Developmental Changes in the Canine Gut Microbiome during Breastfeeding, Weaning, Socialization and Maturation to Adulthood
Authors: Ephraim Eden , Jackson Matthew I. , Cochrane Chun-Yen , Brockel Christoph Ephraim , Jewell Dennis E. 
Published: April 2020

The goal of this study was to identify changes in the canine gut microbiome during breastfeeding, weaning, socialization and maturation to adulthood. Due to rapid changes in the gut microbiome during the first few days after birth, samples were collected every day for the first 15 days from puppies that were born at the Hill’s Pet Nutrition Center. Samples were then collected weekly for 2 weeks, biweekly for the next 4 weeks, quarterly until the dogs were one year old. The 16S rRNA gene sequencing was performed on a total of 254 fresh fecal samples collected from 15 beagles (6 from the first litter and 9 from the second litter) to evaluate developmental changes in the gut microbiome. Puppies were weaned on day 56 and stayed with the same litter until day 150. After day 150, puppies were moved to different rooms and were mixed with other dogs in the colony. This study evaluated changes in the gut microbiome during the four major developmental stages of the dogs. Group 1a, involved samples collected during the first 20 days of the puppies before weaning. Group 1b included samples collected between day 21 and 56 before weaning. Group 2 included samples collected between weaning and the relocation of the litter with other colony dogs (day 56 to 150). Group 3 included all samples collected after day 150. Linear mixed model analysis was performed on Centered‐Log Ratio (CLR) transformed data to evaluate changes in individual OTUs with age in the 4 different groups. Significance was determined at alpha equals 0.05. During the first 20 days after birth, there were no statistically significant changes in levels of the genera Lactobacillus, Faecalibacterium, Sutterella, Oscillospira and unclassified genus in family Enterobacteriacea. However, there was a significant decline in levels of Bifidobacterium, Prevotella and Turicibacter during this period. Between day 20 and day 56, levels of Bifidobacterium, Prevotella Turicibacter and Lactobacillus showed significant increase. Levels of Sutterella and Oscillospira did not change significantly in this period. However, the genus Faecalibacterium and the unclassified genus in the family Enterobacteriaceae declined significantly. No statistical changes were observed in the levels of any of the above OTUs between weaning and the relocation of the puppies with other colony dogs on day 150. Faecalibacterium continued to decline between day 150 and age one, while none of the above OTUs changed. This study showed that during breastfeeding, major shifts in the canine gut microbiome take place between days 20 and 56. Contrary to our expectations, the saccharolytic Faecalibacterium declined in the presence of prebiotics in breast milk and food after weaning. The study continues to evaluate developmental changes in the gut microbiota in additional samples being collected from these and other litters.Support or Funding InformationThe work presented in this study was funded by Hill’s Pet Nutrition, Topeka, KS.