
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3517
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3518
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3519
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3520
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3521
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3522
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3523
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3524
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3525
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3526
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3527
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3528
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3529
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3530
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3531
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3532
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3533
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3534
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3535
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3536
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3537
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3538
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3539
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3540
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3541
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3542
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3543
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3544
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3545
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3546
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3547
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3548
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3549
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3550
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3551
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3552
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3553
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3554
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3555
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3556
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3557
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3558
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3559
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3560
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3561
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3562
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3564
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3565
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3566
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3567
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3568
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3569
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3570
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3571
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3572
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3573
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3574
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3575
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3576
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3577
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3578
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3579
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3580
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3581
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3582
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3583
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3584
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3585
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3586
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3587
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3588
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3589
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3590
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3591
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3592
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3593
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3594
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3595
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3596
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3597
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3598
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3599
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3600
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3601
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3602
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3603
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3604
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3605
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3606
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3607
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3608
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3609
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3610
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3611
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3612
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3613
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3614
+ Extraction O
3615
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3616
+ for O
3617
+ Soil O
3618
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3619
+ MP O
3620
+ Biomedicals O
3621
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3622
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3623
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3624
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3625
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3626
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3627
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3628
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3629
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3630
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3631
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3632
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3633
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3634
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3635
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3636
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3637
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3638
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3639
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3640
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3641
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3642
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3643
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3644
+ conducted O
3645
+ at O
3646
+ Fujia O
3647
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3648
+ farm O
3649
+ , O
3650
+ Changtu O
3651
+ County O
3652
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3653
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3654
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3655
+ Liaoning O
3656
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3657
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3658
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3659
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3660
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3661
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3662
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3663
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3664
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3665
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3666
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3667
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3668
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3669
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3670
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3671
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3672
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3673
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3674
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3675
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3676
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3677
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3678
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3679
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3680
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3681
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3682
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3683
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3684
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3685
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3686
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3687
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3688
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3689
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3690
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3691
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3692
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3693
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3694
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3695
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3696
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3697
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3698
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3699
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3700
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3701
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3702
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3703
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3704
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3705
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3706
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3707
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3708
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3709
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3710
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3711
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3712
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3713
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3714
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3715
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3716
+ of O
3717
+ heterogeneous O
3718
+ disorders O
3719
+ defined O
3720
+ by O
3721
+ characteristic O
3722
+ lymph O
3723
+ node O
3724
+ histopathology O
3725
+ . O
3726
+
3727
+ Infants B
3728
+ reported O
3729
+ to O
3730
+ have O
3731
+ never O
3732
+ been O
3733
+ introduced O
3734
+ to O
3735
+ formula O
3736
+ and O
3737
+ to O
3738
+ be O
3739
+ breastfed O
3740
+ were O
3741
+ considered O
3742
+ to O
3743
+ be O
3744
+ exclusively O
3745
+ breastfed O
3746
+ , O
3747
+ while O
3748
+ those O
3749
+ who O
3750
+ were O
3751
+ ever O
3752
+ breastfed O
3753
+ and O
3754
+ ever O
3755
+ formula O
3756
+ - O
3757
+ fed O
3758
+ were O
3759
+ considered O
3760
+ to O
3761
+ be O
3762
+ fed O
3763
+ with O
3764
+ a O
3765
+ combination O
3766
+ of O
3767
+ breast O
3768
+ milk O
3769
+ and O
3770
+ formula O
3771
+ regardless O
3772
+ of O
3773
+ whether O
3774
+ or O
3775
+ not O
3776
+ the O
3777
+ infant B
3778
+ was O
3779
+ still O
3780
+ breastfed O
3781
+ at O
3782
+ the O
3783
+ time O
3784
+ of O
3785
+ stool O
3786
+ collection O
3787
+ . O
3788
+
3789
+ Most O
3790
+ animals B
3791
+ consumed O
3792
+ the O
3793
+ entire O
3794
+ daily O
3795
+ volume O
3796
+ of O
3797
+ DSSwater O
3798
+ for O
3799
+ the O
3800
+ treatment O
3801
+ duration O
3802
+ , O
3803
+ however O
3804
+ , O
3805
+ some O
3806
+ animals B
3807
+ failed O
3808
+ to O
3809
+ ingest O
3810
+ the O
3811
+ prescribed O
3812
+ dose O
3813
+ and O
3814
+ some O
3815
+ animals B
3816
+ consumed O
3817
+ each O
3818
+ dose O
3819
+ more O
3820
+ rapidly O
3821
+ than O
3822
+ others O
3823
+ , O
3824
+ which O
3825
+ may O
3826
+ be O
3827
+ reflected O
3828
+ in O
3829
+ some O
3830
+ of O
3831
+ the O
3832
+ animal O
3833
+ - O
3834
+ to O
3835
+ - O
3836
+ animal O
3837
+ variability O
3838
+ seen O
3839
+ in O
3840
+ our O
3841
+ measures O
3842
+ of O
3843
+ colitis O
3844
+ . O
3845
+
3846
+ Methods O
3847
+ Animals O
3848
+ and O
3849
+ Sample O
3850
+ Collection O
3851
+ We O
3852
+ obtained O
3853
+ female O
3854
+ individuals O
3855
+ of O
3856
+ Peromyscus B
3857
+ species O
3858
+ ( O
3859
+ P B
3860
+ . I
3861
+ polionotus I
3862
+ , O
3863
+ P B
3864
+ . I
3865
+ maniculatus I
3866
+ , O
3867
+ P B
3868
+ . I
3869
+ leucopus I
3870
+ , O
3871
+ P B
3872
+ . I
3873
+ eremicus I
3874
+ , O
3875
+ P B
3876
+ . I
3877
+ californicus I
3878
+ , O
3879
+ 5 O
3880
+ individuals O
3881
+ per O
3882
+ species O
3883
+ , O
3884
+ except O
3885
+ for O
3886
+ P B
3887
+ . I
3888
+ maniculatus I
3889
+ , O
3890
+ where O
3891
+ n O
3892
+ = O
3893
+ 3 O
3894
+ ) O
3895
+ from O
3896
+ the O
3897
+ Peromyscus B
3898
+ Genetic O
3899
+ Stock O
3900
+ Center O
3901
+ at O
3902
+ the O
3903
+ University O
3904
+ of O
3905
+ South O
3906
+ Carolina O
3907
+ . O
3908
+
3909
+ In O
3910
+ this O
3911
+ cohort O
3912
+ study O
3913
+ , O
3914
+ data O
3915
+ and O
3916
+ rectal O
3917
+ samples O
3918
+ were O
3919
+ collected O
3920
+ at O
3921
+ baseline O
3922
+ and O
3923
+ every O
3924
+ 3 O
3925
+ months O
3926
+ for O
3927
+ up O
3928
+ to O
3929
+ 12 O
3930
+ months O
3931
+ or O
3932
+ until O
3933
+ subject B
3934
+ death O
3935
+ , O
3936
+ and O
3937
+ included O
3938
+ demographics O
3939
+ , O
3940
+ cause O
3941
+ of O
3942
+ dementia O
3943
+ , O
3944
+ comorbidities O
3945
+ , O
3946
+ functional O
3947
+ status O
3948
+ , O
3949
+ and O
3950
+ antimicrobial O
3951
+ exposures O
3952
+ . O
3953
+
3954
+ were O
3955
+ between O
3956
+ 5 O
3957
+ and O
3958
+ 8 O
3959
+ months O
3960
+ old O
3961
+ , O
3962
+ and O
3963
+ were O
3964
+ co O
3965
+ - O
3966
+ housed O
3967
+ ( O
3968
+ within O
3969
+ species O
3970
+ ) O
3971
+ prior O
3972
+ to O
3973
+ our O
3974
+ experiment O
3975
+ . O
3976
+
3977
+ Here O
3978
+ we O
3979
+ show O
3980
+ that O
3981
+ with O
3982
+ 16 O
3983
+ weeks O
3984
+ of O
3985
+ KD O
3986
+ , O
3987
+ mice B
3988
+ had O
3989
+ significant O
3990
+ increases O
3991
+ in O
3992
+ CBF O
3993
+ and O
3994
+ P O
3995
+ - O
3996
+ glycoprotein O
3997
+ transports O
3998
+ on O
3999
+ BBB O
4000
+ to O
4001
+ facilitate O
4002
+ clearance O
4003
+ of O
4004
+ amyloid O
4005
+ - O
4006
+ beta O
4007
+ , O
4008
+ a O
4009
+ hallmark O
4010
+ of O
4011
+ Alzheimers O
4012
+ disease O
4013
+ ( O
4014
+ AD O
4015
+ ) O
4016
+ . O
4017
+
4018
+ mongolica O
4019
+ ( O
4020
+ PS O
4021
+ ) O
4022
+ , O
4023
+ and O
4024
+ Pinus B
4025
+ tabuliformis I
4026
+ ( O
4027
+ PT O
4028
+ ) O
4029
+ . O
4030
+
4031
+ TransITS O
4032
+ amplicons O
4033
+ were O
4034
+ fragmented O
4035
+ using O
4036
+ the O
4037
+ Nextera O
4038
+ kit O
4039
+ ( O
4040
+ Illumina O
4041
+ , O
4042
+ San O
4043
+ Diego O
4044
+ , O
4045
+ CA O
4046
+ ) O
4047
+ , O
4048
+ and O
4049
+ both O
4050
+ libraries O
4051
+ were O
4052
+ barcoded O
4053
+ and O
4054
+ sequenced O
4055
+ with O
4056
+ MiSeq O
4057
+ V3 O
4058
+ ( O
4059
+ 300bp O
4060
+ 2 O
4061
+ ) O
4062
+ ( O
4063
+ Illumina O
4064
+ , O
4065
+ San O
4066
+ Diego O
4067
+ , O
4068
+ CA O
