Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice

Abstract

Understanding the origins of gut microbial community structure is critical for the identification and interpretation of potential fitnessrelated traits for the host. The presence of community clusters characterized by differences in the abundance of signature taxa, referred to as enterotypes, is a debated concept first reported in humans and later extended to other mammalian hosts. In this study, we provide a thorough assessment of their existence in wild house mice using a panel of evaluation criteria. We identify support for two clusters that are compositionally similar to clusters identified in humans, chimpanzees, and laboratory mice, characterized by differences in Bacteroides, Robinsoniella, and unclassified genera belonging to the family Lachnospiraceae. To further evaluate these clusters, we (i) monitored community changes associated with moving mice from the natural to a laboratory environment, (ii) performed functional metagenomic sequencing, and (iii) subjected wild-caught samples to stable isotope analysis to reconstruct dietary patterns. This process reveals differences in the proportions of genes involved in carbohydrate versus protein metabolism in the functional metagenome, as well as differences in plant-versus meat-derived food sources between clusters. In conjunction with wild-caught mice quickly changing their enterotype classification upon transfer to a standard laboratory chow diet, these results provide strong evidence that dietary history contributes to the presence of enterotype-like clustering in wild mice.

Intra- and Interindividual Variations Mask Interspecies Variation in the Microbiota of Sympatric Peromyscus Populations

“…that could not identify a significant effect of environmental contamination or habitat type on cecal diversity (40). They also support recent studies of wild European M. musculus populations that observed that large geographical distances were the most significant factor in explaining microbiota variation and that host genetics and diet had relatively minor effects on variation (41,42). Other natural experiments investigating the structure of the microbiota in insects (13,14), primates (15)(16)(17), and bats (18) also support our results.…”

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

“…Laboratory mice were housed in conventional or specific pathogen-free facilities at the WZW School of Life Sciences (TU München), the Institute for Medical Microbiology and Hygiene (Universitätsklinikum Freiburg) or the Rodent Center (ETH Zurich). Samples from mice captured in the wild were obtained as described previously 42 . Starting materials for bacteria isolation included fresh faeces collected from living mice, mucosal samples, as well as small intestinal, caecal or colonic content collected from mice that had been euthanized by CO 2 inhalation or neck dislocation.…”

Consumption of a Bifidobacterium bifidum Strain for 4 Weeks Modulates Dominant Intestinal Bacterial Taxa and Fecal Butyrate in Healthy Adults

“…The existence of discrete structures for gut microbiota has not been convincingly demonstrated (30) and represents a crucial assumption in applying an appropriate prediction model. Nonetheless, we used the original tutorial to define enterotypes (http://enterotype .embl.de/enterotypes.html) in the present study, because it has been demonstrated to be useful to correlate the gut microbial community structure with host biomarkers and diet (31,32). In our study, enterotyping clustered the microbiota taxonomic structures of the fecal samples in two groups corresponding to the most common enterotypes of healthy adult populations, namely, the Bacteroides-dominant (Ba) and the Prevotella-dominant (Pr) enterotypes (22,33).…”