AUTHOR=Amaretti Alberto , Gozzoli Caterina , Simone Marta , Raimondi Stefano , Righini Lucia , Pérez-Brocal Vicente , García-López Rodrigo , Moya Andrés , Rossi Maddalena 

TITLE=Profiling of Protein Degraders in Cultures of Human Gut Microbiota

JOURNAL=Frontiers in Microbiology

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.02614

DOI=10.3389/fmicb.2019.02614

ISSN=1664-302X

ABSTRACT=<p>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 <italic>Esherichia-Shigella</italic>, <italic>Sutterella</italic>, <italic>Parasutterella</italic>, and <italic>Bilophila</italic>) 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 <italic>p</italic>-cresol. <italic>Anaerotruncus</italic>, <italic>Dorea</italic>, <italic>Oscillibacter</italic>, <italic>Eubacterium oxidoreducens</italic>, <italic>Lachnoclostridium</italic>, <italic>Paeniclostridium</italic>, and <italic>Rombutsia</italic> were among them. Other Firmicutes (e.g., <italic>Roseburia</italic>, <italic>Ruminococcus</italic>, <italic>Lachnospira, Dialister</italic>, Erysipelotrichaceae, and Streptococcaceae) and many Bacteroidetes (e.g., Barnesiellaceae, Prevotellaceae, and Rickenelliaceae) decreased. Sequences attributed to <italic>Bacteroides</italic>, 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.</p>