4069
+ ) O
4070
+ . O
4071
+
4072
+ Mat O
4073
+ samples O
4074
+ and O
4075
+ chimney O
4076
+ and O
4077
+ sediment O
4078
+ sub O
4079
+ - O
4080
+ samples O
4081
+ , O
4082
+ respectively O
4083
+ , O
4084
+ were O
4085
+ snap O
4086
+ - O
4087
+ frozen O
4088
+ in O
4089
+ liquid O
4090
+ N2 O
4091
+ , O
4092
+ and O
4093
+ stored O
4094
+ at O
4095
+ 80C O
4096
+ . O
4097
+
4098
+ Illumina O
4099
+ MiSeq O
4100
+ V3 O
4101
+ - O
4102
+ V4 O
4103
+ 16S O
4104
+ rRNA O
4105
+ metagenomics O
4106
+ library O
4107
+ preparation O
4108
+ and O
4109
+ sequencing O
4110
+ The O
4111
+ hypervariable O
4112
+ V3 O
4113
+ - O
4114
+ V4 O
4115
+ 16S O
4116
+ rRNA O
4117
+ region O
4118
+ of O
4119
+ the O
4120
+ bacterial O
4121
+ gene O
4122
+ was O
4123
+ targeted O
4124
+ by O
4125
+ universal O
4126
+ bacterial O
4127
+ primer O
4128
+ 319F O
4129
+ ( O
4130
+ 5 O
4131
+ - O
4132
+ CCTACGGGNGGCWGCAG O
4133
+ - O
4134
+ 3 O
4135
+ ) O
4136
+ and O
4137
+ 806R O
4138
+ ( O
4139
+ 5 O
4140
+ - O
4141
+ GACTACHVGGGTATCTAATCC O
4142
+ - O
4143
+ 3 O
4144
+ ) O
4145
+ as O
4146
+ previously O
4147
+ described O
4148
+ [ O
4149
+ 34 O
4150
+ ] O
4151
+ . O
4152
+
4153
+ The O
4154
+ selected O
4155
+ pigs B
4156
+ were O
4157
+ slaughtered O
4158
+ at O
4159
+ 141142 O
4160
+ days O
4161
+ of O
4162
+ age O
4163
+ , O
4164
+ after O
4165
+ overnight O
4166
+ fasting O
4167
+ . O
4168
+
4169
+ For O
4170
+ third O
4171
+ - O
4172
+ generation O
4173
+ sequencing O
4174
+ , O
4175
+ purified O
4176
+ fecal O
4177
+ DNA O
4178
+ was O
4179
+ amplified O
4180
+ using O
4181
+ bacterial O
4182
+ 16S O
4183
+ rRNA O
4184
+ full O
4185
+ - O
4186
+ length O
4187
+ primers O
4188
+ and O
4189
+ sequenced O
4190
+ using O
4191
+ Pacbio O
4192
+ RSII O
4193
+ system O
4194
+ ( O
4195
+ Pacific O
4196
+ Biosciences O
4197
+ , O
4198
+ USA O
4199
+ ) O
4200
+ . O
4201
+
4202
+ The O
4203
+ microbiome O
4204
+ in O
4205
+ pediatric O
4206
+ cystic O
4207
+ fibrosis O
4208
+ patients O
4209
+ : O
4210
+ the O
4211
+ role O
4212
+ of O
4213
+ shared O
4214
+ environment O
4215
+ suggests O
4216
+ a O
4217
+ window O
4218
+ of O
4219
+ intervention O
4220
+ Background O
4221
+ Cystic O
4222
+ fibrosis O
4223
+ ( O
4224
+ CF O
4225
+ ) O
4226
+ is O
4227
+ caused O
4228
+ by O
4229
+ mutations O
4230
+ in O
4231
+ the O
4232
+ CFTR O
4233
+ gene O
4234
+ that O
4235
+ predispose O
4236
+ the O
4237
+ airway O
4238
+ to O
4239
+ infection O
4240
+ . O
4241
+
4242
+ A O
4243
+ multi O
4244
+ - O
4245
+ phylum O
4246
+ assessment O
4247
+ of O
4248
+ marine O
4249
+ animal O
4250
+ diversity O
4251
+ that O
4252
+ includes O
4253
+ water O
4254
+ column O
4255
+ and O
4256
+ sediments O
4257
+ , O
4258
+ oxic O
4259
+ and O
4260
+ anoxic O
4261
+ environments O
4262
+ , O
4263
+ and O
4264
+ both O
4265
+ DNA O
4266
+ and O
4267
+ RNA O
4268
+ templates O
4269
+ , O
4270
+ revealed O
4271
+ a O
4272
+ high O
4273
+ percentage O
4274
+ of O
4275
+ novel O
4276
+ 18S O
4277
+ rRNA O
4278
+ sequences O
4279
+ in O
4280
+ most O
4281
+ phyla O
4282
+ , O
4283
+ suggesting O
4284
+ that O
4285
+ marine O
4286
+ environments O
4287
+ have O
4288
+ not O
4289
+ yet O
4290
+ been O
4291
+ fully O
4292
+ sampled O
4293
+ at O
4294
+ a O
4295
+ molecular O
4296
+ level O
4297
+ . O
4298
+
4299
+ On O
4300
+ day O
4301
+ 62 O
4302
+ ( O
4303
+ time O
4304
+ point O
4305
+ A O
4306
+ ) O
4307
+ and O
4308
+ day O
4309
+ 177 O
4310
+ ( O
4311
+ time O
4312
+ point O
4313
+ B O
4314
+ ) O
4315
+ , O
4316
+ all O
4317
+ reactors O
4318
+ were O
4319
+ opened O
4320
+ and O
4321
+ the O
4322
+ carbon O
4323
+ substrate O
4324
+ from O
4325
+ the O
4326
+ center O
4327
+ of O
4328
+ the O
4329
+ reactors O
4330
+ and O
4331
+ the O
4332
+ planktonic O
4333
+ phase O
4334
+ from O
4335
+ between O
4336
+ the O
4337
+ wood O
4338
+ chips O
4339
+ were O
4340
+ sampled O
4341
+ . O
4342
+
4343
+ One O
4344
+ sample O
4345
+ ( O
4346
+ E215m O
4347
+ - O
4348
+ 2014 O
4349
+ _ O
4350
+ f O
4351
+ , O
4352
+ obtained O
4353
+ during O
4354
+ 2014 O
4355
+ from O
4356
+ 215m O
4357
+ depth O
4358
+ in O
4359
+ borehole O
4360
+ 08E140C01 O
4361
+ ) O
4362
+ was O
4363
+ collected O
4364
+ by O
4365
+ passage O
4366
+ of O
4367
+ the O
4368
+ 0 O
4369
+ . O
4370
+ 22m O
4371
+ filtrate O
4372
+ through O
4373
+ a O
4374
+ 10000 O
4375
+ nominal O
4376
+ molecular O
4377
+ weight O
4378
+ limit O
4379
+ filter O
4380
+ ( O
4381
+ type O
4382
+ PLGC O
4383
+ ; O
4384
+ Merck O
4385
+ Millipore O
4386
+ ) O
4387
+ . O
4388
+
4389
+ We O
4390
+ show O
4391
+ that O
4392
+ Bacteroides O
4393
+ LPS O
4394
+ is O
4395
+ structurally O
4396
+ distinct O
4397
+ from O
4398
+ E O
4399
+ . O
4400
+ coli O
4401
+ LPS O
4402
+ and O
4403
+ inhibits O
4404
+ innate O
4405
+ immune O
4406
+ signaling O
4407
+ and O
4408
+ endotoxin O
4409
+ tolerance O
4410
+ ; O
4411
+ furthermore O
4412
+ , O
4413
+ unlike O
4414
+ LPS O
4415
+ from O
4416
+ E O
4417
+ . O
4418
+ coli O
4419
+ , O
4420
+ B O
4421
+ . O
4422
+ dorei O
4423
+ LPS O
4424
+ does O
4425
+ not O
4426
+ decrease O
4427
+ incidence O
4428
+ of O
4429
+ autoimmune O
4430
+ diabetes O
4431
+ in O
4432
+ non O
4433
+ - O
4434
+ obese O
4435
+ diabetic O
4436
+ mice B
4437
+ . O
4438
+
4439
+ Sequencing O
4440
+ Total O
4441
+ RNA O
4442
+ from O
4443
+ each O
4444
+ sample O
4445
+ was O
4446
+ converted O
4447
+ to O
4448
+ Illumina O
4449
+ sequencing O
4450
+ libraries O
4451
+ using O
4452
+ Illuminas O
4453
+ TruSeq O
4454
+ RNA O
4455
+ Sample O
4456
+ Prep O
4457
+ Kit O
4458
+ v2 O
4459
+ according O
4460
+ to O
4461
+ manufacturers O
4462
+ instructions O
4463
+ . O
4464
+
4465
+ Fecal O
4466
+ samples O
4467
+ were O
4468
+ collected O
4469
+ at O
4470
+ the O
4471
+ hospital O
4472
+ between O
4473
+ 24 O
4474
+ and O
4475
+ 48 O
4476
+ h O
4477
+ of O
4478
+ life O
4479
+ and O
4480
+ at O
4481
+ 10 O
4482
+ , O
4483
+ 30 O
4484
+ , O
4485
+ and O
4486
+ 90 O
4487
+ days O
4488
+ of O
4489
+ age O
4490
+ , O
4491
+ immediately O
4492
+ frozen O
4493
+ at O
4494
+ 20 O
4495
+ C O
4496
+ and O
4497
+ processed O
4498
+ as O
4499
+ described O
4500
+ by O
4501
+ Arboleya O
4502
+ and O
4503
+ co O
4504
+ - O
4505
+ workers O
4506
+ [ O
4507
+ 22 O
4508
+ ] O
4509
+ . O
4510
+
4511
+ ABX O
4512
+ - O
4513
+ treated O
4514
+ water O
4515
+ was O
4516
+ sterile O
4517
+ filtered O
4518
+ prior O
4519
+ to O
4520
+ placement O
4521
+ in O
4522
+ mouse B
4523
+ cages O
4524
+ and O
4525
+ provided O
4526
+ to O
4527
+ mice B
4528
+ ad O
4529
+ libitum O
4530
+ . O
4531
+
4532
+ All O
4533
+ fecal O
4534
+ samples O
4535
+ were O
4536
+ collected O
4537
+ from O
4538
+ individual O
4539
+ mice B
4540
+ into O
4541
+ 2 O
4542
+ mL O
4543
+ screw O
4544
+ cap O
4545
+ tubes O
4546
+ ( O
4547
+ Axygen O
4548
+ , O
4549
+ CA O
4550
+ , O
4551
+ USA O
4552
+ ) O
4553
+ . O
4554
+
4555
+ Upon O
4556
+ eclosion O
4557
+ , O
4558
+ 10 O
4559
+ adults O
4560
+ carrying O
4561
+ either O
4562
+ mun O
4563
+ + O
4564
+ or O
4565
+ mun O
4566
+ - O
4567
+ strains O
4568
+ were O
4569
+ dissected O
4570
+ and O
4571
+ their O
4572
+ guts O
4573
+ were O
4574
+ plated O
4575
+ onto O
4576
+ non O
4577
+ - O
4578
+ selective O
4579
+ MRS O
4580
+ agar O
4581
+ ( O
4582
+ S4 O
4583
+ Fig O
4584
+ ) O
4585
+ . O
4586
+
4587
+ All O
4588
+ mice B
4589
+ were O
4590
+ fed O
4591
+ ad O
4592
+ libitum O
4593
+ for O
4594
+ 16 O
4595
+ weeks O
4596
+ , O
4597
+ and O
4598
+ body O
4599
+ weight O
4600
+ was O
4601
+ measured O
4602
+ once O
4603
+ a O
4604
+ week O
4605
+ . O
4606
+
4607
+ The O
4608
+ contents O
4609
+ of O
4610
+ soil O
4611
+ total O
4612
+ C O
4613
+ and O
4614
+ total O
4615
+ N O
4616
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4617
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+ nitrate O
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+ Materials O
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+ good O
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+ - O
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+ quality O
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+ sequencing O
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5000
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+ 3 O
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+ least O
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+ criteria O
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+ dL O
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+ All O
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+ values O
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+ , O
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+ treatments O
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+ , O
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+ collection O
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+ for O
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+ cell O
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+ pellets O
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+ ( O
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+ Biomedicals O
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+ USA O
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+ ) O
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+
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+ Hydrogen O
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+ sulfide O
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+ continuously O
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+ supplied O
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+ and O
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+ dioxide O
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+ dosing O
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+ rates O
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+ were O
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+ pulse O
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+ - O
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+ wise O
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+ controlled O
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+ with O
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+ transmitter O
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+ Hauser O
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+ , O
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+ based O
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+ on O
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+ signals O
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+ from O
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+ a O
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+ redox O
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+ sensor O
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+ , O
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+ equipped O
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+ with O
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+ an O
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+ Ag O
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+ / O
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+ AgCl O
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+ reference O
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+ electrode O
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+ ( O
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+ Orbisint O
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+ 12D O
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+ 7PA41 O
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+ ; O
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+ Endress O
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+ Hauser O
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+ Germany O
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+ ) O
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+ and O
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+ a O
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+ pH O
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+ sensor O
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+ ( O
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+ Orbisint O
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+ 11D O
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+ - O
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+ 7AA41 O
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+ ; O
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+ + O
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+ Hauser O
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+ , O
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+ Germany O
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+
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+ To O
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+ monitor O
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+ reactor O
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+ performance O
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+ , O
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+ mixed O
5203
+ liquor O
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+ and O
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+ effluent O
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+ samples O
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+ were O
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+ collected O
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+ , O
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+ filtered O
5211
+ through O
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+ a O
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+ membrane O
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+ filter O
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+ ( O
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+ Whatman O
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+ , O
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+ Maidstone O
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+ , O
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+ United O
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+ Kingdom O
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+ ) O
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+ ( O
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+ 0 O
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+ . O
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+ 45 O
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+ m O
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+ , O
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+ for O
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+ , O
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+ PO43 O
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+ - O
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+ - O
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+ P O
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+ plus O
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+ NH4 O
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+ + O
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+ - O
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+ N O
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+ , O
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+ NO3 O
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+ - O
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+ - O
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+ N O
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+ , O
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+ and O
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+ NO2 O
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+ - O
