DOI: 10.5061/dryad.b922k
title: Data from: The hindgut-lumen prokaryotic microbiota of the lignocellulose-degrading termite Reticulitermes flavipes and its responses to dietary lignocellulose composition

description: Reticulitermes flavipes (Isoptera: Rhinotermitidae) is a highly eusocial
 insect that thrives on recalcitrant lignocellulosic diets through
 nutritional symbioses with gut-dwelling prokaryotes and eukaryotes. In the
 R. flavipes hindgut, there are up to 12 eukaryotic protozoan symbionts;
 the number of prokaryotic symbionts has been estimated in the hundreds.
 Despite its biological relevance, this diverse community, to date, has
 been investigated only by culture- and cloning-dependent methods.
 Moreover, it is unclear how termite gut microbiomes respond to diet
 changes and what roles they play in lignocellulose digestion. This study
 utilized high-throughput 454 pyrosequencing of 16S V5-V6 amplicons to
 sample the hindgut lumen prokaryotic microbiota of R. flavipes and to
 examine compositional changes in response to lignin-rich and lignin-poor
 cellulose diets after a 7-day feeding period. Of the ~475 000 high-quality
 reads that were obtained, 99.9% were annotated as bacteria and 0.11% as
 archaea. Major bacterial phyla included Spirochaetes (24.9%),
 Elusimicrobia (19.8%), Firmicutes (17.8%), Bacteroidetes (14.1%),
 Proteobacteria (11.4%), Fibrobacteres (5.8%), Verrucomicrobia (2.0%),
 Actinobacteria (1.4%) and Tenericutes (1.3%). The R. flavipes hindgut
 lumen prokaryotic microbiota was found to contain over 4761 species-level
 phylotypes. However, diet-dependent shifts were not statistically
 significant or uniform across colonies, suggesting significant
 environmental and/or host genetic impacts on colony-level microbiome
 composition. These results provide insights into termite gut microbiome
 diversity and suggest that (i) the prokaryotic gut microbiota is much more
 complex than previously estimated, and (ii) environment, founding
 reproductive pair effects and/or host genetics influence microbiome
 composition.
description: TableS3-phylumExcel spread sheet includes a distribution of the filtered 16S 454-reads annotated to phylum from termites collected from three different colonies (S7-S10; S11-S14; and S15-S18) fed paper and wood (S7,S11,S15) and paper (S8, S12, S16), wood (S9,S13, S17). Termites sampled directly from lab colonies are represented by S10, S14, and S18.Table S4. Annotation of total 16S reads to class level.Excel spread sheet includes a distribution of the filtered 16S 454-reads annotated to class level from termites collected from three different colonies (S7-S10; S11-S14; and S15-S18) fed paper and wood (S7,S11,S15) and paper (S8, S12, S16), wood (S9,S13, S17). Termites sampled directly from lab colonies are represented by S10, S14, and S18.TableS4-class.xlsxTableS5-orderExcel spread sheet includes a distribution of the filtered 16S 454-reads annotated to order level from termites collected from three different colonies (S7-S10; S11-S14; and S15-S18) fed paper and wood (S7,S11,S15) and paper (S8, S12, S16), wood (S9,S13, S17). Termites sampled directly from lab colonies are represented by S10, S14, and S18.TableS6-familyExcel spread sheet includes a distribution of the filtered 16S 454-reads annotated to family level from termites collected from three different colonies (S7-S10; S11-S14; and S15-S18) fed paper and wood (S7,S11,S15) and paper (S8, S12, S16), wood (S9,S13, S17). Termites sampled directly from lab colonies are represented by S10, S14, and S18.TableS7-genusExcel spread sheet includes a distribution of the filtered 16S 454-reads annotated to genus level from termites collected from three different colonies (S7-S10; S11-S14; and S15-S18) fed paper and wood (S7,S11,S15) and paper (S8, S12, S16), wood (S9,S13, S17). Termites sampled directly from lab colonies are represented by S10, S14, and S18.TableS8-speciesExcel spread sheet includes a distribution of the filtered 16S 454-reads annotated to species level from termites collected from three different colonies (S7-S10; S11-S14; and S15-S18) fed paper and wood (S7,S11,S15) and paper (S8, S12, S16), wood (S9,S13, S17). Termites sampled directly from lab colonies are represented by S10, S14, and S18.TableS9-OTUsA listing and annotation of the OTUs determined by ESPRITt analysis of the 454 16S data set. The file provides the abundance of the different reads detected within identified species-level OTUs.termite16S_Clean fasAfter pre-processing, 475,980 reads are left, of which 203,223 are non-redundant, these reads are included in the termite16S_Clean.fas filetermite16S_Clean.fastermite16S_Clean frqRepresents the occurrence of each read this in combination with the data in termite16SClean.fas serves as inputs for ESPRIT.termite16S_Clean.frqtermite16S_distributionThe termite16S_distribution.csv is a spreadsheet showing the occurrence of each read in each sample, so that one can easily find out what sequence belongs to what sample. The order of the read names is exactly the same as the sequence file. The output of ESPRIT provides a list of read indices belong to the same OTU (be aware that the indices are zero-based). By summing up the corresponding rows in termite16S_distribution.csv, one will easily get the breakdown of the OTU among samples. The S7 to S18 represent 16S data collected from three different colonies (S7-S10; S11-S14; and S15-S18) fed paper and wood (S7,S11,S15) and paper (S8, S12, S16), wood (S9,S13, S17). Termites sampled directly from lab colonies are represented by S10, S14, and S18.