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Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women


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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  • 09 August 2018

    In the version of this article originally published, the received date was missing. It should have been listed as 2 January 2018. The error has been corrected in the HTML and PDF versions of this article.


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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.

Author information

R.B., J.-M.F.-R., M.F., F.L., F.F., C.P., E.H. and J.K.N. designed the study and supervised all parts of the project. R.B. is the project leader and chaired the consortium. M.-E.D. led data integration and elaborated the primary interpretation of analytical outcomes with L.H., in close collaboration with M.F., J.-M.F.-R. and R.B. L.H. implemented the microarray data analysis workflow. C.T. and M.W. developed the data repository. J.A. developed the metagenomic data analysis pipeline in collaboration with L.H. S.A.B. supervised the development of the data repository and the pipeline. L.H., J.A., R.H.B. and M.-E.D. performed the data analyses. J.-M.F.-R. and M.F. designed the clinical protocol and oversaw the clinical activities. M.C., F.D., I.C., O.P., P.G., J.P., G.X. and W.R. recruited and phenotyped patients and collected biological samples and physiological data. M.S., V.A. and V.B.-B. performed the RNA and DNA extractions. R.B. and M.S. supervised the DNA sequencing and gene profiling. J.L.L. and J.M.M.-N. performed the cell culture experiments. F.B., E.A., J.Charpentier and C.H. performed the animal work. R.H.B., J.Chilloux and L.M.-G. performed the metabolic profiling of plasma and urine by 1H-NMR. E.H. and J.K.N. supervised the metabolic profiling. A.M. performed the methylamine quantifications. L.H. and M.-E.D. drafted the first versions of the paper with critical and substantial contributions from M.F., J.-M.F.-R. and R.B. All authors provided support and constructive criticism throughout the project and approved the final version of the paper.

Competing interests

L.H., J.-M.F.-R., M.F., R.H.B., J.L.L., E.H., J.K.N., C.P., R.B. and M.-E.D. are named as co-inventors on pending patents held by INSERM Transfert, INSERM, University of Rome Tor Vergata, University of Girona and Imperial College on NAFLD diagnostics and have the right to receive royalty payments for inventions or discoveries related to NAFLD diagnostics.

Correspondence to José-Manuel Fernández-Real or Massimo Federici or Rémy Burcelin or Marc-Emmanuel Dumas.

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Fig. 1: Flowchart showing the approach used for the integration of clinical, molecular phenomics and metagenomic information and biological validations.
Fig. 2: Association between liver steatosis, MGR and metagenomic data in obese women.
Fig. 3: Association of metabolomic and transcriptomic data with liver steatosis and MGR.
Fig. 4: Transfer of steatotic and metabolic phenotypes to mice through FMT of material from patients with liver steatosis grade 3.
Fig. 5: Microbial PAA induces liver steatosis and BCAA use in primary human hepatocytes and mice.
Fig. 6: Phenome-wide crosstalk and predictive modeling.