Table_1_Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis.XLSX

Inflammatory bowel diseases (IBD) are associated with compositional and functional changes of the intestinal microbiota, but specific contributions of individual bacteria to chronic intestinal inflammation remain unclear. Enterococcus faecalis is a resident member of the human intestinal core microbiota that has been linked to the pathogenesis of IBD and induces chronic colitis in susceptible monoassociated IL-10-deficient (IL-10−/−) mice. In this study, we characterized the colitogenic activity of E. faecalis as part of a simplified human microbial consortium based on seven enteric bacterial strains (SIHUMI). RNA sequencing analysis of E. faecalis isolated from monoassociated wild type and IL-10−/− mice identified 408 genes including 14 genes of the ethanolamine utilization (eut) locus that were significantly up-regulated in response to inflammation. Despite considerable up-regulation of eut genes, deletion of ethanolamine utilization (ΔeutVW) had no impact on E. faecalis colitogenic activity in monoassociated IL-10−/− mice. However, replacement of the E. faecalis wild type bacteria by a ΔeutVW mutant in SIHUMI-colonized IL-10−/− mice resulted in exacerbated colitis, suggesting protective functions of E. faecalis ethanolamine utilization in complex bacterial communities. To better understand E. faecalis gene response in the presence of other microbes, we purified wild type E. faecalis cells from the colon content of SIHUMI-colonized wild type and IL-10−/− mice using immuno-magnetic separation and performed RNA sequencing. Transcriptional profiling revealed that the bacterial environment reprograms E. faecalis gene expression in response to inflammation, with the majority of differentially expressed genes not being shared between monocolonized and SIHUMI conditions. While in E. faecalis monoassociation a general bacterial stress response could be observed, expression of E. faecalis genes in SIHUMI-colonized mice was characterized by up-regulation of genes involved in growth and replication. Interestingly, in mice colonized with SIHUMI lacking E. faecalis enhanced inflammation was observed in comparison to SIHUMI-colonized mice, supporting the hypothesis that E. faecalis ethanolamine metabolism protects against colitis in complex consortia. In conclusion, this study demonstrates that complex bacterial consortia interactions reprogram the gene expression profile and colitogenic activity of the opportunistic pathogen E. faecalis toward a protective function.

炎症性肠病（Inflammatory bowel diseases, IBD）与肠道菌群的组成及功能改变密切相关，但单一细菌对慢性肠道炎症的具体贡献仍未明确。粪肠球菌（Enterococcus faecalis）是人类肠道核心菌群的常驻成员，其与IBD的发病机制相关，并可在易感的单定植白细胞介素10基因敲除（IL-10-deficient, IL-10−/−）小鼠中诱发慢性结肠炎。本研究以7株肠道细菌构建的简化人类微生物群落（SIHUMI）为模型，解析了粪肠球菌的致结肠炎活性。对从单定植野生型及IL-10−/−小鼠中分离的粪肠球菌进行RNA测序（RNA sequencing）分析，共鉴定出408个基因，其中乙醇胺利用（ethanolamine utilization, eut）基因座的14个基因在炎症刺激下显著上调。尽管eut基因显著上调，但敲除乙醇胺利用通路（ΔeutVW）并未对单定植IL-10−/−小鼠体内粪肠球菌的致结肠炎活性产生影响。但在SIHUMI定植的IL-10−/−小鼠中，用ΔeutVW突变株替换野生型粪肠球菌后，结肠炎症状加重，这提示在复杂细菌群落中，粪肠球菌的乙醇胺利用通路发挥保护性功能。为进一步探究粪肠球菌在其他微生物存在时的基因应答模式，本研究通过免疫磁分离技术，从SIHUMI定植的野生型及IL-10−/−小鼠结肠内容物中纯化野生型粪肠球菌，并进行RNA测序分析。转录组分析显示，细菌微环境会重编程粪肠球菌的炎症应答基因表达谱，且单定植与SIHUMI定植两种条件下的差异表达基因大多不重叠。在粪肠球菌单定植模型中可观察到普遍的细菌应激反应，而在SIHUMI定植小鼠体内，粪肠球菌的基因表达则以参与生长与复制的基因上调为特征。值得注意的是，与完整SIHUMI定植的小鼠相比，缺失粪肠球菌的SIHUMI定植小鼠的肠道炎症更为严重，这验证了“复杂群落中粪肠球菌的乙醇胺代谢可缓解结肠炎”的假说。综上，本研究表明，复杂细菌群落间的相互作用可将机会致病菌粪肠球菌的基因表达谱与致结肠炎活性重编程为保护性功能。