dataesr/scientific-paragraphs-categorization huggingface dataset:
Sequencing the Bacteroides cellulosilyticus WH2 Genome Though at least eight complete and 68 draft genomes of Bacteroides spp. are currently available  [27] , there are numerous examples of distinct clades within this genus where little genomic information exists. To further explore the genome space of one such clade, we obtained a human fecal isolate whose four 16S rRNA gene sequences indicate a close relationship to Bacteroides cellulosilyticus (Figure  S1A, B ). The genome of this isolate, which we have designated B. cellulosilyticus WH2, was sequenced deeply, yielding a high-quality draft assembly (23 contigs with an N50 value of 798,728 bp; total length of all contigs in the assembly, 7. 1 Mb; Table  S1 ). Annotation of its 5,244 predicted proteincoding genes using the carbohydrate active enzyme (CAZy) database  [28]  revealed an extraordinary complement of 503 CAZymes comprising 373 GHs, 23 PLs, 28 carbohydrate esterases (CEs), and 84 glycosyltransferases (GTs) (see Table  S2  for all annotated genes in the B.
cellulosilyticus WH2 genome predicted to have relevance to carbohydrate metabolism). One distinguishing feature of gut Bacteroides genomes is the substantial number of CAZymes they encode relative to those of other intestinal bacteria  [29]. The B. cellulosilyticus WH2 CAZome is enriched in a number of GH families even when compared with prominent representatives of the gut Bacteroidetes (Figure  S2A ). When we expanded this comparison to include all 86 Bacteroidetes in the CAZy database, we found that the B. cellulosilyticus WH2 genome had the greatest number of genes for 19 different GH families, as well as genes from two GH families that had not previously been observed within a Bacteroidetes genome (Figure  S2B ). Altogether, B. cellulosilyticus WH2 has more GH genes at its disposal than any other Bacteroidetes species analyzed to date.
thetaiotaomicron VPI-5482 revealed an unprecedented number of susC/D pairs (a total of 118). Studies of other prominent Bacteroides spp. have found that the evolutionary expansion of these genes has played an important role in endowing the Bacteroides with the ability to degrade a wide range of host-and plant-derived polysaccharides  [25, 33]. Analysis of deeply sampled adult human gut microbiota datasets indicates that B. cellulosilyticus strains are common, colonizing approximately 77% of 124 adult Europeans characterized in one study  [18]  and 62% of 139 individuals living in the United States examined in another survey  [20]. We hypothesized that the apparent success of B. cellulosilyticus in the gut is derived in part from its substantial arsenal of genes involved in carbohydrate utilization.
The second diet switch from phase 2 to 3 resulted in a similar movement along PC1 in the opposite direction, indicating a reversion of the artificial community's configuration to its originally assembled structure in each treatment group. These results, in addition to demonstrating the significant impact of these two diets on the structure of this 12member artificial human gut community, also suggest that an assemblage of this size is capable of demonstrating resilience in the face of substantial diet perturbations. The assembly process and observed diet-induced reconfigurations also proved to be highly reproducible as evidenced by COPRO-Seq results from a replication of E 1 (experiment 2, ''E 2 ''). In this follow-up experiment, fecal samples were collected more frequently than in E 1 , providing a dataset with improved temporal resolution.
We had three goals: (i) to evaluate how our ability to assign peptide-spectrum matches (PSMs) to particular proteins within a theoretical metaproteome is affected by the presence of close homologs within the same species and within other, closely related species; (ii) to test the limits of our ability to characterize protein expression across different species given the substantial dynamic range we documented in microbial species abundance; and (iii) to collect semiquantitative peptide/protein data that might validate and enrich our understanding of Rapid responses  (33)  (higher on HF/HS) Gradual responses  (   3. Top-down analysis of fecal microbiome RNA expression in mice receiving oscillating diets. The fecal metatranscriptomes of four animals in the LF/HPPRHF/HSRLF/HPP treatment group of E 2 were analyzed using microbial RNA-Seq at seven time-points to evaluate the temporal progression of changes in expressed microbial community functions triggered by a change in diet.
These data also allowed us to evaluate whether or not the types of genes considered might influence the degree of correlation between these two datasets. We first performed a spectral count-based correlation analysis on the diet-induced, logtransformed, average fold-differences in expression for all B. cellulosilyticus WH2 genes that were detectable at both the RNA and protein level for both diets. The results revealed a moderate degree of linear correlation between RNA and protein observations (Figure  S8C , black plot; r = 0. 53). However, subsequent division of these genes into functionally related subsets, which were each subjected to their own correlation analysis, revealed striking differences in the degree to which RNA-level and protein-level expression changes agreed with one another.
