Additional file 1: of Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

Table S1. Bile acid deconjugation and transformation genes identified in the 693 analyzed genomes. Table S2. Description of the bile acid metabolism subsystem reconstructed for AGORA: a) metabolites, b) reactions. Table S3. Constraints implemented to simulate the Average European (AE) diet supplemented with taurocholate, glycocholate, taurochenodeoxycholate, and glycochenodeoxycholate. Table S4. Bile acid production potential for each of the 232 AGORA models carrying bile acid reactions. Table S5. Secondary bile acids produced in pairwise AGORA models that could not be produced individually by either model. Table S6. Bile acid production potential (mmol × person-1 × day-1) predicted for the community models representing 194 human microbiomes. Table S7. Features that significantly differed between 15 pediatric Crohn's Disease patients and 25 healthy controls. Table S9. Correlations between total community bile acid production (mmol × person-1 × day-1) and total community reaction abundance across all 194 community models. Table S10. Shadow prices in the flux balance solutions when optimizing for secondary bile acid production in all community models. Shown are metabolites that had a nonzero shadow price in at least one model. Table S11. Description of newly reconstructed strains in this study as an update to the AGORA resource. (XLSX 2194 kb)

补充表S1：在本次分析的693个基因组中鉴定得到的胆汁酸解偶联与转化基因。
补充表S2：为AGORA重构的胆汁酸代谢子系统说明：(a) 代谢物；(b) 反应。
补充表S3：为模拟添加了牛磺胆酸盐、甘氨胆酸盐、牛磺鹅去氧胆酸盐与甘氨鹅去氧胆酸盐的平均欧洲（AE）饮食所设置的约束条件。
补充表S4：232个携带胆汁酸反应的AGORA模型各自的胆汁酸生成潜力。
补充表S5：在成对AGORA模型中生成的、任一单一模型均无法单独合成的次级胆汁酸。
补充表S6：针对代表194个人类微生物组的群落模型所预测的胆汁酸生成潜力（单位：毫摩尔·人⁻¹·天⁻¹）。
补充表S7：15名儿童克罗恩病患者与25名健康对照个体之间存在显著差异的特征。
补充表S9：全部194个群落模型中，群落总胆汁酸生成量（毫摩尔·人⁻¹·天⁻¹）与群落总反应丰度之间的相关性。
补充表S10：所有以次级胆汁酸生成为优化目标的群落模型通量平衡分析求解结果中的影子价格，展示了至少在一个模型中具有非零影子价格的代谢物。
补充表S11：本研究中新重构菌株的相关说明，作为AGORA资源的更新版本。（XLSX 2194 kb）