Abstract
The gut microbiomes of mammals appear to mirror their hosts’ phylogeny, suggesting host-driven microbial community assembly. Yet, much of this evidence stems from comparative studies of distinct wild or captive populations that lack data for disentangling the relative influences of shared phylogeny and environment. Here, we present phylogenetic and multivariate analyses of gut microbiomes from six sympatric (i.e., co-occurring) mammal species inhabiting a 1-km2 area in western Madagascar—three lemur and three non-primate species—that consider genetic, dietary, and ecological predictors of microbiome functionality and composition. Host evolutionary history, indeed, appears to shape gut microbial patterns among both closely and distantly related species. However, we also find that diet—reliance on leaves versus fruit—is the best predictor of microbiome similarity among closely related lemur species, and that host substrate use—ground versus tree—constrains horizontal transmission via incidental contact with feces, with arboreal species harboring far more distinct communities than those of their terrestrial and semi-terrestrial counterparts.
Highlights
The gastrointestinal tracts of mammals are complex ecosystems harboring large and diverse populations of bacteria that are essential for digestion, development, metabolism, behavior, immune function, and protection from pathogens [1,2,3,4,5,6]
The gut microbial communities of the six mammalian host species encompassed two archaeal and 25 bacterial phyla, of which four (Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria) were present in all samples and together constituted 51.2–99.7% of the reads identified in each individual (Fig. 1b)
Bushpig and cattle microbiomes were enriched with Tenericutes, Planctomycetes, and Lentisphaerae whereas fossa microbiomes were deficient in Bacteroidetes and showed higher abundances of microbial taxa related to Firmicutes and Fusobacteria (SAMseq analysis, false discovery rate (FDR)-adjusted P < 0.0001; Table S2)
Summary
The gastrointestinal tracts of mammals are complex ecosystems harboring large and diverse populations of bacteria that are essential for digestion, development, metabolism, behavior, immune function, and protection from pathogens [1,2,3,4,5,6]. These microbial communities are potentially shaped by diverse host factors—heritable (e.g., genetics, evolutionary history), environmental (e.g., geography, diet), as well as behavioral (i.e., social contact patterns) [7]. Some studies of humans and other primates have suggested that social contact patterns
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