Additionally, these data further emphasize the need for enhanced dynamic range metaproteome measurements and better bioinformatic methods to assign/bin unique and nonunique peptides so that deeper and more thorough surveys of the microbial protein landscape can be performed and evaluated alongside more robust transcriptional datasets. Identifying Two Diet-Inducible, Xylanase-Containing PULs Whose Genetic Disruption Results in Diet-Specific Loss of Fitness Several of the most highly expressed and diet-sensitive B. cellulosilyticus WH2 genes in this study fell within two putative PULs. One PUL (BWH2_4044-55) contains 12 ORFs that include a dual susC/D cassette, three putative xylanases assigned to CAZy families GH8 and GH10, a putative multifunctional acetyl xylan esterase/a-L-fucosidase, and a putative hybrid two-component system regulator (Figure  4A ).
To identify specific mono-and/or polysaccharides capable of triggering the activation of these two PULs, as well as the 111 other putative PULs within the B. cellulosilyticus WH2 genome, we used RNA-Seq to characterize its transcriptional profile at mid-log phase in MM (Table  S12 ) plus one of 16 simple sugars or one of 15 complex sugars (Table  S13 ) (see Materials and Methods; n = 2-3 cultures/substrate; 5. 2-14. 0 million raw Illumina HiSeq reads generated for each of the 90 transcriptomes). After mapping each read to the B. cellulosilyticus WH2 reference gene set, counts were normalized using DESeq to allow for direct comparisons across samples and conditions. Hierarchical clustering of the normalized dataset resulted in a well-ordered dendrogram in which samples clustered almost perfectly by the carbohydrate on which B.
Ordination of COPRO-Seq Data Using QIIME COPRO-Seq proportional abundance data were subjected to ordination using scripts found in QIIME v1. 5. 0-dev  [53]. Data from both E 1 and E 2 were combined to generate a single tabdelimited table conforming to QIIME's early (pre-v1. 4. 0-dev) OTU table format. This pseudo-OTU table was subsequently converted into a BIOM-formatted table object that was used as the input for beta_diversity. py to calculate the pairwise distances between all samples using a Hellinger metric. PCoA calculations were performed using principal_coordinates. py. These coordinates and sample metadata were passed to make_3d_plots. py to generate PCoA plots. Plots shown are visualized using v2. 21 of the KiNG software package  [54].
Metatranscriptomics GeneChip. A custom Affymetrix GeneChip (''SynComm1'') with perfect match/mismatch (PM/MM) probe sets targeting 97. 6% of the predicted protein-coding genes within the genomes of the 12 bacterial species in this study (plus three additional species not included in the model human gut microbiota) was designed and manufactured in collaboration with the Affymetrix chip design team. Control probes targeting intergenic regions from each genome were also tiled onto the array to allow detection of any contaminating gDNA. Hybridizations were carried out with 0. 9-5. 1 mg cDNA using the manufacturer's recommended protocols. Details regarding the design of this GeneChip are deposited under Gene Expression Omnibus (GEO) accession GPL9803. Custom mask files were generated for each species on the GeneChip for the purpose of performing data normalization one species at a time.
Normalization of raw intensity values was carried out in Affymetrix Microarray Suite (MAS) v5. 0. MAS output was exported to Excel where advanced filtering was used to identify those probe sets called present in at least five of seven cecal RNA samples in at least one diet tested. Data from probe sets that did not meet these criteria (i. e. , genes that were not expressed on either condition) were not included in subsequent analyses. Normalized, filtered data were evaluated using the Cyber-T web server  [55]  to identify differentially expressed genes. Genes were generally considered significantly differentially expressed in cases meeting the following three criteria: p , 0. 01, PPDE(,p) $ 0. 99, and |fold-change|$ 2. Microbial RNA-Seq. Methods for extracting total microbial RNA from mouse feces and cecal contents, depleting small RNAs (e.
