Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

• Published in: Science (American Association for the Advancement of Science) Vol. 352; no. 6285; pp. 565 - 569
• Main Authors: Zhernakova, Alexandra, Kurilshikov, Alexander, Bonder, Marc Jan, Tigchelaar, Ettje F., Schirmer, Melanie, Vatanen, Tommi, Mujagic, Zlatan, Vila, Arnau Vich, Falony, Gwen, Vieira-Silva, Sara, Wang, Jun, Imhann, Floris, Brandsma, Eelke, Jankipersadsing, Soesma A., Joossens, Marie, Cenit, Maria Carmen, Deelen, Patrick, Swertz, Morris A., study, LifeLines cohort, Weersma, Rinse K., Feskens, Edith J. M., Netea, Mihai G., Gevers, Dirk, Jonkers, Daisy, Franke, Lude, Aulchenko, Yurii S., Huttenhower, Curtis, Raes, Jeroen, Hofker, Marten H., Xavier, Ramnik J., Wijmenga, Cisca, Fu, Jingyuan
• Format: Journal Article
• Language: English
• Published: United States American Association for the Advancement of Science 29.04.2016; The American Association for the Advancement of Science
• Subjects: Analysis; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Biomarkers; Chair Nutrition and Health over the Lifecourse; Chromogranin A - analysis; Chromogranin A - metabolism; Clinical trials; Diet; Enteroendocrine Cells - metabolism; Feces - chemistry; Feces - microbiology; Gastrointestinal Microbiome - genetics; Gastrointestinal Tract - microbiology; Genetic Markers; Global Nutrition; High-Throughput Nucleotide Sequencing; HNE Nutrition and Health over the Lifecourse; HNE Voeding en Gezondheid in de Levenscyclus; Humans; Metagenomics; Microbiology; Netherlands; Phylogeny; RNA, Ribosomal, 16S - genetics; VLAG; Wereldvoeding; Netherlands
• ISSN: 0036-8075; 1095-9203; 1095-9203
• DOI: 10.1126/science.aad3369

Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition. We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions.