Hepatic steatosis is a multifactorial condition that is often observed in obese patients and is a prelude to non-alcoholic fatty liver disease. Here, we combine shotgun sequencing of fecal metagenomes with molecular phenomics (hepatic transcriptome and plasma and urine metabolomes) in two well-characterized cohorts of morbidly obese women recruited to the FLORINASH study. We reveal molecular networks linking the gut microbiome and the host phenome to hepatic steatosis. Patients with steatosis have low microbial gene richness and increased genetic potential for the processing of dietary lipids and endotoxin biosynthesis (notably from Proteobacteria), hepatic inflammation and dysregulation of aromatic and branched-chain amino acid metabolism. We demonstrated that fecal microbiota transplants and chronic treatment with phenylacetic acid, a microbial product of aromatic amino acid metabolism, successfully trigger steatosis and branched-chain amino acid metabolism. Molecular phenomic signatures were predictive (area under the curve = 87%) and consistent with the gut microbiome having an effect on the steatosis phenome (>75% shared variation) and, therefore, actionable via microbiome-based therapies.
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We thank N. J. Gooderham for critical reading of the manuscript. This work was supported by EU-FP7 FLORINASH (Health-F2-2009-241913) to R.B., M.F., J.-M.F.-R., F.F., C.P., E.H. and J.K.N. This work used the computing resources of the UK MEDical BIOinformatics partnership—aggregation, integration, visualization and analysis of large, complex data (UK MED-BIO), which is supported by the Medical Research Council (grant number MR/L01632X/1). L.H. is in receipt of an MRC Intermediate Research Fellowship in Data Science (MR/L01632X/1, UK MED-BIO). This work was also supported by funding to R.B. ((Région Midi-Pyrénées 2009-2014 RPV09003BBA), Agence Nationale de la Recherche ANR 09-GEN TRANSFLORAP and GAD 08-2_378258), to M.F. (Ministry of University (MIUR) Progetti di Ricerca di Interesse Nazionale (PRIN) protocol number 2015MPESJS_004, Ministry of Health Ricerca Finalizzata RF-2011-02349921, Fondazione Roma call for Non-Communicable Diseases NCD 2014), to J.-M.F.-R. (Ministry of Health FIS project 15/01934, CIBERobn Pathophysiology of Obesity and Nutrition and FEDER funds) and to M.-E.D. (EU METACARDIS under agreement HEALTH-F4-2012-305312, Neuron II under agreement 291840 and the MRC MR/M501797/1). We acknowledge the support of the Imperial College National Institute of Biomedical Research andthe Clinical Phenotyping Centre for support.
About this article
Nature Communications (2019)
Nature Reviews Gastroenterology & Hepatology (2019)
Nature Reviews Endocrinology (2019)
Diet-induced metabolic changes of the human gut microbiome: importance of short-chain fatty acids, methylamines and indoles
Acta Diabetologica (2019)