g. , tRNA) and ribosomal RNA (5S, 16S, and 23S rRNA), and for converting depleted RNA to double-stranded cDNA were described previously  [14]. Illumina libraries were prepared  [11]  from 26 fecal samples obtained from the second diet oscillation experiment (four animals, 6-7 time-points surveyed per animal), using 500 ng of input double-stranded cDNA/sample/library. RNA-Seq reads were aligned to the reference genomes using the SSAHA2 aligner  [56]. Normalization of the resulting raw counts was performed using the DESeq package in R  [57]. Raw counts derived from the metatranscriptome were normalized either at the community level (i. e. , counts from all genes were included in the same table during normalization) for purposes of looking at community-level representation of functions (ECs) of interest, or at the species level (i.
e. , counts from each species were independently normalized) for purposes of looking at gene expression changes within individual species. Data adjustment (logarithmic transformation) and hierarchical clustering were performed using Cluster 3. 0  [58]  and GENE-E. Heatmap visualizations of expression data were prepared using JavaTreeview  [59]  and Microsoft Excel. The B. cellulosilyticus WH2 in vitro gene expression dendrogram presented was prepared using GENE-E. Bootstrap probabilities at each edge of the dendrogram were calculated using the ''pvclust'' package in R (10,000 replications). Clusters with bootstrap p values. 0. 95 were considered strongly supported and statistically significant.
Protein samples (1 mg) were subsequently diluted with 100 mM Tris?HCl and 10 mM CaCl 2 (pH 8. 0) to a final urea concentration below 4 M. Proteolytic digestions were initiated with sequencing grade trypsin (1/100, w/w; Promega) and incubated overnight at room temperature. A second aliquot of trypsin was added (1/100) after the reactions were diluted with 100 mM Tris?HCl (pH 8. 0) to a final urea concentration below 2 M. After incubation for 4 h at room temperature, samples were reduced by incubation in 10 mM DTT for 1 h at room temperature. Finally, the peptides were acidified (protonated) in 200 mM NaCl and 0. 1% formic acid, filtered, and concentrated with a 10 kDa molecular weight cutoff spin column (Sartorius). LC-MS/MS Data Collection. The peptide mixture from each mouse was analyzed in technical duplicate via twodimensional liquid chromatography (LC)-MS/MS on a hybrid LTQ Orbitrap Velos mass spectrometer (Thermo Fisher Scientific).
Peptides (,100 mL per sample) were separated using a split phase 2D (strong-cation exchange (SCX) and C 18 reverse phase (RP))-LC column over a 12-step gradient for each run. All MS analyses were performed in positive ion mode. Mass spectral data were acquired using Xcalibur (v2. 0. 7) in data-dependent acquisition mode for each chromatographic separation (22 h run). One precursor MS scan was acquired in the Orbitrap at 30K resolution followed by 10 data-dependent MS/MS scans (m/z 400-1,700) at 35% normalized collision energy with dynamic exclusion enabled at a repeat count of 1. MS/MS spectra were searched with SEQUEST (v. 27;  [60] ) using the following settings: enzyme type = trypsin; precursor ion mass tolerance = 3. 0 Da; fragment mass tolerance = 0. 5 Da; fully tryptic peptides and those resulting from up to four missed cleavages only.
All datasets were filtered with DTASelect (v1. 9;  [61] ) using the following parameters: Xcorrs of 1. 8, 2. 5, and 3. 5 for singly, doubly, and triply charged precursor ions; DeltCN $ 0. 08; $2 fully tryptic peptides per protein. A custom-built FASTA target-decoy database  [62, 63]  was generated and searched with SEQUEST at a peptide-level false positive rate (FPR) estimated at #0. 5%. The database contained theoretical proteomes predicted from the genomes of the 12 bacterial species characterized in this study (see Tables  S4  and S8 ), some diet components (e. g. , rice and yeast), and common contaminants (e. g. , keratins). Three additional theoretical bacterial proteomes predicted from the genomes of Eubacterium rectale, Faecalibacterium prausnitzii, and Ruminococcus torques were included as distractors (negative controls) that were not expected to be present in any of the samples analyzed.
An in silico tryptically digested protein sequence database was also used to generate a theoretical peptidome of unique peptides within a mass range of 600-4,890 Da and #1 miscleavages. Analysis of Proteomic Datasets. Spectral counts for each protein were normalized by either the total number of spectra collected for all species in a sample (normalization by community, ''NBC''), or by the total number of spectra collected for all proteins from a given species (normalization by species, ''NBS''). p values for each protein were calculated using the Mann-Whitney U test. To correct for multiple comparisons, q values were calculated using an optimized false discovery rate (FDR) approach with the ''qvalue'' package in BioConductor. Regardless of the normalization strategy employed, p and q values were only calculated for proteins with at least three valid runs, where a valid run was one with more than five spectral counts.
