A comprehensive metagenomic analysis of the canine gut microbiome utilizing high-resolution, full-length 16S rRNA gene sequencing of fecal samples from 90 healthy dogs, including 61 puppies with their mothers, as well as other adult male and female counterparts.

Stool samples were collected from six kennels of Hungarian Pumi dogs, including puppies and their mothers, as well as adult male and female counterparts, across multiple time points beginning from the mothers' gestation period and under various feeding conditions. The study included both naturally whelped and cesarean section-delivered puppies. The primary objective was to examine the dynamics of the gut microbiome in mother dogs during gestation and lactation, in puppies throughout their first year of life and into adulthood, and to assess the impact of different feeding regimes on the gut microbiota of both puppies and adult dogs. In total, 463 stool samples from 90 individuals were analyzed using high-coverage, full-length 16S rRNA gene sequencing on Oxford Nanopore Technologies' MinION platform. This high-quality dataset provides valuable insights into the microbiome dynamics of pregnant and lactating dogs, heritable microbiome patterns in newborn puppies, and the influence of nutrition on early microbiome establishment in puppies, as well as differences in microbiome composition between puppies and adult dogs.