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+ - O
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+ N O
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+
5262
+ For O
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5267
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5268
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5269
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5270
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5271
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5272
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5273
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5274
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5275
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5277
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5278
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5279
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5280
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5281
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5282
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5283
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5285
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+ extraction O
5288
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+ performed O
5290
+ . O
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+
5292
+ For O
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+ inflammation O
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+ , O
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+ 0 O
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+ to O
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5300
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5301
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+ ; O
5303
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+ to O
5305
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5306
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5307
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5308
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5309
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5310
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5311
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5312
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5313
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5315
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5317
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5318
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5319
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5320
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5321
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+ smooth O
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+ Alpha O
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+ phases O
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+ ( O
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+ menstrual O
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+ , O
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+ follicular O
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+ model O
5390
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+ and O
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+ a O
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5397
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+ - O
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+ effects O
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+ model O
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+ for O
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+ Chao1 O
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5408
+ Approximately O
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+ ( O
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+ 32 O
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+ currently O
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+ smokers O
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+
5427
+ Microbial O
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+ Community O
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+ Analysis O
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+ using O
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+ a O
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+ total O
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+ kit O
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+ ( O
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+ MP O
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+ Biomedicals O
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+ , O
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+ Solon O
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+ , O
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+ OH O
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+ , O
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+ USA O
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+ accordance O
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+ manufacturers O
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+ instructions O
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+ . O
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+
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+ coluzzii O
5458
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+ mating O
5461
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5462
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5463
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5464
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5466
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+ Bobo O
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+ - O
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+ Dioulasso O
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+ , O
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+ Burkina O
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+ Faso O
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+ Valle O
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+ du O
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+ Kou O
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+ 5 O
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+ VK5 O
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+ Kou O
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+ VK7 O
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+ populated O
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+ An O
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+
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+ Second O
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5507
+ using O
5508
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5509
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5510
+ plasma O
5511
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5512
+ as O
5513
+ an O
5514
+ internal O
5515
+ control O
5516
+ . O
5517
+
5518
+ Sequences O
5519
+ of O
5520
+ the O
5521
+ primers O
5522
+ used O
5523
+ for O
5524
+ 16S O
5525
+ rRNA O
5526
+ gene O
5527
+ amplicon O
5528
+ sequencing O
5529
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5530
+ the O
5531
+ bacterial O
5532
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5533
+ archaeal O
5534
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5535
+ Primer O
5536
+ name O
5537
+ Sequence O
5538
+ of O
5539
+ the O
5540
+ primers O
5541
+ Archaea O
5542
+ Fwd O
5543
+ Ar0787 O
5544
+ AATGATACGGCGACCACCGAGATCTACACACACTCTTTCCCTACACGACGCTCTTCCGATCT O
5545
+ ATTAGATACCCSBGTAGTCC O
5546
+ Rev O
5547
+ Ar1059 O
5548
+
5549
+ CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT O
5550
+ GCCATGCACCWCCTCT O
5551
+ Bacteria O
5552
+ Fwd O
5553
+ Ba0027 O
5554
+ AATGATACGGCGACCACCGAGATCTACACTATGGTAATTGT O
5555
+ AGAGTTTGATCCTGGCTCAG O
5556
+ Rev O
5557
+ Ba0338 O
5558
+ CAAGCAGAAGACGGCATACGAGATAGTCAGTCAGCC O
5559
+ TGCTGCCTCCCGTAGGAGT O
5560
+
5561
+ Primer O
5562
+ sequence O
5563
+ consisted O
5564
+ of O
5565
+ an O
5566
+ initial O
5567
+ standardized O
5568
+ Illumina O
5569
+ adapter O
5570
+ ( O
5571
+ regular O
5572
+ ) O
5573
+ , O
5574
+ followed O
5575
+ by O
5576
+ an O
5577
+ eight O
5578
+ nucleotide O
5579
+ barcode O
5580
+ ( O
5581
+ X O
5582
+ ' O
5583
+ s O
5584
+ ) O
5585
+ and O
5586
+ a O
5587
+ primer O
5588
+ sequence O
5589
+ ( O
5590
+ bold O
5591
+ ) O
5592
+ . O
5593
+
5594
+ Genomic O
5595
+ DNA O
5596
+ extraction O
5597
+ from O
5598
+ the O
5599
+ nine O
5600
+ sampling O
5601
+ points O
5602
+ ( O
5603
+ P0 O
5604
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5605
+ P8 O
5606
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5607
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5608
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5609
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5610
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5611
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5612
+ SPIN O
5613
+ kit O
5614
+ for O
5615
+ soil O
5616
+ ( O
5617
+ MP O
5618
+ Biomedicals O
5619
+ , O
5620
+ Solon O
5621
+ , O
5622
+ OH O
5623
+ ) O
5624
+ following O
5625
+ the O
5626
+ manufacturers O
5627
+ protocol O
5628
+ with O
5629
+ additional O
5630
+ washing O
5631
+ steps O
5632
+ before O
5633
+ starting O
5634
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5635
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5636
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5637
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5638
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5639
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5640
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5641
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5642
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5643
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5644
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5645
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5646
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5647
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5648
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5649
+ Primers O
5650
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5651
+ for O
5652
+ the O
5653
+ amplification O
5654
+ of O
5655
+ the O
5656
+ amplification O
5657
+ of O
5658
+ the O
5659
+ bacterial O
5660
+ and O
5661
+ archaeal O
5662
+ 16SrRNA O
5663
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5664
+ fragments O
5665
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5666
+ listed O
5667
+ in O
5668
+ Table2 O
5669
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5670
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5671
+ previously O
5672
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5673
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5674
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5675
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5676
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5677
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5678
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5679
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5680
+ in O
5681
+ biogas O
5682
+ environments O
5683
+ ( O
5684
+ Fischer O
5685
+ etal O
5686
+ . O
5687
+ , O
5688
+ 2016 O
5689
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5690
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5691
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5692
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5693
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5694
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5695
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5696
+ were O
5697
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5698
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5699
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5700
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5701
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5702
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5703
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5704
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5705
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5706
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5707
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5708
+ for O
5709
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5710
+ characterisation O
5711
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5712
+
5713
+ Within O
5714
+ 24h O
5715
+ after O
5716
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5717
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5718
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5719
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5720
+ aspirate O
5721
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5722
+ NPA O
5723
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5724
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5725
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5726
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5727
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5728
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5729
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5730
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5731
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5732
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5733
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5734
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5735
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5736
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5737
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5738
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5739
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5740
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5741
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5742
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5743
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5744
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5745
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5746
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5747
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5748
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5749
+ To O
5750
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5751
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5752
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5753
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5754
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5755
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5756
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5757
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5758
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5759
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5760
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5761
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5762
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5763
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5764
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5765
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5766
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5767
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5768
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5769
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5770
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5771
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5772
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5773
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5774
