Initial colonization of the mammalian gut microbiome defines a critical window in early life during which both host immunity and future ecosystem structure are established. Several factors influence early gut colonization, including parental and environmental transmission, introduction of solid foods, cohabitation, and medication use. Here, we evaluated a canine cohort to elucidate the trajectory of gut microbiome assembly and stabilization, comprising 664 stool samples from 79 colony dogs sampled approximately every three months from three months to three years of age. Detailed records of each individual’s food intake, housing, breed, medical histories, and lineage were collected. Metagenomic shotgun sequencing was used to quantify each individual’s taxonomic and functional gut composition.

Preliminary results indicate that age effects were primarily observed at the level of individual microbes. Notably, members of the Fusobacteriaceae family showed increased prevalence with age, alongside increases in taxa such as Phocaeicola plebeius and decreases in members of the Eubacteriaceae family. In addition, longitudinal analysis identified both stable and transient colonizers, highlighting dynamic microbial turnover in early life. Further, food showed modest but significant associations with community composition, consistent with known nutritional influences on the gut microbiome. In contrast, co-housing had no effect on overall community similarity; further work is needed to assess potential strain-level transmission. Preliminary functional analyses also indicated age-associated gene content carriage within species, including processes such as DNA integration and transcriptional regulation, suggesting strain-level functional shifts accompanying microbial succession.

Further work within this cohort will provide an opportunity to explore strain transmission events among interacting individuals, disease development, and short- and long-term dietary effects on the canine gut microbiome. Taken together, these data will provide an understanding of early life gut microbiome ecological patterns.