Divergent gut microbiota in two closely related house mouse subspecies under common garden conditions

Sequencing data associated with this project are archived in the European Nucleotide Archive (project accession number: PRJEB51786). Accession numbers for each sample are presented in Table S1 (Supporting Information).Care of all mice mentioned in this manuscript, all procedures and experiments were performed according to the National Institutes of Health and the Office of Laboratory Animal Welfare guidelines for appropriate animal husbandry (OLAW assurance A3292-01), and all live mice were handled by an authorized person.

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إنجليزي. The gastrointestinal microbiota (GM) is considered an important component of the vertebrate holobiont. GM–host interactions influence the fitness of holobionts and are, therefore, an integral part of evolution. The house mouse is a prominent model for GM–host interactions, and evidence suggests a role for GM in mouse speciation. However, previous studies based on short 16S rRNA GM profiles of wild house mouse subspecies failed to detect GM divergence, which is a prerequisite for the inclusion of GM in Dobzhansky–Muller incompatibilities. Here, we used standard 16S rRNA GM profiling in two mouse subspecies, Mus musculus musculus and M. m. domesticus, including the intestinal mucosa and content of three gut sections (ileum, caecum, and colon). We reduced environmental variability by sampling GM in the offspring of wild mice bred under seminatural conditions. Although the breeding conditions allowed a contact between the subspecies, we found a clear differentiation of GM between them, in all three gut sections. Differentiation was mainly driven by several Helicobacters and two H. ganmani variants showed a signal of codivergence with their hosts. Helicobacters represent promising candidates for studying GM–host coadaptations and the fitness effects of their interactions.