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Fig. S1. Relative abundance of all transcripts assigned to major SEED categories that were recovered from forestomachs and hindguts (A), and (B) relative abundance of transcripts of Lactobacillales and Clostridiales in forestomachs and hindguts. From the hindguts, we obtained enough mRNA transcripts for functional analysis (n > 400) from only two samples.

Fig. S2. Host niche-dependent gene expression. Principal component analysis based on relative abundance of SEED categories in the forestomach and the hindgut of either the entire community (hindgut, forestomach), or of Lactobacillales and Clostridiales residing in forestomach or hindgut. As only two hindgut samples of the six C57BL/6 investigated yielded enough Lactobacillales mRNA reads for functional analysis, we strengthened our analysis including two additional samples obtained from Tyk2-/- mice on a C57BL/6 background with n = 1504 and n = 1071 Lactobacillales mRNA reads.

Table S1. Metatranscriptome sequencing. Forestomach metatranscriptomes were sequenced using an IonTorrent PGM sequencer. Double-stranded cDNA libraries derived from the hindgut were paired-end sequenced using an Illumina HiSeq (Campus Science Support Facilities GmbH, Vienna). Read pairs were overlapped using FLASH (Magoč and Salzberg, 2011). Metatranscriptomic sequencing data were analysed following an established double RNA analysis pipeline (Urich et al., 2008; Berry et al., 2012).

Table S2. Quantitative PCR of 16S rRNA gene of lactic acid bacteria and Clostridium clusters IV and XIV. Shown are 16S rRNA gene copies μg−1 DNA of individual forestomachs (FS1-5) and the mean of six hindgut samples. To determine the gene copies of 16S rRNA genes of Clostridium clusters IV and XIVa, primers targeting the respective clusters were used in separate reactions, gene copies were added and the sum was logarithmized.

Table S3. Major glycoside hydrolase (GH) families in forestomach and hindgut according to Pfam analysis.

Table S4. Selected features of the genome of L. vaginalis ATCC 49540 (NZ_GG693412).

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