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5775
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5776
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5777
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5778
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5779
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5780
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5781
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5782
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5783
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5784
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5785
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5786
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5787
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5788
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5789
+ , O
5790
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5791
+ also O
5792
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5793
+ surface O
5794
+ , O
5795
+ DCM O
5796
+ and O
5797
+ mesopelagic O
5798
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5799
+ generated O
5800
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5801
+ the O
5802
+ TARA O
5803
+ expedition O
5804
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5805
+ 37 O
5806
+ ] O
5807
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5808
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5809
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5810
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5811
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5812
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5813
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5814
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5815
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5816
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5817
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5819
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5820
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5821
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5822
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5823
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5824
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5825
+ either O
5826
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5827
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5828
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5829
+ standard O
5830
+ diet O
5831
+ supplemented O
5832
+ with O
5833
+ COLOSTRONONI O
5834
+ ( O
5835
+ Product O
5836
+ Number O
5837
+ 934744602 O
5838
+ , O
5839
+ Lot O
5840
+ # O
5841
+ A04268 O
5842
+ , O
5843
+ Guna O
5844
+ S O
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+ . O
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+ p O
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+ . O
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+ a O
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+ . O
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+ , O
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5852
+ , O
5853
+ Italy O
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+ dissolved O
5856
+ in O
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+ sucrose O
5858
+ solution O
5859
+ ( O
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+ 2 O
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+ % O
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+ ) O
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+ CN O
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5870
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5874
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5875
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5877
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5878
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5879
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5880
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5881
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5882
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5883
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5884
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5885
+ standard O
5886
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5887
+ supplemented O
5888
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5889
+ sucrose O
5890
+ solution O
5891
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5892
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5893
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5894
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5895
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5896
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5897
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5898
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5899
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5900
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5901
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5902
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5903
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5904
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5905
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5906
+ 16S O
5907
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5908
+ gene O
5909
+ V4 O
5910
+ sequencing O
5911
+ Microbiota O
5912
+ profiling O
5913
+ was O
5914
+ performed O
5915
+ targeting O
5916
+ the O
5917
+ V4 O
5918
+ region O
5919
+ of O
5920
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5921
+ 16S O
5922
+ rRNA O
5923
+ gene O
5924
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5925
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5926
+ The O
5927
+ packer O
5928
+ leak O
5929
+ was O
5930
+ repaired O
5931
+ and O
5932
+ pumping O
5933
+ continued O
5934
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5935
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5936
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5937
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5938
+ not O
5939
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5940
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5941
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5942
+ and O
5943
+ sampling O
5944
+ resumed O
5945
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5946
+ August O
5947
+ . O
5948
+
5949
+ Collection O
5950
+ of O
5951
+ sample O
5952
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5953
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5954
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5955
+ from O
5956
+ two O
5957
+ hot O
5958
+ springs O
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+ 65C O
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+ 54C O
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5965
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5966
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5968
+ A O
5969
+ major O
5970
+ feature O
5971
+ of O
5972
+ all O
5973
+ deserts O
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5975
+ the O
5976
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5977
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5978
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5979
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5980
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5982
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5983
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5984
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5985
+ crusts O
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+ BSC O
5988
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5991
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5992
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5993
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5994
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5995
+ such O
5996
+ as O
5997
+ sandstone O
5998
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5999
+ Pointing O
6000
+ and O
6001
+ Belnap O
6002
+ , O
6003
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6004
+ ; O
6005
+ Makhalanyane O
6006
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6007
+ al O
6008
+ . O
6009
+ , O
6010
+ 2015 O
6011
+ ) O
6012
+ . O
6013
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6014
+ Overall O
6015
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6016
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6017
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6018
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6019
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6020
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6021
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6022
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6023
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6024
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6025
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6026
+ active O
6027
+ late O
6028
+ in O
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+ the O
6030
+ baseflow O
6031
+ period O
6032
+ of O
6033
+ perennial O
6034
+ streams O
6035
+ ( O
6036
+ December O
6037
+ to O
6038
+ April O
6039
+ ) O
6040
+ . O
6041
+
6042
+ Metaproteomics O
6043
+ Samples O
6044
+ used O
6045
+ for O
6046
+ metaproteomics O
6047
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6048
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6049
+ collected O
6050
+ from O
6051
+ in O
6052
+ situ O
6053
+ nylon O
6054
+ bags O
6055
+ containing O
6056
+ 5g O
6057
+ of O
6058
+ air O
6059
+ - O
6060
+ dried O
6061
+ switch O
6062
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6063
+ or O
6064
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6065
+ stover O
6066
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6067
+ were O
6068
+ placed O
6069
+ in O
6070
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6071
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6072
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6073
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6074
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6075
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6076
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6077
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6078
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6079
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6080
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6081
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6082
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6083
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6084
+ For O
6085
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6086
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6087
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6088
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6089
+ a O
6090
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6091
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6092
+ to O
6093
+ show O
6094
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6095
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6096
+ of O
6097
+ diffuse O
6098
+ hyperintensity O
6099
+ on O
6100
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6101
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6102
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6103
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6104
+ scans O
6105
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6106
+ Fig O
6107
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6108
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6109
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6110
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6111
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6112
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6113
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6114
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6115
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6116
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6117
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6118
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6119
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6120
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6121
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6122
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6123
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6124
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6125
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6126
+ To O
6127
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6128
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6129
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6130
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6131
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6132
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6133
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6134
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6135
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6136
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6137
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6138
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6139
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6140
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6141
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6142
+ environmental O
6143
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6144
+ amplicon O
6145
+ datasets O
6146
+ from O
6147
+ NCBIs O
6148
+ SRA O
6149
+ ( O
6150
+ March O
6151
+ 2016 O
6152
+ ) O
6153
+ using O
6154
+ fastq O
6155
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6156
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6157
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6158
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6159
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6160
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6161
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6162
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6163
+ R O
6164
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6165
+ ( O
6166
+ List O
6167
+ of O
6168
+ amplicons O
6169
+ available O
6170
+ in O
6171
+ the O
6172
+ online O
6173
+ supplementary O
6174
+ material O
6175
+ : O
6176
+ https O
6177
+ : O
6178
+ / O
6179
+ / O
6180
+ figshare O
6181
+ . O
6182
+ com O
6183
+ / O
6184
+ articles O
6185
+ / O
6186
+ Supplementary O
6187
+ _ O
6188
+ Data O
6189
+ _ O
6190
+ Lopez O
6191
+ - O
6192
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6193
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6194
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6195
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6196
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6197
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6198
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6199
+ / O
6200
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6201
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6202
+ , O
6203
+ which O
6204
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6205
+ the O
6206
+ high O
6207
+ quality O
6208
+ reads63 O
6209
+ . O
6210
+
6211
+ MATERIALS O
6212
+ AND O
6213
+ METHODS O
6214
+ Bioelectrochemical O
6215
+ cell O
6216
+ . O
6217
+
6218
+ ( O
6219
+ B O
6220
+ and O
6221
+ C O
6222
+ ) O
6223
+ Linear O
6224
+ strips O
6225
+ of O
6226
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6227
+ tissue O
6228
+ , O
6229
+ extending O
6230
+ from O
6231
+ the O
6232
+ squamocolumnar O
6233
+ junction O
6234
+ to O
6235
+ the O
6236
+ proximal O
