Microbiomics, metabolomics, predicted metagenomics and hepatic steatosis in a population‐based study of 1355 adults


Background & Aims

Previous small studies have appraised the gut microbiome (GM) in steatosis, but large‐scale studies are lacking. We studied the association of GM diversity and composition, plasma metabolites, predicted functional metagenomics and steatosis.

Approach & Results

This is a cross‐sectional analysis of the prospective population‐based Rotterdam Study. We used 16Sribosomal‐RNA gene sequencing and determined taxonomy using the Silva‐reference database. Alpha‐and beta‐diversity were calculated using Shannon‐index and Bray‐Curtis dissimilarities. Differences were tested across steatosis using PerMANOVA. Hepatic steatosis was diagnosed by ultrasonography. We subsequently selected genera using regularized regression. The functional metagenome was predicted based on the GM using KEGG‐pathways. Serum metabolomics were assessed using high‐throughput proton nuclear magnetic resonance. All analyses were adjusted for age, sex, BMI, alcohol, diet, and proton‐pump inhibitors. We included 1355 participants of which 472 had steatosis. Alpha‐diversity was lower in steatosis (P=1.1×109) and beta‐diversity varied across steatosis strata (P=0.001). Lasso selected 37 genera of which three remained significantly associated after adjustment (Coprococcus3: β=‐65; Ruminococcus Gauvreauiigroup: β=62; and Ruminococcus Gnavusgroup: β=45, Q‐value =0.037). Predicted metagenome analyses revealed that pathways of secondary bile‐acid synthesis and biotin metabolism were present and D‐alanine metabolism was absent in steatosis. Metabolic profiles showed positive associations for aromatic‐and branched chain amino acids and glycoprotein acetyls with steatosis and R. Gnavusgroup, whereas these metabolites were inversely associated with alpha‐diversity and Coprococcus3.


We confirmed, for the first time on a large‐scale, the lower microbial diversity and association of Coprococcus and Ruminococcus Gnavus with steatosis. We additionally showed that steatosis and alpha-diversity share -opposite- metabolic profiles.

Hepatology, 2020