Interspecies comparative metagenomics reveals correlated gut microbiome functional capacities among vertebrates

While recent research reveals that the gut microbiome drives vertebrate health, little is known about whether the mechanisms these microbes employ to interact with physiology are consistent across host species. To help close this knowledge gap, we compared gut metagenomes across 10 vertebrate species, including biomedical animal models, to define the inter-species variation in the biochemical pathways encoded by gut microbiota. Doing so revealed gut-enriched pathways conserved across vertebrates, as well as pathways that vary concordantly with host evolutionary history. Overall, the functional capacity of the non-human gut microbiome generally reflects that of humans, though a subset of the pathways encoded by human gut microbiota are not well represented in non-human microbiomes. Collectively, these results support the use of animal models to study the mechanisms through which gut microbes impact human health, but suggest that researchers should cautiously consider which model will optimally represent a specific mechanism of interest.