6237
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6238
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6239
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6240
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6241
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6242
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6243
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6244
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6245
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6246
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6247
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6248
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6249
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6250
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6251
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6252
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6253
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6254
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6255
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6256
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6257
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6258
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6259
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6260
+ The O
6261
+ Association O
6262
+ of O
6263
+ Specific O
6264
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6265
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6266
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6267
+ Fecal O
6268
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6269
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6270
+ Immune O
6271
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6272
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6273
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6274
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6275
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6276
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6277
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6278
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6279
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6280
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6281
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6282
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6283
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6284
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6285
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6286
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6287
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6288
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6289
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6290
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6291
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6292
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6293
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6294
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6295
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6296
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6297
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6298
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6299
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6300
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6301
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6302
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6303
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6304
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6305
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6306
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6307
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6308
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6309
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6310
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6311
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6312
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6313
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6314
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6315
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6316
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6317
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6318
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6319
+ Immunohistochemistry O
6320
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6321
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6322
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6323
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6324
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6325
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6326
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6327
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6328
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6329
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6330
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6331
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6332
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6333
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6334
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6335
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6336
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6337
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6338
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6339
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6340
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6341
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6342
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6343
+ activated O
6344
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6345
+ sorting O
6346
+ analysis O
6347
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6348
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6349
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6350
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6351
+ freshly O
6352
+ prepared O
6353
+ neutral O
6354
+ buffered O
6355
+ 4 O
6356
+ % O
6357
+ paraformaldehyde O
6358
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6359
+ 24h O
6360
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6361
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6362
+ temperature O
6363
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6364
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6365
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6366
+ extraction O
6367
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6368
+ PCR O
6369
+ amplification O
6370
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6371
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6372
+ sequencing O
6373
+ Total O
6374
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6375
+ DNA O
6376
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6377
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6378
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6379
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6380
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6381
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6382
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6383
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6384
+ Soil O
6385
+ GenomeTM O
6386
+ DNA O
6387
+ Isolation O
6388
+ kit O
6389
+ ( O
6390
+ Qiagen O
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+ , O
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+ Germany O
6393
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+ , O
6395
+ according O
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+ to O
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+ the O
6398
+ manufacturer O
6399
+ instructions O
6400
+ . O
6401
+
6402
+ For O
6403
+ RT O
6404
+ - O
6405
+ PCR O
6406
+ , O
6407
+ total O
6408
+ RNA O
6409
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6410
+ the O
6411
+ remaining O
6412
+ spinal O
6413
+ cord O
6414
+ sample O
6415
+ was O
6416
+ extracted O
6417
+ using O
6418
+ a O
6419
+ Qiagen O
6420
+ RNeasy O
6421
+ Plus O
6422
+ Micro O
6423
+ Kit O
6424
+ with O
6425
+ RNA O
6426
+ carrier O
6427
+ ( O
6428
+ Hilden O
6429
+ , O
6430
+ GER O
6431
+ ) O
6432
+ to O
6433
+ facilitate O
6434
+ RNA O
6435
+ pull O
6436
+ - O
6437
+ down O
6438
+ from O
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+ this O
6440
+ small O
6441
+ tissue O
6442
+ . O
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+
6444
+ The O
6445
+ CSTRs O
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+ were O
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+ inoculated O
6448
+ from O
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+ a O
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+ lab O
6451
+ - O
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+ scale O
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+ digester O
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+ operated O
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+ at O
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+ a O
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+ dilution O
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+ rate O
6459
+ of O
6460
+ 0 O
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+ . O
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+ 125 O
6463
+ days O
6464
+ - O
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+ 1 O
6466
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6467
+ the O
6468
+ same O
6469
+ synthetic O
6470
+ substrate O
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+ for O
6472
+ 7 O
6473
+ months O
6474
+ . O
6475
+
6476
+ When O
6477
+ three O
6478
+ or O
6479
+ more O
6480
+ of O
6481
+ the O
6482
+ MRI O
6483
+ criteria O
6484
+ for O
6485
+ inflammation O
6486
+ were O
6487
+ present O
6488
+ , O
6489
+ the O
6490
+ segment O
6491
+ was O
6492
+ judged O
6493
+ severely O
6494
+ inflamed O
6495
+ ( O
6496
+ grade O
6497
+ 3 O
6498
+ ) O
6499
+ . O
6500
+
6501
+ All O
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+ the O
6503
+ experiments O
6504
+ were O
6505
+ conducted O
6506
+ in O
6507
+ triplicate O
6508
+ inside O
6509
+ a O
6510
+ shaker O
6511
+ ( O
6512
+ Multitron O
6513
+ Standard O
6514
+ , O
6515
+ Infors O
6516
+ HT O
6517
+ , O
6518
+ Switzerland O
6519
+ ) O
6520
+ under O
6521
+ thermophilic O
6522
+ conditions O
6523
+ ( O
6524
+ 62C O
6525
+ , O
6526
+ 120rpm O
6527
+ ) O
6528
+ . O
6529
+
6530
+ Sequencing O
6531
+ was O
6532
+ conducted O
6533
+ with O
6534
+ an O
6535
+ Illumina O
6536
+ MiSeq O
6537
+ system O
6538
+ ( O
6539
+ Illumina O
6540
+ ) O
6541
+ with O
6542
+ the O
6543
+ 500 O
6544
+ cycle O
6545
+ V2chemistry O
6546
+ at O
6547
+ Auckland O
6548
+ University O
6549
+ of O
6550
+ Technology O
6551
+ , O
6552
+ New O
6553
+ Zealand O
6554
+ . O
6555
+
6556
+ For O
6557
+ comparison O
6558
+ , O
6559
+ we O
6560
+ also O
6561
+ collected O
6562
+ one O
6563
+ barite O
6564
+ - O
6565
+ rich O
6566
+ silica O
6567
+ chimney O
6568
+ ( O
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+ SiCh O
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+ ) O
6571
+ from O
6572
+ the O
6573
+ extinct O
6574
+ vent O
6575
+ area O
6576
+ ( O
6577
+ Figure O
6578
+ 1G O
6579
+ ) O
6580
+ at O
6581
+ 7333 O
6582
+ . O
6583
+ 99N O
6584
+ and O
6585
+ 0809 O
6586
+ . O
6587
+ 58E O
6588
+ at O
6589
+ a O
6590
+ water O
6591
+ depth O
6592
+ of O
6593
+ 2367 O
6594
+ m O
6595
+ . O
6596
+ An O
6597
+ overview O
6598
+ of O
6599
+ examined O
6600
+ mat O
6601
+ - O
6602
+ samples O
6603
+ and O
6604
+ chimney O
6605
+ sub O
6606
+ - O
6607
+ samples O
6608
+ , O
6609
+ respectively O
6610
+ , O
6611
+ are O
6612
+ given O
6613
+ in O
6614
+ Table O
6615
+ 1 O
6616
+ . O
6617
+
6618
+ A O
6619
+ total O
6620
+ of O
6621
+ 12l O
6622
+ of O
6623
+ blood O
6624
+ sample O
6625
+ were O
6626
+ used O
6627
+ to O
6628
+ measure O
6629
+ blood O
6630
+ glucose O
6631
+ level O
6632
+ using O
6633
+ a O
6634
+ blood O
6635
+ glucose O
6636
+ meter O
6637
+ and O
6638
+ a O
6639
+ test O
6640
+ strip O
6641
+ ( O
6642
+ Clarity O
6643
+ Plus O
6644
+ , O
6645
+ Boca O
6646
+ Raton O
6647
+ , O
6648
+ FL O
6649
+ , O
6650
+ USA O
6651
+ ) O
6652
+ . O
6653
+
6654
+ To O
6655
+ investigate O
6656
+ potential O
6657
+ sources O
6658
+ of O
6659
+ the O
6660
+ microorganisms O
6661
+ in O
6662
+ the O
6663
+ cryoconite O
6664
+ holes O
6665
+ we O
6666
+ also O
6667
+ collected O
6668
+ a O
6669
+ total O
6670
+ of O
6671
+ eleven O
6672
+ samples O
6673
+ from O
6674
+ different O
6675
+ surface O
6676
+ habitats O
6677
+ nearby O
6678
+ for O
6679
+ DNA O
6680
+ sequencing O
6681
+ . O
6682
+
6683
+ Three O
6684
+ biopsies O
6685
+ were O
6686
+ obtained O
6687
+ from O
6688
+ the O
6689
+ greater O
6690
+ curvature O
6691
+ sides O
6692
+ of O
6693
+ the O
6694
+ mid O
6695
+ - O
6696
+ antrum O
6697
+ and O
6698
+ mid O
6699
+ - O
6700
+ body O
6701
+ , O
6702
+ in O
6703
+ addition O
6704
+ to O
6705
+ the O
6706
+ descending O
6707
+ duodenum O
6708
+ . O
6709
+
6710
+ DNA O
6711
+ extraction O
6712
+ and O
6713
+ real O
6714
+ - O
6715
+ time O
6716
+ quantitative O
6717
+ PCR O
6718
+ gDNAs O
6719
+ were O
6720
+ extracted O
6721
+ from O
6722
+ the O
6723
+ freeze O
6724
+ dried O
6725
+ sediments O
6726
+ ( O
6727
+ each O
6728
+ 0 O
6729
+ . O
6730
+ 25g O
6731
+ dry O
6732
+ weight O
6733
+ ) O
6734
+ using O
6735
+ the O
6736
+ MOBIOs O
6737
+ PowerSoil O
6738
+ DNA O
6739
+ extraction O
6740
+ kit O
6741
+ and O
6742
+ PowerClean O
6743
+ Pro O
6744
+ DNA O
6745
+ Clean O
6746
+ - O
6747
+ Up O
6748
+ Kit O
6749
+ ( O
6750
+ MOBIO O
6751
+ , O
6752
+ Carlsbad O
6753
+ , O
6754
+ CA O
6755
+ ) O
6756
+ according O
6757
+ to O
6758
+ the O
6759
+ manufacturers O
6760
+ specifications O
6761
+ . O
6762
+
6763
+ For O
6764
+ 16S O
6765
+ rRNA O
6766
+ gene O
6767
+ amplification O
6768
+ for O
6769
+ denaturing O
6770
+ gradient O
6771
+ gel O
6772
+ electrophoresis O
6773
+ ( O
6774
+ DGGE O
6775
+ ) O
6776
+ , O
6777
+ primers O
6778
+ set O
6779
+ 1401r O
6780
+ / O
6781
+ 968GCf O
6782
+ was O
6783
+ used O
6784
+ for O
6785
+ bacteria O
6786
+ and O
6787
+ 515GCr O
6788
+ / O
6789
+ A109 O
6790
+ ( O
6791
+ T O
6792
+ ) O
6793
+ f O
6794
+ for O
6795
+ archaea O
6796
+ ( O
6797
+ Sousa O
6798
+ etal O
6799
+ . O
6800
+ , O
6801
+ 2007 O
6802
+ ) O
6803
+ . O
6804
+
6805
+ Domain O
6806
+ - O
6807
+ specific O
6808
+ primers O
6809
+ , O
6810
+ 958F O
6811
+ and O
6812
+ 1048R O
6813
+ for O
6814
+ Archaea O
6815
+ and O
6816
+ 967F O
6817
+ and O
6818
+ 1064R O
6819
+ for O
6820
+ Bacteria O
6821
+ , O
6822
+ targeted O
6823
+ the O
6824
+ V6 O
6825
+ hypervariable O
6826
+ region O
6827
+ of O
6828
+ the O
6829
+ 16S O
6830
+ rRNA O
6831
+ gene O
6832
+ ( O
6833
+ Sogin O
6834
+ et O
6835
+ al O
6836
+ . O
6837
+ , O
6838
+ 2006 O
6839
+ ) O
6840
+ . O
6841
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6842
+ Seven O
6843
+ individuals B
6844
+ collected O
6845
+ in O
6846
+ 2016 O
6847
+ were O
6848
+ treated O
6849
+ similarly O
6850
+ , O
6851
+ with O
6852
+ the O
6853
+ exception O
6854
+ that O
6855
+ whole O
6856
+ , O
6857
+ sediment O
6858
+ - O
6859
+ free O
6860
+ animals B
6861
+ were O
6862
+ transferred O
6863
+ to O
6864
+ centrifuge O
6865
+ tubes O
6866
+ with O
6867
+ Lifeguard O
6868
+ . O
6869
+
6870
+ MATERIALS O
6871
+ AND O
6872
+ METHODS O
6873
+ Sampling O
6874
+ and O
6875
+ physiochemical O
6876
+ measurements O
6877
+ Benthic O
6878
+ mat O
6879
+ samples O
6880
+ were O
6881
+ collected O
6882
+ on O
6883
+ 26 O
6884
+ June O
6885
+ 2012 O
6886
+ at O
6887
+ 16 O
6888
+ : O
6889
+ 00 O
6890
+ PDT O
6891
+ ( O
6892
