Reactions Added Without Genome Annotation.

Bacteroides fragilis is a universal member of the dominant commensal gut phylum Bacteroidetes. Its fermentation products and abundance have been linked to obesity, inflammatory bowel disease, and other disorders through its effects on host metabolic regulation and the immune system. As of yet, there has been no curated systems-level characterization of B. fragilis’ metabolism that provides a comprehensive analysis of the link between human diet and B. fragilis’ metabolic products. To address this, we developed a genome-scale metabolic model of B. fragilis strain 638R. The model iMN674 contains 1,634 reactions, 1,362 metabolites, three compartments, and reflects the strain’s ability to utilize 142 metabolites. Predictions made with this model include its growth rate and efficiency on these substrates, the amounts of each fermentation product it produces under different conditions, and gene essentiality for each biomass component. The model highlights and resolves gaps in knowledge of B. fragilis’ carbohydrate metabolism and its corresponding transport proteins. This high quality model provides the basis for rational prediction of B. fragilis’ metabolic interactions with its environment and its host.脆弱拟杆菌（Bacteroides fragilis）是肠道优势共生菌门拟杆菌门（Bacteroidetes）的普遍存在成员。其发酵产物与丰度可通过调控宿主代谢与免疫系统，与肥胖、炎症性肠病及其他疾病密切相关。迄今为止，尚未有经过整理的系统级别的脆弱拟杆菌代谢特征研究，能够全面解析人类饮食与脆弱拟杆菌代谢产物之间的关联。为解决这一研究空白，我们构建了脆弱拟杆菌638R菌株的基因组规模代谢模型（genome-scale metabolic model）。该模型iMN674包含1634个反应、1362种代谢物、3个区室，可反映该菌株利用142种代谢物的能力。基于该模型的预测结果包括：该菌株在这些底物上的生长速率与生长效率、不同条件下各发酵产物的生成量，以及各生物量组分对应的基因必需性。该模型阐明并填补了当前关于脆弱拟杆菌碳水化合物代谢及其对应转运蛋白的认知缺口。这一高质量模型为合理预测脆弱拟杆菌与其生存环境及宿主之间的代谢互作奠定了基础。