Metabolic reprogramming of the intestinal microbiome with functional bile acid changes underlie the development of NAFLD.

"CONFLICTS OF INTEREST Andrew N. Billin owns stock in and is employed by Gilead Sciences. Jen‐Chieh Chuang owns stock in and is employed by Gilead Sciences and The Liver Company. Ryan S. Huss owns stock in and is employed by The Liver Company. He owns stock in Gilead Sciences. Robert P. Myers owns stock in and is employed by The Liver Company. He owns stock in Gilead Sciences. Nicole Narayan owns stock in and is employed by Second Genome. Arun J. Sanyal consults and received grants from Conatus, Gilead, Malinckrodt, Immuron, Boehringer Ingelhiem, Novartis, Bristol Myers Squibb, Merck, Lilly, Novo Nordisk, Fractyl, Siemens, Madrigal, Inventiva, and Covance. He owns stock in and consults for Genfit and Hemoshear. He consults for Intercept, Pfizer, Salix, Galectin, Sequana, Terns, Albireo, Sanofi, Jannsen, Takeda, Northsea, AMRA, Perspectum, Poxel, 89 Bio, AstraZeneca, NGM Bio, Amgen, Regeneron, Genetech, Roche, Albireo, Prosciento, Histoindex, Path AI, and Biocellvia. He received grants from Echosense‐Sandhill, OWL, and Second Genome. He received royalties from Elsevier and UptoDate. He owns stock in Sanyal Bio, Exhalenz, Durect, Indalo, Tiziana, and Rivus."

"Funding information National Institutes of Health (NIH) grant NIH RO1 DK105961 (to Arun J. Sanyal); NIH grant T32 DK07150‐40 (to Arun J. Sanyal); NIH grant CTSA UL1TR002649 (to Ekaterina Smirnova) from VCU BERD Core; NIH grant CTSA 5KL2TR002648 (to Ekaterina Smirnova ) from VCU Institutional Career Development Core; and National Medical Research Council Singapore Research Training Fellowship MOH‐000193 (to Mark D. Muthiah). This work was primarily funded by NIH RO1 DK105961 and T32 DK07150‐40 to Dr. Arun Sanyal, and CTSA UL1TR002649 and VCU CCTR KL2TR002648 emerging scholar award to Dr. Ekaterina Smirnova for the proposed analyses. Samples were also collected in the VCU CCTR, which is supported by the CTSA award to VCU. These NIH institutes did not have a direct role in the design and conduct of the studies. Second genome provided in kind contribution with analysis of microbial transcriptome."