+ photon O
6893
+ flux O
6894
+ 490 O
6895
+ mol O
6896
+ photons O
6897
+ PAR O
6898
+ m2 O
6899
+ s1 O
6900
+ ; O
6901
+ due O
6902
+ to O
6903
+ partial O
6904
+ cloudiness O
6905
+ ) O
6906
+ and O
6907
+ 27 O
6908
+ June O
6909
+ 2012 O
6910
+ at O
6911
+ 01 O
6912
+ : O
6913
+ 00 O
6914
+ PDT O
6915
+ ( O
6916
+ photon O
6917
+ flux O
6918
+ 0 O
6919
+ mol O
6920
+ photons O
6921
+ PAR O
6922
+ m2 O
6923
+ s1 O
6924
+ ) O
6925
+ and O
6926
+ at O
6927
+ 16 O
6928
+ : O
6929
+ 00 O
6930
+ PDT O
6931
+ ( O
6932
+ photon O
6933
+ flux O
6934
+ 1225 O
6935
+ mol O
6936
+ photon O
6937
+ PAR O
6938
+ m2 O
6939
+ s1 O
6940
+ ) O
6941
+ from O
6942
+ a O
6943
+ water O
6944
+ depth O
6945
+ of O
6946
+ 3540cm O
6947
+ located O
6948
+ in O
6949
+ northeastern O
6950
+ Washington O
6951
+ state O
6952
+ ( O
6953
+ USA O
6954
+ ) O
6955
+ ( O
6956
+ 48 O
6957
+
6958
+ . O
6959
+ 97347119 O
6960
+ . O
6961
+ 476322 O
6962
+ ) O
6963
+ . O
6964
+
6965
+ To O
6966
+ test O
6967
+ viral O
6968
+ extractions O
6969
+ for O
6970
+ putative O
6971
+ bacterial O
6972
+ contamination O
6973
+ , O
6974
+ each O
6975
+ DNA O
6976
+ sample O
6977
+ was O
6978
+ assessed O
6979
+ using O
6980
+ the O
6981
+ 16S O
6982
+ 63F O
6983
+ / O
6984
+ 1087R O
6985
+ primer O
6986
+ pair O
6987
+ following O
6988
+ standard O
6989
+ PCR O
6990
+ protocols O
6991
+ [ O
6992
+ 6 O
6993
+ ] O
6994
+ . O
6995
+
6996
+ Sequences O
6997
+ analyzed O
6998
+ in O
6999
+ a O
7000
+ previous O
7001
+ study O
7002
+ of O
7003
+ the O
7004
+ microbial O
7005
+ diversity O
7006
+ of O
7007
+ Mono O
7008
+ Lake O
7009
+ by O
7010
+ Humayoun O
7011
+ et O
7012
+ al O
7013
+ . O
7014
+ ( O
7015
+ 2003 O
7016
+ ) O
7017
+ , O
7018
+ who O
7019
+ sampled O
7020
+ different O
7021
+ depths O
7022
+ from O
7023
+ the O
7024
+ same O
7025
+ redox O
7026
+ zones O
7027
+ at O
7028
+ Station O
7029
+ 6 O
7030
+ ( O
7031
+ 2 O
7032
+ m O
7033
+ , O
7034
+ aerobic O
7035
+ ; O
7036
+ 17 O
7037
+ . O
7038
+ 5 O
7039
+ m O
7040
+ , O
7041
+ microaerophilic O
7042
+ , O
7043
+ 23 O
7044
+ m O
7045
+ , O
7046
+ anoxic O
7047
+ ; O
7048
+ and O
7049
+ 35 O
7050
+ m O
7051
+ , O
7052
+ sulfidic O
7053
+ , O
7054
+ see O
7055
+ Humayoun O
7056
+ et O
7057
+ al O
7058
+ . O
7059
+ , O
7060
+ 2003 O
7061
+ ) O
7062
+ , O
7063
+ were O
7064
+ downloaded O
7065
+ from O
7066
+ NCBI O
7067
+ GenBank O
7068
+ ( O
7069
+ n O
7070
+ = O
7071
+ 274 O
7072
+ ) O
7073
+ . O
7074
+
7075
+ Preparation O
7076
+ of O
7077
+ Libraries O
7078
+ , O
7079
+ Shotgun O
7080
+ Metagenomic O
7081
+ Sequencing O
7082
+ , O
7083
+ and O
7084
+ Data O
7085
+ Preprocessing O
7086
+ All O
7087
+ materials O
7088
+ and O
7089
+ apparatus O
7090
+ were O
7091
+ from O
7092
+ Thermo O
7093
+ Fisher O
7094
+ Scientific O
7095
+ ( O
7096
+ Wilmington O
7097
+ , O
7098
+ DE O
7099
+ , O
7100
+ United O
7101
+ States O
7102
+ ) O
7103
+ , O
7104
+ unless O
7105
+ stated O
7106
+ otherwise O
7107
+ . O
7108
+
7109
+ An O
7110
+ aliquot O
7111
+ of O
7112
+ 300l O
7113
+ was O
7114
+ analyzed O
7115
+ for O
7116
+ cholesterol O
7117
+ , O
7118
+ triglyceride O
7119
+ , O
7120
+ high O
7121
+ - O
7122
+ and O
7123
+ low O
7124
+ - O
7125
+ density O
7126
+ lipoproteins O
7127
+ . O
7128
+
7129
+ Paired O
7130
+ - O
7131
+ end O
7132
+ sequencing O
7133
+ with O
7134
+ a O
7135
+ 100 O
7136
+ cycle O
7137
+ Illumina O
7138
+ HiSeq O
7139
+ run O
7140
+ generated O
7141
+ partial O
7142
+ ~ O
7143
+ 30 O
7144
+ bp O
7145
+ overlaps O
7146
+ , O
7147
+ and O
7148
+ six O
7149
+ libraries O
7150
+ were O
7151
+ multiplexed O
7152
+ per O
7153
+ lane O
7154
+ . O
7155
+
7156
+ To O
7157
+ sequence O
7158
+ the O
7159
+ library O
7160
+ preparation O
7161
+ , O
7162
+ Illumina O
7163
+ adapters O
7164
+ were O
7165
+ attached O
7166
+ to O
7167
+ the O
7168
+ amplicons O
7169
+ by O
7170
+ using O
7171
+ an O
7172
+ Illumina O
7173
+ TruSeq O
7174
+ DNA O
7175
+ sample O
7176
+ preparation O
7177
+ kit O
7178
+ , O
7179
+ v2 O
7180
+ . O
7181
+
7182
+ Major O
7183
+ capsid O
7184
+ protein O
7185
+ fragments O
7186
+ were O
7187
+ sequenced O
7188
+ with O
7189
+ three O
7190
+ strategies O
7191
+ , O
7192
+ i O
7193
+ . O
7194
+ e O
7195
+ . O
7196
+ , O
7197
+ clone O
7198
+ - O
7199
+ library O
7200
+ Sanger O
7201
+ sequencing O
7202
+ ( O
7203
+ about O
7204
+ 100 O
7205
+ reads O
7206
+ ) O
7207
+ , O
7208
+ shallow O
7209
+ Illumina O
7210
+ sequencing O
7211
+ ( O
7212
+ 1 O
7213
+ , O
7214
+ 0002 O
7215
+ , O
7216
+ 000 O
7217
+ reads O
7218
+ ) O
7219
+ , O
7220
+ and O
7221
+ deep O
7222
+ Illumina O
7223
+ sequencing O
7224
+ ( O
7225
+ more O
7226
+ than O
7227
+ 100 O
7228
+ , O
7229
+ 000 O
7230
+ reads O
7231
+ ) O
7232
+ . O
7233
+
7234
+ Gnotobiotic O
7235
+ mouse B
7236
+ experiments O
7237
+ All O
7238
+ experiments O
7239
+ involving O
7240
+ mice B
7241
+ were O
7242
+ performed O
7243
+ using O
7244
+ protocols O
7245
+ approved O
7246
+ by O
7247
+ the O
7248
+ Animal O
7249
+ Studies O
7250
+ Committee O
7251
+ of O
7252
+ the O
7253
+ Washington O
7254
+ University O
7255
+ School O
7256
+ of O
7257
+ Medicine O
7258
+ . O
7259
+
7260
+ All O
7261
+ mothers B
7262
+ attending O
7263
+ the O
7264
+ clinics O
7265
+ during O
7266
+ the O
7267
+ recruitment O
7268
+ periods O
7269
+ at O
7270
+ each O
7271
+ location O
7272
+ were O
7273
+ invited O
7274
+ to O
7275
+ participate O
7276
+ in O
7277
+ the O
7278
+ study O
7279
+ and O
7280
+ written O
7281
+ consent O
7282
+ was O
7283
+ obtained O
7284
+ from O
7285
+ all O
7286
+ who O
7287
+ agreed O
7288
+ to O
7289
+ participate O
7290
+ . O
7291
+
7292
+ Animal O
7293
+ models O
7294
+ such O
7295
+ as O
7296
+ adjuvant O
7297
+ - O
7298
+ induced O
7299
+ arthritis O
7300
+ ( O
7301
+ AIA O
7302
+ ) O
7303
+ , O
7304
+ one O
7305
+ of O
7306
+ the O
7307
+ most O
7308
+ widely O
7309
+ accepted O
7310
+ animal O
7311
+ models O
7312
+ [ O
7313
+ 1316 O
7314
+ ] O
7315
+ , O
7316
+ may O
7317
+ provide O
7318
+ new O
7319
+ knowledge O
7320
+ on O
7321
+ the O
7322
+ relationship O
7323
+ between O
7324
+ the O
7325
+ microbiota O
7326
+ and O
7327
+ RA O
7328
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7329
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7330
+ contribute O
7331
+ to O
7332
+ the O
7333
+ development O
7334
+ of O
7335
+ novel O
7336
+ microbial O
7337
+ - O
7338
+ based O
7339
+ drugs O
7340
+ . O
7341
+
7342
+ Nucleotide O
7343
+ sequence O
7344
+ accession O
7345
+ and O
7346
+ contextual O
7347
+ data O
7348
+ availability O
7349
+ 16S O
7350
+ rRNA O
7351
+ amplicon O
7352
+ and O
7353
+ shotgun O
7354
+ metagenomic O
7355
+ data O
7356
+ are O
7357
+ publicly O
7358
+ available O
7359
+ under O
7360
+ SRA O
7361
+ Bioproject O
7362
+ PRJNA248084 O
7363
+ ( O
7364
+ https O
7365
+ : O
7366
+ / O
7367
+ / O
7368
+ www O
7369
+ . O
7370
+ ncbi O
7371
+ . O
7372
+ nlm O
7373
+ . O
7374
+ nih O
7375
+ . O
7376
+ gov O
7377
+ / O
7378
+ bioproject O
7379
+ / O
7380
+ PRJNA248084 O
7381
+ / O
7382
+ ) O
7383
+ . O
7384
+
7385
+ Symptoms O
7386
+ with O
7387
+ respect O
7388
+ to O
7389
+ Cough O
7390
+ , O
7391
+ Sputum O
7392
+ Production O
7393
+ , O
7394
+ Shortness O
7395
+ of O
7396
+ Breath O
7397
+ , O
7398
+ Wheezing O
7399
+ , O
7400
+ Nasal O
7401
+ Irritation O
7402
+ , O
7403
+ Throat O
7404
+ Irritation O
7405
+ , O
7406
+ Fatigue O
7407
+ , O
7408
+ and O
7409
+ Appetite O
7410
+ were O
7411
+ independently O
7412
+ scored O
7413
+ relative O
7414
+ to O
7415
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7416
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7417
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7418
+ s O
7419
+ norm O
7420
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7421
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7422
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7423
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7424
+ 0 O
7425
+ ) O
7426
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7427
+ increased O
7428
+ symtomatology O
7429
+ scored O
7430
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7431
+ 1 O
7432
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7433
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7434
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7435
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7436
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7437
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7438
+ , O
7439
+ or O
7440
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7441
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7442
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7443
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7444
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7445
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7446
+ A O
7447
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7448
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7449
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7450
+ E O
7451
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7452
+ site O
7453
+ Underwater O
7454
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7455
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7456
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7457
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7458
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7459
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7460
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7461
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7462
+ 24 O
7463
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7464
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7465
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7466
+ Bottom O
7467
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7468
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7469
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7470
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7471
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7472
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7473
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7474
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7475
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7476
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7477
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7478
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7479
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7480
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7481
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7482
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7483
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7484
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7485
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7486
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7487
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7488
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7489
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7490
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7491
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7492
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7493
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7494
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7495
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7496
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7497
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7498
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7499
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7500
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7501
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7502
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7503
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7504
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7505
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7506
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7507
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7508
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7509
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7510
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7511
+ 5 O
7512
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7513
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7515
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7517
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7519
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7520
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7521
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7522
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7523
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7524
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7525
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7526
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7527
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7528
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7529
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7530
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7531
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7532
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7533
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7534
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7535
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7536
+ grain O
7537
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7538
+ [ O
7539
+ Q50 O
7540
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7541
+ 5 O
7542
+ 11 O
7543
+ 12 O
7544
+ 3377 O
7545
+ 10 O
7546
+ Sediment O
7547
+ type O
7548
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7549
+
7550
+ silt O
7551
+ Middle O
7552
+ silt O
7553
+ Middle O
7554
+ silt O
7555
+ Silty O
7556
+ - O
7557
+ sandy O
7558
+ Middle O
7559
+ silt O
7560
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7561
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7562
+ [ O
7563
+ % O
7564
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7565
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7566
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7567
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7568
+ 33 O
7569
+ 87 O
7570
+ Total O
7571
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7572
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7573
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7574
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7575
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7576
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7577
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7578
+ 0 O
7579
+ . O
7580
+ 3 O
7581
+ 0 O
7582
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7583
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7584
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7585
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7586
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7587
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7588
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7589
+ 0 O
7590
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7591
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7592
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7593
+ 0 O
7594
+ . O
7595
+ 3 O
7596
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7597
+ . O
7598
+ 04 O
7599
+ 0 O
7600
+ . O
7601
+ 0 O
7602
+ 0 O
7603
+ . O
7604
+ 4 O
7605
+ 0 O
7606
+ . O
7607
+ 0 O
7608
+ Total O
7609
+ organic O
7610
+ carbon O
7611
+
7612
+ ALOHA O
7613
+ ( O
7614
+ A O
7615
+ Long O
7616
+ - O
7617
+ term O
7618
+ Oligotrophic O
7619
+ Habitat O
7620
+ Assessment O
7621
+ ; O
7622
+ 22 O
7623
+ . O
7624
+ 45N O
7625
+ , O
7626
+ 158W O
7627
+ ) O
7628
+ , O
