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A mole rat’s gut microbiota suggests selective influence of diet on microbial niche space and evolution

The coevolution of mammals with their gut microbiota is heavily influenced by diet. Here we investigate the evolution of the gut microbiota in an African mole rat, which has a highly fibrous diet that includes underground storage organs of plants. For this purpose, microbial DNA was isolated from the digesta of a Cape dune mole rat gut, and 23 of 62 partial length 16S rRNA sequences were chosen for full length sequence determination. In addition, V4 regions of 16S rRNA were sequenced using Illumina technology. These sequences were then compared to previously identified sequences in the NCBI and Greengenes databases. Treponeme-related sequences within the mole rat showed evidence of a substantial adaptive radiation, with considerable diversity found within the mole rat (81% minimum sequence identity) as well as substantial divergence (87.3% average sequence identity to nearest neighbor) from previously identified organisms. It also appears likely that Desulfovibrio and several other bacterial clades, but not Clostridia-related organisms, have undergone substantial evolutionary changes during the evolution of mole rats and their ancestors. These findings support the intuitive view that some enteric bacteria can be described as “housekeeping,” with a niche defined by the host gut largely independent of diet. This diet-independent niche space and the microbes occupying it appear to be stable despite substantial alteration of diet-dependent niches and adaptive radiation of microbes occupying those niches. Impact statement The composition of the microbiota is of critical importance for health and disease, and is receiving increased scientific and medical scrutiny. Of particular interest is the role of changing diets as a function of agriculture and, perhaps to an even greater extent, modern food processing. To probe the connection between diet and the gut’s microbial community, the microbiota from a mole rat, a rodent with a relatively unusual diet, was analyzed in detail, and the microbes found were compared with previously identified organisms. The results show evidence of an adaptive radiation of some microbial clades, but relative stability in others. This suggests that the microbiota, like the genome, carries with it housekeeping components as well as other components which can evolve rapidly when the environment changes. This study provides a very broad view of the niche space in the gut and how factors such as diet might influence that niche space.