Evaluation of neonatal oral and rectal microbiota in dogs delivered by c-section, from birth to weaning.

In recent years, the role of the microbiota in early-life health has gained increasing attention; however, data on the initial phases of microbial colonization in dogs remain limited. This study investigated the development of oral and rectal microbiota in puppies delivered by cesarean section from birth to weaning, and the contribution of maternal microbial sources. Four French Bulldog dams and their litters (18 puppies) were enrolled under uniform management conditions. Oral and rectal swabs were collected from puppies at birth and at 15, 30, 45, and 60 days of age, together with maternal oral, teat-skin, and rectal samples, and analyzed by 16S rRNA gene sequencing. Longitudinal analyses revealed a marked, time-dependent increase in microbial richness and diversity in both oral and rectal niches, reflecting a clear ecological succession from pioneer facultative anaerobes to taxa associated with a mature microbiota. Alpha diversity significantly increased from birth to weaning in both oral and rectal samples (p < 0.001), while beta diversity analyses showed progressive convergence toward maternal microbial profiles over time, particularly after the dietary transition from milk to solid food. Source tracking analysis identified maternal teat-skin microbiota as the primary contributor during early life, while maternal oral and rectal sources became increasingly dominant as puppies matured. These findings demonstrate that microbial colonization in dogs begins very early and undergoes dynamic, site-specific maturation throughout the neonatal period. From a One Health perspective, the observed mother-offspring microbial interactions highlight the translational value of canine models for studying early-life microbiota development.