Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

Abstract

Co-evolution of mammals and their gut microbiota has profoundly effected their radiation into myriad habitats. We used shotgun sequencing of microbial community DNA and targeted sequencing of bacterial 16S rRNA genes to understand how microbial communities adapt to extremes of diets, sampling fecal DNAs from 33 mammalian species and 18 humans who kept detailed diet records. We found that microbiota adaptation to diet is reproducible across different mammalian lineages. Functional repertoires of microbiome genes, such as those encoding carbohydrate-active enzymes and proteases, can be predicted from bacterial species assemblages. These results illustrate the value of characterizing vertebrate gut microbiomes to fully understand host evolutionary histories at a supra-organismal level.

Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus

“…The impact of diet in shaping gut microflora communities in humans and other vertebrates has been well studied (De Filippo et al., 2010; Muegge et al., 2011). Even in insects, gut microflora has been implicated in adaptation to crop rotation (Chu et al., 2013) and novel food sources (Otani et al., 2014).…”

Integrating nutrition and immunology: A new frontier

“…The reasons why host diet has a strong impact on the gut microbial composition are still not well understood (De Filippo et al, 2010;Muegge et al, 2011;Turnbaugh et al, 2009), but presumably reflects a combination of influences on the physical and chemical milieu of the gut (Clissold et al, 2010;Duncan et al, 2008;Faith et al, 2011;Flint et al, 2008;Ley et al, 2008;Sorensen et al, 2010), and effects on immune responses (see above). Also, the diet itself is a vector of commensals, and different diets will provide microbial inoculates of different community compositions.…”

Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

“…Most studies have been focusing on feces of human or other mammalian origin, but the number of studies on other vertebrates is increasing [2]. Gut microbiota analysis may be regarded as a twenty-first-century science, but the field was pioneered already in the late nineteenth century [4].…”