Means for all panels were calculated from data from four animals at each time-point, except day 26 (n = 2). In each of the first four panels (A-D), the differences between day 13 and day 27 were deemed statistically significant by Mann-Whitney U test (p = 0. 03 for each of the four tests performed). (EPS) Figure S8 Shotgun metaproteomic analysis of cecal samples from gnotobiotic mice colonized with the 12member artificial community. (A) Each species' theoretical proteome was subjected to in silico trypsinization (see Materials and Methods). Of the resulting peptides, those specific to a single protein within our database of all predicted proteins encoded by the genomes of the 12 assemblage members, the mouse, and three bacterial ''distractors'' (E. rectale, F. prausnitzii, and R. torques) were classified as ''unique,'' while all others were considered ''nonunique.
'' The ''unique'' fraction of a species' predicted peptides indicates how many can be unambiguously traced back to a single protein of origin if detected by LC-MS/MS. (B) Comparison of the average relative cecal abundance of each assemblage member (dark gray bars) with the percentage of proteins within its theoretical proteome that were detected by LC-MS/MS (red bars), and the percentage of all genes within its genome whose expression was detected using our custom GeneChip (light gray bars). Data shown are mean values 6 SEM. (C) Scatter plots illustrating the Pearson correlation coefficient (r) between logtransformed averages of diet-specific fold-differences in expression as determined by GeneChip assay (RNA, x-axis) and LC-MS/MS (protein, y-axis) in E 1. Data points within the black scatter plot represent the 448 B.
Data Deposition All short read Illumina data used for COPRO-Seq and RNA-Seq analyses, GeneChip data, and genome sequencing/assembly data are available through GEO SuperSeries GSE48537 and NCBI BioProject ID PRJNA183545. The draft genome assembly for B. cellulosilyticus WH2 has been deposited at DDBJ/EMBL/ GenBank under accession number ATFI00000000. Raw MS data are available from the Dryad Digital Repository: http://dx. doi. org/10. 5061/dryad. 7fj1k.
Erythrocytes osmotic fragility The procedure of EOF was a slightly modified method of  O'Dell et al. (1987). A 100 l aliquot of washed erythrocyte suspension was added to test tubes containing 5 mL of 0. 2 %, 0. 3 %, or 0. 9 % buffered salt solutions (BSS, pH 7. 4). The contents of these tubes were gently mixed by inverting them five times and were allowed to stand at 37 °C for 30 min. There after,Then these tubes were centrifuged at 1270 x g for 10 min to pellet the cells. The supernatant was then transferred into a glass cuvette and the absorbance was measured at 540 nm, measure data wave length of 540 nm using a spectrophotometer by reading the absorbance. The profile of the EOF of our camels was previously analysed by using a BSS (pH 7. 4) concentrations, ranging from 0. 1 % to 0. 9 %.
Although it is important to take into account the results obtained here, it could be different with conventional animals as the strains would need to successfully compete with endogenous bacteria. The bacteria were alive and metabolically active in the caecum of rats as shown by agar plate counts, by the analysis of lactate production and by the transcripts measured by real time PCR. The primers for binding related genes were the same for the three Lactobacillus strains. So that even if they showed specific amplification of the targeted genes in each of the three Lactobacillus strains, as revealed by dissociations curves (data not shown), they did not distinguish between the transcripts of each strain when they are together. Therefore the transcriptional analysis corresponded to the general expression of the pool of genes investigated.
Mild rectal bleeding may be isolated or not. When it is associated with mild clinical or radiological signs, it is classified as "suspected NEC" or NEC stage 1B  [3]. According to our protocol, infants with rectal bleeding went through a fasting period and were fed only parenterally. The fasting period lasted between 1 and 10 days depending on the duration of rectal bleeding and the clinical (mild abdominal distention, elevated pre-gavage residuals or emesis) or radiological (intestinal dilation, mild ileus) signs associated with the bleeding. Wide spectrum antibiotics were prescribed when there were associated clinical or radiological signs. In addition, we collected data from systematic weekly stool cultures routinely performed in all VLBW infants to monitor for the emergence of multi-resistant bacteria.