7629
+ an O
7630
+ open O
7631
+ - O
7632
+ ocean O
7633
+ field O
7634
+ site O
7635
+ ~ O
7636
+ 100 O
7637
+ km O
7638
+ north O
7639
+ of O
7640
+ Oahu O
7641
+ ( O
7642
+ Table O
7643
+ 1 O
7644
+ ) O
7645
+ . O
7646
+
7647
+ Patients O
7648
+ in O
7649
+ the O
7650
+ cohort O
7651
+ had O
7652
+ scheduled O
7653
+ visits O
7654
+ every O
7655
+ three O
7656
+ months O
7657
+ from O
7658
+ their O
7659
+ inclusion O
7660
+ and O
7661
+ unscheduled O
7662
+ visits O
7663
+ when O
7664
+ exacerbations O
7665
+ symptoms O
7666
+ appeared O
7667
+ , O
7668
+ as O
7669
+ described O
7670
+ elsewhere O
7671
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7672
+ 15 O
7673
+ ] O
7674
+ . O
7675
+
7676
+ Foods O
7677
+ and O
7678
+ portions O
7679
+ from O
7680
+ 24 O
7681
+ - O
7682
+ hour O
7683
+ dietary O
7684
+ recalls O
7685
+ were O
7686
+ entered O
7687
+ into O
7688
+ the O
7689
+ USDA O
7690
+ SuperTracker O
7691
+ system O
7692
+ ( O
7693
+ Britten O
7694
+ , O
7695
+ 2013 O
7696
+ ) O
7697
+ . O
7698
+
7699
+ Findings O
7700
+ Background O
7701
+ Cystic O
7702
+ fibrosis O
7703
+ ( O
7704
+ CF O
7705
+ ) O
7706
+ is O
7707
+ an O
7708
+ inherited O
7709
+ disease O
7710
+ that O
7711
+ affects O
7712
+ over O
7713
+ 70 O
7714
+ , O
7715
+ 000 O
7716
+ people B
7717
+ worldwide O
7718
+ . O
7719
+
7720
+ For O
7721
+ shotgun O
7722
+ pyrosequenced O
7723
+ data O
7724
+ , O
7725
+ sequences O
7726
+ were O
7727
+ first O
7728
+ analysed O
7729
+ with O
7730
+ the O
7731
+ MOTHUR O
7732
+ software O
7733
+ package O
7734
+ 1 O
7735
+ . O
7736
+ 27 O
7737
+ to O
7738
+ remove O
7739
+ sequences O
7740
+ shorter O
7741
+ than O
7742
+ 100 O
7743
+ bp O
7744
+ . O
7745
+
7746
+ Establishment O
7747
+ of O
7748
+ light O
7749
+ and O
7750
+ heavy O
7751
+ oil O
7752
+ - O
7753
+ degrading O
7754
+ produced O
7755
+ water O
7756
+ cultures O
7757
+ Oil O
7758
+ - O
7759
+ free O
7760
+ produced O
7761
+ water O
7762
+ from O
7763
+ all O
7764
+ five O
7765
+ PW O
7766
+ samples O
7767
+ was O
7768
+ combined O
7769
+ in O
7770
+ equal O
7771
+ ratios O
7772
+ and O
7773
+ 500 O
7774
+ mL O
7775
+ aliquots O
7776
+ were O
7777
+ dispensed O
7778
+ into O
7779
+ five O
7780
+ sterile O
7781
+ , O
7782
+ custom O
7783
+ - O
7784
+ made O
7785
+ glass O
7786
+ vessels O
7787
+ . O
7788
+
7789
+ Methods O
7790
+ Materials O
7791
+ and O
7792
+ methods O
7793
+ Fecal O
7794
+ samples O
7795
+ were O
7796
+ collected O
7797
+ from O
7798
+ dogs B
7799
+ ( O
7800
+ Cases O
7801
+ ) O
7802
+ diagnosed O
7803
+ with O
7804
+ MUO O
7805
+ at O
7806
+ the O
7807
+ veterinary O
7808
+ hospitals O
7809
+ of O
7810
+ Iowa O
7811
+ State O
7812
+ University O
7813
+ ( O
7814
+ ISU O
7815
+ ) O
7816
+ and O
7817
+ Texas O
7818
+ A O
7819
+ & O
7820
+ M O
7821
+ University O
7822
+ ( O
7823
+ TAMU O
7824
+ ) O
7825
+ and O
7826
+ stored O
7827
+ in O
7828
+ a O
7829
+ - O
7830
+ 80C O
7831
+ freezer O
7832
+ for O
7833
+ analysis O
7834
+ at O
7835
+ completion O
7836
+ of O
7837
+ case O
7838
+ recruitment O
7839
+ . O
7840
+
7841
+ Sequencing O
7842
+ of O
7843
+ 16S O
7844
+ rRNA O
7845
+ genes O
7846
+ by O
7847
+ Illumina O
7848
+ MiSeq O
7849
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7850
+ performed O
7851
+ to O
7852
+ check O
7853
+ the O
7854
+ purity O
7855
+ of O
7856
+ the O
7857
+ culture O
7858
+ . O
7859
+
7860
+ The O
7861
+ cohort O
7862
+ included O
7863
+ COPD O
7864
+ patients O
7865
+ with O
7866
+ a O
7867
+ FEV1 O
7868
+ below O
7869
+ 50 O
7870
+ % O
7871
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7872
+ the O
7873
+ reference O
7874
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7875
+ 16 O
7876
+ ] O
7877
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7878
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7879
+ reported O
7880
+ three O
7881
+ or O
7882
+ more O
7883
+ exacerbations O
7884
+ in O
7885
+ the O
7886
+ previous O
7887
+ year O
7888
+ and O
7889
+ who O
7890
+ had O
7891
+ attended O
7892
+ the O
7893
+ Day O
7894
+ Care O
7895
+ Unit O
7896
+ of O
7897
+ Sabadell O
7898
+ University O
7899
+ Hospital O
7900
+ since O
7901
+ 2005 O
7902
+ . O
7903
+
7904
+ Briefly O
7905
+ , O
7906
+ vertical O
7907
+ profiles O
7908
+ of O
7909
+ relevant O
7910
+ environmental O
7911
+ variables O
7912
+ : O
7913
+ photosynthetically O
7914
+ active O
7915
+ radiation O
7916
+ ( O
7917
+ PAR O
7918
+ , O
7919
+ LiCor O
7920
+ 2 O
7921
+ quantum O
7922
+ sensor O
7923
+ , O
7924
+ 400700 O
7925
+ nm O
7926
+ , O
7927
+ E O
7928
+ m2 O
7929
+ s2 O
7930
+ ) O
7931
+ , O
7932
+ fluorescence O
7933
+ ( O
7934
+ WetLabs O
7935
+ fluorometer O
7936
+ , O
7937
+ relative O
7938
+ fluorescence O
7939
+ units O
7940
+ ) O
7941
+ , O
7942
+ dissolved O
7943
+ oxygen O
7944
+ ( O
7945
+ SBE O
7946
+ 43 O
7947
+ , O
7948
+ mg O
7949
+ L1 O
7950
+ ) O
7951
+ and O
7952
+ attenuation O
7953
+ coefficient O
7954
+ ( O
7955
+ WetLabs O
7956
+ transmissometer O
7957
+ , O
7958
+ 600 O
7959
+ nm O
7960
+ wavelength O
7961
+ light O
7962
+ source O
7963
+ , O
7964
+ 10 O
7965
+ cm O
7966
+ path O
7967
+ length O
7968
+ , O
7969
+ m1 O
7970
+ ) O
7971
+ were O
7972
+ obtained O
7973
+ using O
7974
+ sensors O
7975
+ mounted O
7976
+ on O
7977
+ the O
7978
+ frame O
7979
+ holding O
7980
+ a O
7981
+ SeaBird O
7982
+ SBE O
7983
+ 19 O
7984
+ CTD O
7985
+ ( O
7986
+ conductivity O
7987
+ , O
7988
+ temperature O
7989
+ , O
7990
+ depth O
7991
+ ) O
7992
+
7993
+ recorder O
7994
+ , O
7995
+ modified O
7996
+ and O
7997
+ calibrated O
7998
+ for O
7999
+ use O
8000
+ in O
8001
+ Mono O
8002
+ Lake O
8003
+ . O
8004
+
8005
+ Enrichments O
8006
+ were O
8007
+ set O
8008
+ up O
8009
+ in O
8010
+ triplicates O
8011
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8012
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8013
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8014
+ 40 O
8015
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8016
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8017
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8018
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8019
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8020
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8021
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8022
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8023
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8024
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8025
+ 21 O
8026
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8027
+ 5 O
8028
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8029
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8030
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8031
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8032
+ electron O
8033
+ acceptor O
8034
+ . O
8035
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8036
+ All O
8037
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8038
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8039
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8040
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8041
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8042
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8043
+ 37C O
8044
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8045
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8046
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8047
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8048
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8049
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8050
+ Saudi O
8051
+ Arabia O
8052
+ , O
8053
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8054
+ continuously O
8055
+ mixed O
8056
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8057
+ 100rpm O
8058
+ for O
8059
+ sludge O
8060
+ acclimation O
8061
+ . O
8062
+
8063
+ Metabolic O
8064
+ Potential O
8065
+ of O
8066
+ As O
8067
+ - O
8068
+ yet O
8069
+ - O
8070
+ uncultured O
8071
+ Archaeal O
8072
+ Lineages O
8073
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8074
+ Candidatus O
8075
+ Hydrothermarchaeota O
8076
+ Thriving O
8077
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8078
+ Deep O
8079
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8080
+ sea O
8081
+ Metal O
8082
+ Sulfide O
8083
+ Deposits O
8084
+ Candidatus O
8085
+ Hydrothermarchaeota O
8086
+ , O
8087
+ formally O
8088
+ called O
8089
+ Marine O
8090
+ Benthic O
8091
+ Group O
8092
+ E O
8093
+ , O
8094
+ has O
8095
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8096
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8097
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8098
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8099
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8100
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8101
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8102
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8103
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8104
+ rich O
8105
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8106
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8107
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8108
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8109
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8110
+ hydrothermal O
8111
+ vents O
8112
+ and O
8113
+ cold O
8114
+ seeps O
8115
+ . O
8116
+
8117
+ The O
8118
+ overlapping O
8119
+ paired O
8120
+ - O
8121
+ end O
8122
+ reads O
8123
+ were O
8124
+ stitched O
8125
+ together O
8126
+ ( O
8127
+ approximately O
8128
+ 97bp O
8129
+ overlap O
8130
+ ) O
8131
+ , O
8132
+ and O
8133
+ size O
8134
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8135
+ to O
8136
+ reduce O
8137
+ non O
8138
+ - O
8139
+ specific O
8140
+ amplification O
8141
+ products O
8142
+ from O
8143
+ host O
8144
+ DNA O
8145
+ ( O
8146
+ 225275bp O
8147
+ ) O
8148
+ . O
8149
+
8150
+ Adaptor O
8151
+ - O
8152
+ appended O
8153
+ fragments O
8154
+ were O
8155
+ sequenced O
8156
+ on O
8157
+ Illumina O
8158
+ MiSeq O
8159
+ desktop O
8160
+ sequencer O
8161
+ ( O
8162
+ 2300bp O
8163
+ paired O
8164
+ - O
8165
+ end O
8166
+ run O
8167
+ , O
8168
+ San O
8169
+ Diego O
8170
+ , O
8171
+ CA O
8172
+ ) O
8173
+ according O
8174
+ to O
8175
+ standard O
8176
+ protocols O
8177
+ . O
8178
+
8179
+ The O
8180
+ PCRs O
8181
+ included O
8182
+ about O
8183
+ 5ng O
8184
+ of O
8185
+ DNA O
8186
+ extract O
8187
+ , O
8188
+ 15pmol O
8189
+ of O
8190
+ each O
8191
+ forward O
8192
+ primer O
8193
+ U341F O
8194
+ 5 O
8195
+ - O
8196
+ NNNNNNNNNNCCTAYGGGRBGCASCAG O
8197
+ and O
8198
+ reverse O
8199
+ primer O
8200
+ U806R O
8201
+ 5 O
8202
+ - O
8203
+ NNNNNNNNNNGGACTACNNGGGTATCTAAT O
8204
+ in O
8205
+ a O
8206
+ 20L O
8207
+ volume O
8208
+ of O
8209
+ MyTaq O
8210
+ buffer O
8211
+ containing O
8212
+ 1 O
8213
+ . O
8214
+ 5 O
8215
+ units O
8216
+ MyTaq O
8217
+ DNA O
8218
+ polymerase O
8219
+ ( O
8220
+ Bioline O
8221
+ ) O
8222
+ and O
8223
+ 2L O
8224
+ of O
8225
+ BioStabII O
8226
+ PCR O
8227
+ Enhancer O
8228
+ ( O
8229
+ Sigma O
8230
+ ) O
8231
+ . O
8232
+
8233
+ Further O
8234
+ bioinformatic O
8235
+ analysis O
8236
+ of O
8237
+ the O
8238
+ 16S O
8239
+ rRNA O
8240
+ gene O
8241
+ amplicon O
8242
+ sequencing O
8243
+ ( O
8244
+ primer O
8245
+ cutting O
8246
+ , O
8247
+ quality O
8248
+ and O
8249
+ length O
8250
+ trimming O
8251
+ , O
8252
+ merging O
8253
+ , O
8254
+ OTU O
8255
+ clustering O
8256
+ , O
8257
+ and O
8258
+ phylogenetic O
8259
+ analysis O
8260
+ ) O
8261
+ was O
8262
+ conducted O
8263
+ using O
8264
+ the O
8265
+ CLC O
8266
+ Genomic O
8267
+ Workbench O
8268
+ software O
8269
+ 10 O
8270
+ . O
8271
+ 0 O
8272
+ . O
8273
+ 1 O
8274
+ with O
8275
+ the O
8276
+ additional O
8277
+ microbial O
8278
+ genomic O
8279
+ module O
8280
+ 2 O
8281
+ . O
8282
+ 0 O
8283
+ . O
8284
+
8285
+ Bacterial O
8286
+ and O
8287
+ archaeal O
8288
+ 16S O
8289
+ rRNA O
8290
+ gene O
8291
+ fragments O
8292
+ were O
8293
+ amplified O
8294
+ as O
8295
+ described O
8296
+ before O
8297
+ ( O
8298
+ Gonzalez O
8299
+ - O
8300
+ Gil O
8301
+ et O
8302
+ al O
8303
+ . O
8304
+ , O
8305
+ 2015 O
8306
+ ) O
8307
+ . O
8308
+
8309
+ The O
8310
+ 16S O
8311
+ and O
8312
+ 18S O
8313
+ rRNA O
8314
+ amplicons O
8315
+ were O
8316
+ prepared O
8317
+ according O
8318
+ to O
8319
+ the O
8320
+ Illumina O
8321
+ 16S O
8322
+ Metagenomic O
8323
+ Sequencing O
8324
+ Library O
8325
+ Preparation O
8326
+ guide O
8327
+ [ O
8328
+ 19 O
8329
+ ] O
8330
+ and O
8331
+ as O
8332
+ described O
8333
+ previously O
8334
+ [ O
8335
+ 20 O
8336
+ ] O
8337
+ . O
8338
+
8339
+ Definition O
8340
+ of O
8341
+ carriage O
8342
+ by O
8343
+ lytA O
8344
+ Pcr O
8345
+ The O
8346
+ presence O
8347
+ of O
8348
+ S O
8349
+ . O
8350
+ pneumoniae O
8351
+ was O
8352
+ assessed O
8353
+ using O
8354
+ a O
8355
+ lytA O
8356
+ qPCR O
8357
+ as O
8358
+ described O
8359
+ ( O
8360
+ WHO O
8361
+ and O
8362
+ CDC O
8363
+ , O
8364
+ 2011 O
8365
+ ) O
8366
+ using O
8367
+ primers O
8368
+ F373 O
8369
+ : O
8370
+ 5 O
8371
+ - O
8372
+ ACGCAATCTAGCAGATGAAGCA O
8373
+ - O
8374
+ 3 O
8375
+ and O
8376
+ R424 O
8377
+ : O
8378
+ 5 O
8379
+ TCGTGCGTTTTAATTCCAGCT O
8380
+ - O
8381
+ 3 O
8382
+ . O
8383
+
8384
+ All O
8385
+ samples O
8386
+ were O
8387
+ de O
8388
+ - O
8389
+ identified O
8390
+ , O
8391
+ and O
8392
+ by O
8393
+ using O
8394
+ information O
8395
+ from O
8396
+ participants B
8397
+ assigned O
8398
+ to O
8399
+ a O
8400
+ menstrual O
8401
+ phase O
8402
+ by O
8403
+ using O
8404
+ a O
8405
+ calendar O
8406
+ - O
8407
+ based O
8408
+ method O
8409
+ : O
8410
+ menstrual O
8411
+ , O
8412
+ day O
8413
+ 1 O
8414
+ ( O
8415
+ onset O
8416
+ of O
8417
+ menstruation O
8418
+ ) O
8419
+ to O
8420
+ cessation O
8421
+ of O
8422
+ bleeding O
8423
+ ( O
8424
+ day O
8425
+ 4 O
8426
+ to O
8427
+ 7 O
8428
+ ) O
8429
+ ; O
8430
+ follicular O
8431
+ , O
8432
+ cessation O
8433
+ of O
8434
+ bleeding O
8435
+ to O
8436
+ day O
8437
+ 12 O
8438
+ ; O
8439
+ periovulatory O
8440
+ , O
8441
+ day O
8442
+ 13 O
8443
+ to O
8444
+ day O
8445
+ 16 O
8446
+ ; O
8447
+ luteal O
8448
+ , O
8449
+ day O
8450
+ 17 O
8451
+ to O
8452
+ days O
8453
+ 26 O
8454
+ to O
8455
+ 32 O
8456
+ ( O
8457
+ commencement O
8458
+ of O
8459
+ bleeding O
8460
+ ) O
8461
+ . O
8462
+
8463
+ Donors B
8464
+ stated O
8465
+ that O
8466
+ their O
8467
+ last O
8468
+ menstrual O
8469
+ period O
8470
+ had O
8471
+ ended O
8472
+ at O
8473
+ least O
8474
+ 3days O
8475
+ prior O
8476
+ to O
8477
+ donating O
8478
+ and O
8479
+ that O
8480
+ they O
8481
+ had O
8482
+ not O
8483
+ used O
8484
+ vaginal O
8485
+ products O
8486
+ or O
8487
+ participated O
8488
+ in O
8489
+ intercourse O
8490
+ within O
8491
+ 24h O
8492
+ prior O
8493
+ to O
8494
+ donating O
8495
+ . O
8496
+
8497
+ Genomic O
8498
+ DNA O
8499
+ libraries O
8500
+ were O
8501
+ generated O
8502
+ using O
8503
+ TruSeq O
8504
+ Nano O
8505
+ DNA O
8506
+ Sample O
8507
+ Prep O
8508
+ Kit O
8509
+ ( O
8510
+ Illumina O
8511
+ , O
8512
+ San O
8513
+ Diego O
8514
+ , O
8515
+ CA O
8516
+ , O
8517
+ USA O
8518
+ ) O
8519
+ according O
8520
+ to O
8521
+ the O
8522
+ manufacturers O
8523
+ instructions O
8524
+ . O
8525
+
8526
+ Flour O
8527
+ ( O
8528
+ 120 O
8529
+ g O
8530
+ ) O
8531
+ and O
8532
+ sterile O
8533
+ tap O
8534
+ water O
8535
+ ( O
8536
+ 60 O
8537
+ g O
8538
+ ) O
8539
+ were O
8540
+ kneaded O
8541
+ with O
8542
+ a O
8543
+ continuous O
8544
+ high O
8545
+ - O
8546
+ speed O
8547
+ mixer O
8548
+ ( O
8549
+ 60 O
8550
+ g O
8551
+ , O
8552
+ dough O
8553
+ mixing O
8554
+ time O
8555
+ 5 O
8556
+ min O
8557
+ ) O
8558
+ ( O
8559
+ Chopin O
8560
+ & O
8561
+ Co O
8562
+ . O
8563
+ , O
8564
+ Boulogne O
8565
+ , O
8566
+ Seine O
8567
+ , O
8568
+ France O
8569
+ ) O
8570
+ . O
8571
+
8572
+ The O
8573
+ pH O
8574
+ of O
