1. Alterations in bile acid metabolizing gut microbiota and specific bile acid genes as a precision medicine to subclassify NAFLD
- Author
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Na Jiao, Zi-Huan Yang, Lixin Zhu, Richele Bettencourt, Dingfeng Wu, Sa Fang, Ruixin Zhu, Ping Lan, and Rohit Loomba
- Subjects
0301 basic medicine ,Male ,Physiology ,medicine.drug_class ,Disease ,Biology ,Gut flora ,Genome ,digestive system ,Pathogenesis ,Bile Acids and Salts ,03 medical and health sciences ,0302 clinical medicine ,Non-alcoholic Fatty Liver Disease ,Nonalcoholic fatty liver disease ,Coenzyme A Ligases ,Genetics ,medicine ,Humans ,Precision Medicine ,Gene ,Bile acid ,Fatty liver ,Hydroxysteroid Dehydrogenases ,Reproducibility of Results ,Middle Aged ,medicine.disease ,biology.organism_classification ,Precision medicine ,3-alpha-Hydroxysteroid Dehydrogenase (B-Specific) ,digestive system diseases ,Gut microbiome ,Gastrointestinal Microbiome ,030104 developmental biology ,Metagenomics ,Case-Control Studies ,Immunology ,030211 gastroenterology & hepatology ,Female ,Research Article - Abstract
Background & AimsMultiple mechanisms for the gut microbiome contributing to the pathogenesis of non-alcoholic fatty liver disease (NAFLD) have been implicated. Here, we aim to investigate the contribution and potential application for altered bile acid (BA) metabolizing microbe in NAFLD using whole metagenome sequencing (WMS) data.Methods86 well-characterized biopsy-proven NAFLD patients and 38 healthy controls were included in the discovery cohort. Assembly-based analysis was performed to identify BA-metabolizing microbes. Statistical tests, feature selection and microbial interaction analysis were integrated to identify microbial alterations and markers in NAFLD. An independent validation cohort was subjected to similar analyses.ResultsNAFLD microbiota exhibited decreased diversity and microbial interactions. We established a classifier model with 53 differential species exhibiting a robust diagnostic accuracy (AUC=0.97) for dectecting NAFLD. Next, 8 important differential pathway markers including secondary BA biosynthesis were identified. Specifically, increased abundance of 7α-HSDH, baiA and baiB were detected in NAFLD. Further, 10 of 50 BA-metabolizing metagenome-assembled genomes (MAG)s, from Bacteroides ovatus and Eubacterium biforme, were dominant in NAFLD and interplayed as a synergetic ecological guild. Importantly, two subtypes of NAFLD patients were observed according to secondary BA metabolism potentials. Elevated capability for secondary BA biosynthesis was also observed in the validation cohort.ConclusionsWe identified novel bacterial BA-metabolizing genes and microbes that may contribute to NAFLD pathogenesis and serve as disease markers. Microbial differences in BA-metabolism and strain-specific differences among patients highlight the potential for precision medicine in NAFLD treatment.
- Published
- 2021