Extended Data Fig. 11: T cell targets are highly expressed in vitro and in vivo.
From: Mapping the T cell repertoire to a complex gut bacterial community
a, The SBP is highly expressed in in vitro transcriptomic data from two species in our community: Clostridium bolteae and Clostridium hathewayi. In C. bolteae, it is the 10th most highly expressed gene out of 5,982, and in C. hathewayi, it is the 4th most highly expressed gene out of 6,712. The expression level was normalized to transcripts per million (TPM). b, The SBP and TPRL are highly expressed in vivo. Reads were recruited from 378 metatranscriptomic samples38 and mapped to the whole genomes of select SBP and TPRL-encoding strains in our community (Tyzzerella nexilis DSM 1787 and Clostridium bolteae DSM 15670 (SBP); Bacteroides stercoris ATCC 43183, Bacteroides eggerthii DSM 20697, and Bacteroides cellulosilyticus DSM 14838 (TPRL)). To account for gene copy number variation, we measured expression as the ratio between RNA and DNA level from paired metagenomic and metatranscriptomic samples. In all cases, we found that the protein is very highly expressed in vivo.
