(P20-048-23) Beagle Dogs Living in Household and in Controlled Environments Show Different Gut Microbiome Profiles When Fed an Identical Diet or the Same Diet Type

Objectives: To compare the fecal microbiome of beagle dogs living in household and in controlled environments when fed an identical diet or the same diet type.

Methods: Beagles were recruited from U.S. households (pets, n = 54), an academic facility (FAC1, n = 34), and a private kennel (FAC2, n = 39). All were fed an identical diet (fresh, Nom Nom Chicken) or diet type (kibble, various brands) for ≥ 1 week. Stool samples were collected at the end of the feeding period and the fecal microbiome at the strain level was characterized with shotgun metagenomic sequencing. Diversity metrics (captured at rarefied depth 230,000) and the abundance (using Linear discriminant analysis Effect Size, LEfSe) were compared among the three cohorts.

Results: When fed a fresh diet, the Shannon diversity index (SDI) was different among the three cohorts with FAC2 having higher SDI than pets (adjusted p = 2.5e-3) and FAC1 (adjusted p = 5.3e-5). Similarly, SDI for kibble were different among the three cohorts with FAC2 having higher SDI than pets (adjusted p = 0.003) but comparable to FAC1. Centered and rescaled principal coordinate analysis axes 1 and 2 explained 29.1% and 10.4% of the variance, and clusters of three cohorts were observed along the two axes within only the fresh samples, as well as within only the kibble samples (PERMANOVA with the Bray-Curtis dissimilarity, p < 0.05 for fresh, p < 0.05 for kibble). With the fresh diet, taxa with higher abundances in pets were Bacteroidia, Gammaproteobacteria and Negativicutes, while Actinomycetia was largely more abundant in FAC1, and Clostridia and Fusobacteriia in FAC2. With the kibble diet, taxa with higher abundances in pets were Gammaproteobacteria, Negativicutes, and Fusobacteriia, while Actinomycetia was largely more abundant in FAC1, and Clostridia, Erysipelotrichia, and Bacilli in FAC2.

Conclusions: The findings highlight dogs’ living environment as an important factor to consider when conducting diet and microbiome studies. Given such research is often conducted in dogs living in controlled environments and applied to wider populations, this trial suggests microbiome research conducted within household pets may have greater applicability.

Funding Sources: NomNomNow (project started 12/1/2021, prior to the acquisition by Mars, Inc)