Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut

The metabolism of bile acids (BAs) by gut bacteria plays an important role in human health. This study identified and characterized 7 alpha-dehydroxylating bacteria, which are majorly responsible for converting primary BAs to secondary BAs, in the human gut and investigated their association with human disease. Six 7 alpha-dehydratase (BaiE) clusters were identified from human gut metagenomes through sequence similarity network and genome neighborhood network analyses. Abundance analyses of gut metagenomes and metatranscriptomes identified a cluster of bacteria (cluster 1) harboring baiE genes that may be key 7 alpha-dehydroxylating bacteria in the human gut. The baiE gene abundance of cluster 1 was significantly and positively correlated with the ratio of secondary BAs to primary BAs. Furthermore, the baiE gene abundances of cluster 1 were significantly negatively correlated with inflammatory bowel disease, including Crohn's disease and ulcerative colitis, as well as advanced nonalcoholic fatty liver disease, liver cirrhosis, and ankylosing spondylitis. Phylogenetic and metagenome-assembled genome analyses showed that the 7 alpha-dehydroxylating bacterial Glade of cluster 1 was affiliated with the family Oscillospiraceae and may demonstrate efficient BA dehydroxylation ability by harboring both a complete bai operon, for proteins which produce secondary BAs from primary BAs, and a gene for bile salt hydrolase, which deconjugates BAs, in the human gut. IMPORTANCE In this study, we identified a key 7 alpha-dehydroxylating bacterial group predicted to be largely responsible for converting primary bile acids (BAs) to secondary BAs in the human gut through sequence similarity network, genome neighborhood network, and gene abundance analyses using human gut metagenomes. The key bacterial group was phylogenetically quite different from known 7 alpha-dehydroxylating bacteria, and their abundance was highly correlated with the occurrence of diverse diseases associated with bile acid 7 alpha-dehydroxylation. In addition, we characterized the metabolic features of the key bacterial group using their metagenome-assembled genomes. This approach is useful to identify and characterize key gut bacteria highly associated with human health and diseases.

Automated summary

In this study, a key group of 7 alpha-dehydroxylating bacteria responsible for converting primary bile acids (BAs) to secondary BAs in the human gut was identified through sequence similarity network, genome neighborhood network, and gene abundance analyses using human gut metagenomes. The abundance of this bacterial group was highly correlated with the occurrence of diverse diseases associated with bile acid 7 alpha-dehydroxylation. The metabolic features of this key bacterial group were characterized using their metagenome-assembled genomes. This approach is useful for identifying and characterizing key gut bacteria highly associated with human health and diseases.