Identifying a common set of genes that mediate host-microbial interactions across populations and species of mammals has broad relevance for human health and animal biology. However, the genetic basis of the gut microbial composition in natural populations remains largely unknown outside of humans. Here, we used wild house mouse populations as a model system to ask three major questions: (a) Does host genetic relatedness explain interindividual variation in gut microbial composition? (b) Do population differences in the microbiota persist in a common environment? (c) What are the host genes associated with microbial richness and the relative abundance of bacterial genera? We found that host genetic distance is a strong predictor of the gut microbial composition as characterized by 16S amplicon sequencing. Using a common garden approach, we then identified differences in microbial composition between populations that persisted in a shared laboratory environment. Finally, we used exome sequencing to associate host genetic variants with microbial diversity and relative abundance of microbial taxa in wild mice. We identified 20 genes that were associated with microbial diversity or abundance including a macrophage-derived cytokine (IL12a) that contained three nonsynonymous mutations. Surprisingly, we found a significant overrepresentation of candidate genes that were previously associated with microbial measurements in humans. The homologous genes that overlapped between wild mice and humans included genes that have been associated with traits related to host immunity and obesity in humans. Gene-bacteria associations identified in both humans and wild mice suggest some commonality to the host genetic determinants of gut microbial composition across mammals.
Host genetic determinants of the gut microbiota of wild mice
Creators
Taichi A. Suzuk - Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA
Megan Phifer-Rixey - Monmouth University
Katya L. Mack - Museum of Vertebrate Zoology
Michael J. Sheehan - Cornell University
Dana Lin - Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA
Ke Bi - QB3
Michael W. Nachman - Museum of Vertebrate Zoology
Publication Details
Molecular ecology, v 28(13), pp 3197-3207
Publisher
Wiley
Number of pages
11
Grant note
R01 GM127468; R01 GM074245 / NIGMS NIH HHS; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS)
R01GM127468 / NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS)
Resource Type
Journal article
Language
English
Academic Unit
Biology
Web of Science ID
WOS:000477750800006
Scopus ID
2-s2.0-85067388127
Other Identifier
991021229903504721
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