"sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053"	"characteristics_ch1.1"
"After dividing sequence runs by barcode, we mapped the reads to the relevant genomes using the ssaha2 algorithm. Minimum score thresholds for ssaha were selected based on the distribution of scores for all mapped reads of a 32nt barcoded sample and a 36-nt non-barcoded sample (29 was selected as the minimum score for 32nt barcoded samples; 33 was the minimum score used for 36-nt non-barcoded samples). Although an 18-nt read is sufficient to map more than 90% of the sequencing reads, even at 32-36nt there is a large fraction of the reads that map to multiple locations within a genome or across genomes. Reads that map non-uniquely were discarded."	"data_processing.1"
"Double stranded cDNA was generated using Superscript II (Invitrogen) to generate the first strand followed by E. coli DNA polymerase, RNaseH, and E.coli DNA ligase (NEB) to generate the second strand."	"extract_protocol_ch1.1"
"Fecal samples obtained from mice were immediately frozen in liquid nitrogen and stored at -80 °C until processing. All of the samples were suspended in a solution containing 500 ul of acid-washed glass beads (Sigma-Aldrich), 500 ul of extraction buffer A (200 mM Tris [pH 8], 200 mM NaCl, 20 mM EDTA), 200 ul of 20% SDS, and 500 ul of a mixture of phenol:chloroform:isoamyl alcohol (25:24:1, pH 8.0; Ambion) and lysed by using a bead beater (BioSpec Products). Cellular debris was removed by centrifugation (8,000g; 3 min). The nucleic acids were precipitated with isopropanol and sodium acetate and resuspended in 100 ul TE. The resuspension was further purified with a Qiagen PCR column and eluted into 30 ul of EB buffer."	"extract_protocol_ch1.2"
"Libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample Kit. Briefly, cDNA was sonicated in a biorupter sonicator, cleaned up/concentrated through a Qiagen PCR column, and end-repaired. The blunt DNA was treated with Klenow fragment (exo minus) to add an A-overhang, and ligated to the relevant Illumina adapter sequence (either with our without a barcode).  Adaptered-DNA was then size-selected on a agarose gel and PCR amplified. The purified PCR was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols."	"extract_protocol_ch1.3"
"Fecal samples obtained from mice were immediately frozen in liquid nitrogen and stored at -80 °C until processing. All of the samples were treated with RNAProtect (Qiagen) and suspended in a solution containing 500 μl of acid-washed glass beads (Sigma-Aldrich), 500 μl of extraction buffer A (200 mM NaCl, 20 mM EDTA), 210 μl of 20% SDS, and 500 μl of a mixture of phenol:chloroform:isoamyl alcohol (125:24:1, pH 4.5; Ambion) and lysed by using a bead beater (BioSpec Products). Cellular debris was removed by centrifugation (8,000 × g; 3 min). The nucleic acids were precipitated with isopropanol and sodium acetate (pH 5.5)."	"growth_protocol_ch1.1"
"[Clostridium] symbiosum"	"organism_ch1.1"
"Bacteroides thetaiotaomicron VPI-5482"	"organism_ch1.2"
"Bacteroides ovatus ATCC 8483"	"organism_ch1.3"
"Bacteroides caccae ATCC 43185"	"organism_ch1.4"
"Collinsella aerofaciens ATCC 25986"	"organism_ch1.5"
"Blautia hydrogenotrophica DSM 10507"	"organism_ch1.6"
"Marvinbryantia formatexigens DSM 14469"	"organism_ch1.7"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.8"
"[Eubacterium] rectale ATCC 33656"	"organism_ch1.9"
"Desulfovibrio piger GOR1"	"organism_ch1.10"
"mouse feces"	"source_name_ch1.1"
"D3_10_m11"	"title.1"
"rRNA depletion: Genomic DNA was removed with TURBO DNAse (Ambion), and then total RNA was run over two MEGAClear columns (Ambion) to deplete tRNAs and 5S rRNA. In between the two column purifications, a second DNAse digestion was performed (Baseline-ZERO Epicenter).  16S and 23S rRNA were depleted using MICROBExpress (Ambion) and custom depletion oligos (Rey et.al. 2010; JBC)."	"treatment_protocol_ch1.1"
"RNA-Seq"	"library_strategy.1"
"sample source: Fecal pellet from a mouse (c57Bl6) colonized with 10-gut bacteria. Mouse was fed Harlan Teklad Diet TD.09053"	"characteristics_ch1.1"
"Fecal samples obtained from mice were immediately frozen in liquid nitrogen and stored at -80 °C until processing. All of the samples were treated with RNAProtect (Qiagen) and suspended in a solution containing 500 μl of acid-washed glass beads (Sigma-Aldrich), 500 μl of extraction buffer A (200 mM NaCl, 20 mM EDTA), 210 μl of 20% SDS, and 500 μl of a mixture of phenol:chloroform:isoamyl alcohol (125:24:1, pH 4.5; Ambion) and lysed by using a bead beater (BioSpec Products). Cellular debris was removed by centrifugation (8,000 × g; 3 min). The nucleic acids were precipitated with isopropanol and sodium acetate (pH 5.5)."	"growth_protocol_ch1.1"
"[Clostridium] symbiosum"	"organism_ch1.1"
"Bacteroides thetaiotaomicron VPI-5482"	"organism_ch1.2"
"Bacteroides ovatus ATCC 8483"	"organism_ch1.3"
"Bacteroides caccae ATCC 43185"	"organism_ch1.4"
"Collinsella aerofaciens ATCC 25986"	"organism_ch1.5"
"Blautia hydrogenotrophica DSM 10507"	"organism_ch1.6"
"Marvinbryantia formatexigens DSM 14469"	"organism_ch1.7"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.8"
"[Eubacterium] rectale ATCC 33656"	"organism_ch1.9"
"Desulfovibrio piger GOR1"	"organism_ch1.10"
"mouse feces"	"source_name_ch1.1"
"rRNA depletion: Genomic DNA was removed with TURBO DNAse (Ambion), and then total RNA was run over two MEGAClear columns (Ambion) to deplete tRNAs and 5S rRNA. In between the two column purifications, a second DNAse digestion was performed (Baseline-ZERO Epicenter).  16S and 23S rRNA were depleted using MICROBExpress (Ambion) and custom depletion oligos (Rey et.al. 2010; JBC)."	"treatment_protocol_ch1.1"