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GM\u2013host interactions influence the fitness of holobionts and are, therefore, an integral part of evolution. The house mouse is a prominent model for GM\u2013host 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\u2013Muller 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\u2013host coadaptations and the fitness effects of their interactions.<\/jats:p>","DOI":"10.1093\/femsec\/fiac078","type":"journal-article","created":{"date-parts":[[2022,6,29]],"date-time":"2022-06-29T21:03:36Z","timestamp":1656536616000},"source":"Crossref","is-referenced-by-count":10,"title":["Divergent gut microbiota in two closely related house mouse subspecies under common garden conditions"],"prefix":"10.1093","volume":"98","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1701-9878","authenticated-orcid":false,"given":"Barbora","family":"Bendov\u00e1","sequence":"first","affiliation":[{"name":"Department of Zoology, Faculty of Science, Charles University , Prague, Czech Republic"},{"name":"Studenec Research Facility, Institute of Vertebrate Biology, Czech Academy of Sciences , Brno, Czech 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