Microbiomics, Metabolomics, Predicted Metagenomics, and Hepatic Steatosis in a Population-Based Study of 1,355 Adults

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Background and Aims: Previous small studies have appraised the gut microbiome (GM) in steatosis, but large-scale studies are lacking. We studied the association of the GM diversity and composition, plasma metabolites, predicted functional metagenomics, and steatosis. Approach and Results: This is a cross-sectional analysis of the prospective population-based Rotterdam Study. We used 16S ribosomal RNA gene sequencing and determined taxonomy using the SILVA reference database. Alpha diversity and beta diversity were calculated using the Shannon diversity index and Bray–Curtis dissimilarities. Differences were tested across steatosis using permutational multivariate analysis of variance. Hepatic steatosis was diagnosed by ultrasonography. We subsequently selected genera using regularized regression. The functional metagenome was predicted based on the GM using Kyoto Encyclopedia of Genes and Genomes pathways. Serum metabolomics were assessed using high-throughput proton nuclear magnetic resonance. All analyses were adjusted for age, sex, body mass index, alcohol, diet, and proton-pump inhibitors. We included 1,355 participants, of whom 472 had steatosis. Alpha diversity was lower in steatosis (P = 1.1∙10−9), 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. Conclusions: We confirmed, 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.

Original languageEnglish
Pages (from-to)968-982
Number of pages15
Issue number3
Publication statusPublished - Mar 2021

Bibliographical note

Funding Information:
The authors thank the Rotterdam Study participants and staff, and in particular, the collaborating general practitioners and pharmacists. The authors are also deeply grateful to Mrs. van Wijngaarden (P.W.), nurse ultrasonographeer, for performing the abdominal ultrasonography and LSMs. The generation and management of stool microbiome data for the Rotterdam Study (RSIII-2) was executed by the Human Genotyping Facility of the Genetic Laboratory of the Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands. We thank Nahid El Faquir and Jolande Verkroost-Van Heemst for their help in sample collection and registration, and Pelle van der Wal, Kamal Arabe, Hedayat Razawy, and Karan Singh Asra for their help in DNA isolation and sequencing. Furthermore, we thank Drs. Jeroen Raes and Jun Wang (KU Leuven, Belgium) for their guidance in 16S rRNA profiling and data-set generation.

Publisher Copyright:
© 2020 by the American Association for the Study of Liver Diseases.


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