Data collection We collected antenatal data (maternal illness, medications during pregnancy, mode of delivery), infant characteristics at birth (Apgar score, GA and birth weight). Infants were considered growth restricted when birth weight was less than -2 standard deviations (SD)  [9]. We collected history before the occurrence of rectal bleeding: drugs, ventilatory support, oxygen therapy, feeding, and proportion of infants who received thickeners. At the time of rectal bleeding (or an equivalent postnatal age in Controls), we collected postnatal age, duration of rectal bleeding, treatment, and type of enteral feeding. For each Control, we collected the characteristics between birth and the postnatal age at the onset of rectal bleeding in the corresponding Case. We collected the results of the stool cultures performed for identification of pathogens (Staphylococcus aureus, Coagulase negative Staphylococcus, Clostridium difficile, Escherichia coli, Enterococcus, Klebsiella pneumoniae, Proteus mirabilis, Proteus mirabilis, Klebsiella oxytoca) in the week before the occurrence of rectal bleeding in Cases and at equivalent GA and postnatal age in Controls.
Statistical analysis Results are expressed as numbers (percentage) or medians [min; max]. Case and Control groups were compared using the Wilcoxon test for quantitative parameters and the CHI-2 or Fisher's exact test when appropriate for categorical variables. All parameters with a p value below 0. 1 were stepwise introduced into a multiple logistic regression where being a Case or a Control was the dependent variable. We used SPSS 16 Software (SPSS Inc. , Chicago, IL) to perform statistical analysis. The study protocol was approved by the ethics committee of Lyon (Comité de protection des personnes Sud Est IV Lyon).
Results Between January 2007 and December 2010, 823 children with a birth weight ≤ 1500 g or GA ≤ 32 weeks were admitted consecutively to the neonatal unit of Croix Rousse University Hospital. Of these, 75 had MRB. Three children were excluded. The first one had a foetopathy due to cytomegalovirus. The second died at day 67 (corrected GA: 35 weeks) from intestinal perforation and sepsis. The last had a severe malformation (chylothorax and chylous ascites). We then analysed the data in the 72 infants corresponding to the inclusion criteria, which was 8. 8% (72/ 820) of the population. Among the 72 VLBW infants included in our study, over one third (28/72, 39%) had isolated rectal bleeding and the others (44/72, 61%) had rectal bleeding associated with mild clinical or radiological signs. It represented respectively 3.
2A ). Substitutions within the R2 repeat (sup35-M2) in half of the tested transformants, as well as the PNM2 mutation (in all transformants tested) abolished growth on adenine-deficient medium, indicating elimination of [PSI ϩ ] in these isolates (Fig. 2B ). Thus, in some transformants the sup35-M2 allele can cause an effective [PSI ϩ ] loss in a dominant manner. In contrast, other sup35 KK alleles (sup35-M1, sup35-M3, sup35-M4, and sup35-M5) failed to eliminate the nonsense suppression phenotype in the presence of wild type SUP35. To determine whether sup35 KK alleles themselves have a nonsense suppression phenotype, we transformed an isogenic [psi Ϫ ] strain (7A-D832) with plasmids bearing mutant alleles. Transformants failed to grow on media lacking adenine (data not shown). In addition, we measured steady-state levels of Sup35p in cells ectopically expressing the sup35 KK alleles.
Acknowledgments-We are very grateful to A. Borchsenius and M. D. Ter-Avanesyan for plasmids and yeast strains, A. Masharsky for sequencing, E. Besedina and N. Trubicina for help in some experiments, A. Galkin and P. Drozdova for critical reading of the manuscript, Y. Chernoff and members of the Physiological Genetics laboratory of Saint Petersburg State University for fruitful discussions and a " Dynasty Foundation " for travel grant (to A. V. K. ).
Participant selection and recruitment Participant selection was a two phase process; firstly selection of villages and secondly selection of households within villages. For village selection, data concerning 56 villages were obtained from The National Institute of Statistics, Ministry of Planning, Royal Government of Cambodia (http://www. nis. gov. kh/index. php/online-statistics/resultonline). This data included the number of homes in the village, the population, % male, % children <14, % children <5, % of population >25 years with no, some, completed primary and completed secondary education, % migrants, % with access to improved water supplies, % with no toilet facility, % adult female literacy and % employed in primary, secondary and tertiary sectors. Of the 56 villages, 27 had access to 1001 F water.