8575
+ the O
8576
+ water O
8577
+ was O
8578
+ measured O
8579
+ varying O
8580
+ from O
8581
+ 7 O
8582
+ . O
8583
+ 8 O
8584
+ to O
8585
+ 8 O
8586
+ . O
8587
+ 0 O
8588
+ . O
8589
+
8590
+ The O
8591
+ sandstone O
8592
+ and O
8593
+ lignite O
8594
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8595
+ were O
8596
+ preserved O
8597
+ in O
8598
+ sterile O
8599
+ glass O
8600
+ bottles O
8601
+ under O
8602
+ anaerobic O
8603
+ conditions O
8604
+ with O
8605
+ filtered O
8606
+ N2 O
8607
+ gas O
8608
+ , O
8609
+ and O
8610
+ stored O
8611
+ at O
8612
+ 4C O
8613
+ in O
8614
+ the O
8615
+ dark O
8616
+ prior O
8617
+ to O
8618
+ use O
8619
+ in O
8620
+ the O
8621
+ shore O
8622
+ - O
8623
+ based O
8624
+ laboratory O
8625
+ . O
8626
+
8627
+ Dissolved O
8628
+ oxygen O
8629
+ and O
8630
+ temperature O
8631
+ ( O
8632
+ Oxymeter O
8633
+ YSI O
8634
+ 550A O
8635
+ ) O
8636
+ , O
8637
+ conductivity O
8638
+ ( O
8639
+ Digimed O
8640
+ DM O
8641
+ - O
8642
+ 3P O
8643
+ ) O
8644
+ , O
8645
+ turbidity O
8646
+ ( O
8647
+ Motte O
8648
+ 202VE O
8649
+ ) O
8650
+ , O
8651
+ and O
8652
+ water O
8653
+ transparency O
8654
+ ( O
8655
+ Secchi O
8656
+ disk O
8657
+ ) O
8658
+ were O
8659
+ measured O
8660
+ in O
8661
+ the O
8662
+ field O
8663
+ . O
8664
+
8665
+ 16S O
8666
+ rDNA O
8667
+ sequencing O
8668
+ of O
8669
+ selected O
8670
+ samples O
8671
+ DNA O
8672
+ samples O
8673
+ ( O
8674
+ from O
8675
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8676
+ independent O
8677
+ replicates O
8678
+ ) O
8679
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8680
+ on O
8681
+ days O
8682
+ 30 O
8683
+ , O
8684
+ 37 O
8685
+ and O
8686
+ 50 O
8687
+ ( O
8688
+ phase O
8689
+ 2 O
8690
+ ) O
8691
+ , O
8692
+ and O
8693
+ days O
8694
+ 178 O
8695
+ , O
8696
+ 192 O
8697
+ and O
8698
+ 206 O
8699
+ ( O
8700
+ phase O
8701
+ 4 O
8702
+ ) O
8703
+ from O
8704
+ the O
8705
+ fermenter O
8706
+ and O
8707
+ post O
8708
+ - O
8709
+ digester O
8710
+ were O
8711
+ selected O
8712
+ for O
8713
+ high O
8714
+ throughput O
8715
+ sequencing O
8716
+ of O
8717
+ the O
8718
+ amplified O
8719
+ 16S O
8720
+ rDNA O
8721
+ fragments O
8722
+ as O
8723
+ described O
8724
+ by O
8725
+ Sundberg O
8726
+ et O
8727
+ al O
8728
+ . O
8729
+ ( O
8730
+ 2013 O
8731
+ ) O
8732
+ . O
8733
+
8734
+ The O
8735
+ samples O
8736
+ ( O
8737
+ 27 O
8738
+ pooled O
8739
+ and O
8740
+ 4 O
8741
+ individual O
8742
+ replicates O
8743
+ ) O
8744
+ were O
8745
+ next O
8746
+ individually O
8747
+ barcoded O
8748
+ and O
8749
+ sequenced O
8750
+ using O
8751
+ the O
8752
+ Illumina O
8753
+ MiSeq O
8754
+ platform O
8755
+ via O
8756
+ the O
8757
+ MiSeq O
8758
+ Reagent O
8759
+ Kit O
8760
+ v2 O
8761
+ ( O
8762
+ 500 O
8763
+ cycle O
8764
+ ) O
8765
+ , O
8766
+ producing O
8767
+ paired O
8768
+ - O
8769
+ end O
8770
+ reads O
8771
+ each O
8772
+ 250 O
8773
+ nucleotides O
8774
+ in O
8775
+ length O
8776
+ . O
8777
+
8778
+ Spring O
8779
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8780
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8781
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8782
+ according O
8783
+ to O
8784
+ following O
8785
+ criteria O
8786
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8787
+ evidence O
8788
+ of O
8789
+ continuous O
8790
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8791
+ flow O
8792
+ from O
8793
+ the O
8794
+ rock O
8795
+ , O
8796
+ close O
8797
+ to O
8798
+ bubbling O
8799
+ zones O
8800
+ , O
8801
+ and O
8802
+ near O
8803
+ the O
8804
+ most O
8805
+ reductive O
8806
+ point O
8807
+ . O
8808
+
8809
+ Introduction O
8810
+ Anaerobic O
8811
+ digestion O
8812
+ ( O
8813
+ AD O
8814
+ ) O
8815
+ involves O
8816
+ the O
8817
+ conversion O
8818
+ of O
8819
+ organics O
8820
+ to O
8821
+ valuable O
8822
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8823
+ , O
8824
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8825
+ is O
8826
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8827
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8828
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8829
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8830
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8831
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8832
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8833
+ of O
8834
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8835
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8836
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8837
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8838
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8839
+ Duplicate O
8840
+ filters O
8841
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8842
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8843
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8844
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8845
+ 2008 O
8846
+ and O
8847
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8848
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8849
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8850
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8851
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8852
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8853
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8854
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8855
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8856
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8857
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8858
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8859
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8860
+ days O
8861
+ ( O
8862
+ 11 O
8863
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8864
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8865
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8866
+ Study O
8867
+ on O
8868
+ a O
8869
+ Fermented O
8870
+ Whole O
8871
+ Wheat O
8872
+ : O
8873
+ Phenolic O
8874
+ Content O
8875
+ , O
8876
+ Activity O
8877
+ on O
8878
+ PTP1B O
8879
+ Enzyme O
8880
+ and O
8881
+ In O
8882
+ Vitro O
8883
+ Prebiotic O
8884
+ Properties O
8885
+ Fermented O
8886
+ cereals O
8887
+ , O
8888
+ staple O
8889
+ foods O
8890
+ in O
8891
+ Asia O
8892
+ and O
8893
+ Africa O
8894
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8895
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8896
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8897
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8898
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8899
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8900
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8901
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8902
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8903
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8904
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8905
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8906
+ The O
8907
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8908
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8909
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8910
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8911
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8912
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8913
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8914
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8915
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8916
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8917
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8918
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8919
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8920
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8921
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8922
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8923
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8924
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8925
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8926
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8927
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8928
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8929
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8930
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8931
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8932
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8933
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8934
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8935
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8936
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8937
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8938
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8939
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8940
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8941
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8942
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8943
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8944
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8945
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8946
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8947
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8948
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8949
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8950
+ R806 O
8951
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8952
+ PCR O
8953
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8954
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8955
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8956
+ ] O
8957
+ ; O
8958
+ for O
8959
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8960
+ , O
8961
+ primers O
8962
+ ITS3 O
8963
+ and O
8964
+ ITS4 O
8965
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8966
+ PCR O
8967
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8968
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8969
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8970
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8971
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8972
+ . O
8973
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8974
+ SamplingReadsEnvironmental O
8975
+ parametersSiteCoordinatesDateDepth O
8976
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8977
+ m O
8978
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8979
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8980
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8981
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8982
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8983
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8984
+ a O
8985
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8986
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8987
+ L1 O
8988
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8989
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8990
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8991
+ 0248E09 O
8992
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8993
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8994
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8995
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8996
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8997
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8998
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8999
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9000
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9001
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9002
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9003
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9004
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9005
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9006
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9007
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9008
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9009
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9010
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9011
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9012
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9013
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9014
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9015
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9016
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9017
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9018
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9019
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9020
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9021
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9022
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9023
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9024
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9025
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9026
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9027
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9028
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9029
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9030
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9031
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9032
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9033
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9034
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9035
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9036
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9037
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9038
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9039
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9040
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9041
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9042
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9043
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9044
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9045
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9046
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9048
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9049
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9050
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9051
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9052
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9053
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9054
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9055
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9056
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9057
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9058
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9059
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9060
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9061
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9062
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9063
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9064
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9065
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9066
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9068
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9609
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9628
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9661
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9743
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9827
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9874
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test_results.txt ADDED
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