Plasticity in gene expression allows bacteria to adapt to diverse environments. This is particularly relevant in the dynamic niche of the human intestinal tract; however, transcriptional networks remain largely unknown for gut-resident bacteria. Here we apply differential RNA sequencing (RNA-seq) and conventional RNA-seq to the model gut bacterium Bacteroides thetaiotaomicron to map transcriptional units and profile their expression levels across 15 in vivo-relevant growth conditions. We infer stress- and carbon source-specific transcriptional regulons and expand the annotation of small RNAs (sRNAs). Integrating this expression atlas with published transposon mutant fitness data, we predict conditionally important sRNAs. These include MasB, which downregulates tetracycline tolerance. Using MS2 affinity purification and RNA-seq, we identify a putative MasB target and assess its role in the context of the MasB-associated phenotype. These data—publicly available through the Theta-Base web browser (http://micromix.helmholtz-hiri.de/bacteroides/)—constitute a valuable resource for the microbiome community.

基因表达的可塑性使细菌能够适应不同的环境。这与人类肠道的动态生态位尤其相关；然而，肠道驻留细菌的转录网络在很大程度上仍然未知。在这里，我们将差异 RNA 测序 (RNA-seq) 和常规 RNA-seq 应用于模型肠道细菌Bacteroides thetaiotaomicron，以绘制转录单位图谱并分析其在 15 种体内相关生长条件下的表达水平。我们推断了胁迫和碳源特异性转录调节子，并扩展了小 RNA (sRNA) 的注释。将该表达图谱与已发表的转座子突变体适应度数据相结合，我们预测了有条件重要的 sRNA。其中包括 MasB，它可以下调四环素耐受性。使用 MS2 亲和纯化和 RNA-seq，我们确定了假定的 MasB 靶点并评估其在 MasB 相关表型背景中的作用。这些数据可通过 Theta-Base 网络浏览器 (http://micromix.helmholtz-hiri.de/bacteroides/) 公开获取，为微生物界构成了宝贵的资源。