Characterization of the fecal microbiome during neonatal and early pediatric development in puppies

Abstract

Limited information is available describing the development of the neonatal fecal microbiome in dogs. Feces from puppies were collected at 2, 21, 42, and 56 days after birth. Feces were also collected from the puppies’ mothers at a single time point within 24 hours after parturition. DNA was extracted from fecal samples and 454-pyrosequencing was used to profile 16S rRNA genes. Species richness continued to increase significantly from 2 days of age until 42 days of age in puppies. Furthermore, microbial communities clustered separately from each other at 2, 21, and 42 days of age. The microbial communities belonging to dams clustered separately from that of puppies at any given time point. Major phylogenetic changes were noted at all taxonomic levels with the most profound changes being a shift from primarily Firmicutes in puppies at 2 days of age to a co-dominance of Bacteroidetes, Fusobacteria, and Firmicutes by 21 days of age. Further studies are needed to elucidate the relationship between puppy microbiota development, physiological growth, neonatal survival, and morbidity.

Gut microbiome features associated withClostridium difficilecolonization in puppies

“…As has been found in other studies (14, 25), both colonization with C. difficile and reduced gut microbial diversity in puppies were significantly associated with young age. Similar associations have also been found in human studies (17, 19, 36, 39).…”

“…It is unclear why these discrepancies were observed in our study. Both Bacteroides spp, which are used as markers of a healthy gut in people (50), and E. coli are found in the feces of healthy puppies (25, 51). Bacteroides spp are found in increasing relative abundance with increasing age, while E. coli levels are significantly higher in younger (less than 21 days) puppies than in older (greater than 42 days) puppies (25).…”

“…No such association has been demonstrated in dogs, and studies of the association between the administration of antibiotics (and the consequent disruption of the gut microbiota) and C. difficile colonization/infection in dogs have yielded mixed results (23, 24). The evolution of the neonatal canine gut microbiome has been described, with increasing diversity and taxonomic shifts occurring with increasing age (25). As has been found in human infants (17), it is possible that certain taxonomic patterns and a lack of microbial community diversity in the gut may be associated with a lack of colonization resistance to C. difficile .…”

Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features

“…Historically, characterization of the GI microbiota was performed by means of culture-dependent methods, allowing biochemical and physiological investigations of isolated strains. The high throughput and low cost of NGS technologies has facilitated the study of the intestinal microbiota of not only humans but also of other mammals, including livestock animals (Kim et al, 2011;Ferrario et al, 2017) and companion animals (Suchodolski et al, 2015;Guard et al, 2017). In recent years, the availability of constantly advancing next-generation sequencing (NGS) technologies, together with tailor-made bioinformatics tools, have provided novel culture-independent approaches to better assess the composition, functionality and dynamics of this microbial intestinal ecosystem.…”

“…In recent years, the availability of constantly advancing next-generation sequencing (NGS) technologies, together with tailor-made bioinformatics tools, have provided novel culture-independent approaches to better assess the composition, functionality and dynamics of this microbial intestinal ecosystem. The high throughput and low cost of NGS technologies has facilitated the study of the intestinal microbiota of not only humans but also of other mammals, including livestock animals (Kim et al, 2011;Ferrario et al, 2017) and companion animals (Suchodolski et al, 2015;Guard et al, 2017).…”