Barking up the microbiome tree: a multi-cavity characterization of maternal postpartum and pup early colonization dynamics

Early-life microbial colonization plays a pivotal role in shaping host development, yet site-specific microbial dynamics in domestic dogs remain poorly characterized. Here, we explored microbial colonization and maturation of oral and rectal microbiota in puppies during the first postnatal week and assessed the contributions of maternal sources (oral, vaginal, rectal, and milk microbiota) to early colonization. We collected 505 samples from 33 dams and their litters across two timepoints (day 1 and day 8 postpartum) and characterized microbial communities using 16S rRNA gene sequencing. We found that the pup oral microbiome on day 1 closely resembled maternal milk and vaginal microbiota, highlighting the importance of maternal seeding via these routes. In contrast, the rectal microbiome of pups was initially distinct from all maternal body sites, suggesting a more complex colonization route, potentially involving environmental exposure. However, both oral and rectal microbiomes in pups exhibited signs of early maturation by day 8, with decreased abundance of opportunistic taxa such as Clostridium and increased resemblance to maternal profiles. Among maternal body sites, only the vaginal microbiome showed significant shifts postpartum, while other sites remained relatively stable. Our results reveal differential maternal contributions to microbial development across body sites in pups and support the notion of a dynamic but directed colonization process during early life. The observed patterns mirror key features of microbial transmission in humans, supporting the relevance of dogs as a valuable model for studying early-life microbiome dynamics and maternal-offspring microbial transmission in mammals.