Data_Sheet_3_Profiling of Protein Degraders in Cultures of Human Gut Microbiota.docx

Unabsorbed proteins reach the colon and are fermented by the microbiota, yielding a variety of harmful metabolites. In the present study, a 16S rRNA gene survey identified the bacterial taxa flourishing in 11 batch fermentations with proteins and peptones as the sole fermentable substrates, inoculated with the feces of six healthy adults. Organic acids, ammonia, and indole resulting from protein breakdown and fermentation accumulated in all of the cultures. Analysis of differential abundances among time-points identified Enterobacteriaceae, Burkholderiaceae, and Desulfovibrionaceae (including Esherichia-Shigella, Sutterella, Parasutterella, and Bilophila) among the bacteria that especially in the cultures with low inoculation load. Lachnospiraceae and Ruminococcaceae also encompassed many taxa that significantly expanded, mainly in cultures inoculated with high inoculation load, and showed the strongest correlation with the production of ammonium, indole, and p-cresol. Anaerotruncus, Dorea, Oscillibacter, Eubacterium oxidoreducens, Lachnoclostridium, Paeniclostridium, and Rombutsia were among them. Other Firmicutes (e.g., Roseburia, Ruminococcus, Lachnospira, Dialister, Erysipelotrichaceae, and Streptococcaceae) and many Bacteroidetes (e.g., Barnesiellaceae, Prevotellaceae, and Rickenelliaceae) decreased. Sequences attributed to Bacteroides, unresolved at the level of species, presented opposite contributions, resulting in no significant changes in the genus. This study sheds light on the multitude of bacterial taxa putatively participating in protein catabolism in the colon. Protein fermentation was confirmed as unfavorable to health, due to both the production of toxic metabolites and the blooming of opportunistic pathogens and pro-inflammatory bacteria.

未被吸收的蛋白质可抵达结肠，并由微生物群（microbiota）发酵，进而产生多种有害代谢物。本研究通过16S rRNA基因测序分析，对11批以蛋白质和蛋白胨（peptones）为唯一可发酵底物、接种6名健康成人粪便的批量发酵体系中旺盛生长的细菌分类群（taxa）进行了鉴定。蛋白质分解与发酵产生的有机酸、氨及吲哚在所有培养体系中均出现积累。对不同时间点的差异丰度进行分析后发现，在低接种量培养体系中尤为富集的细菌类群包括肠杆菌科（Enterobacteriaceae）、伯克霍尔德菌科（Burkholderiaceae）和脱硫弧菌科（Desulfovibrionaceae），其下涵盖埃希氏菌-志贺氏菌属（Esherichia-Shigella）、萨特氏菌属（Sutterella）、副萨特氏菌属（Parasutterella）以及嗜胆菌属（Bilophila）。毛螺菌科（Lachnospiraceae）和瘤胃球菌科（Ruminococcaceae）同样包含大量显著增殖的分类群，这类增殖主要发生在高接种量的培养体系中，且它们与氨、吲哚及对甲酚（p-cresol）的生成呈现最强的相关性。其中包括厌氧杆状菌属（Anaerotruncus）、多尔氏菌属（Dorea）、振荡杆菌属（Oscillibacter）、还原真杆菌（Eubacterium oxidoreducens）、毛洛梭菌属（Lachnoclostridium）、近梭菌属（Paeniclostridium）以及罗氏菌属（Rombutsia）。其他厚壁菌门（Firmicutes）类群（如罗氏菌属Roseburia、瘤胃球菌属Ruminococcus、毛螺菌属Lachnospira、Dialister属、丹毒丝菌科Erysipelotrichaceae以及链球菌科Streptococcaceae）以及大量拟杆菌门（Bacteroidetes）类群（如Barnesiellaceae、普雷沃氏菌科Prevotellaceae以及Rickenelliaceae）的丰度均出现下降。无法鉴定到物种水平的拟杆菌属（Bacteroides）相关序列则呈现出相反的丰度变化趋势，最终导致该属未出现显著的丰度改变。本研究揭示了结肠内推测参与蛋白质分解代谢的大量细菌分类群。本研究证实蛋白质发酵过程对健康存在不利影响，这既源于其产生有毒代谢物，也因为其会促使机会致病菌与促炎性细菌大量增殖。