Gastrointestinal diseases are the most frequently reported clinical problem in captive common marmosets (Callithrix jacchus), often affecting the health and welfare of the animal and ultimately their use as a research subject. The microbiome has been shown to be intimately connected to diet and gastrointestinal health. Here we use shotgun metagenomics and untargeted metabolomics of fecal samples collected before, during and after a dietary transition, from a biscuit to a gel diet, in common marmosets. Overall health of marmosets, measured as weight recovery and reproductive success, improved after the diet transition. Microbial and metabolic responses varied by individually paired marmosets. The genes and functions of the microbes appeared to be of greater importance than the microbes themselves. In at least one breeding pair, Bifidobacterium and Prevotella spp were found to increase (compared to Escherichia and Bacteroidetes spp) after diet change during clinical improvement, supporting previous literature. Untargeted metabolic profiles indicated that polyamines levels, specifically cadaverine and putrescine, were high after diet transition, suggesting either an increase in excretion or decrease in intestinal reabsorption at the intestinal level. In conclusion, our data suggests that Bifidobacterium species could potentially be useful as probiotic supplements to the laboratory marmoset diet.
Appropriate diet and health of the common marmoset in captivity is essential to both the welfare of the animal and to improve experimental outcomes. Our study shows that a gel diet compared to a biscuit diet improves the health of a marmoset colony, and correlates with fecal microbiome and metabolomic changes. The diet transition had an influence on the molecular changes at both the individual-pair and group level but only at the individual-pair level for the microbial changes. Similar to results seen in humans, responses were individualized. It appears to be more important which genes and functions present changed rather than specific microbes. Further study is needed to identify specific components that should be considered when choosing an appropriate diet and additional supplementary foods as well as to validate the benefits of providing probiotics. Probiotics containing Bifidobacterium species appear to be useful as probiotic supplements to the laboratory marmoset diet, but additional work is needed to validate these findings.