Captive animal gut microbiota is populated with microorganisms that are relevant to the digestion of host dominant diet

Abstract

Diet contributes to changes in animal gut microbiomes, which in turn impacts host fitness and immune system development. Drastic changes in diet are often inevitable when animals adjust to captive lifestyles in facilities and could influence host health status by shifting gut microbiome composition. In this study, we evaluated the effects of the dominant diet component on the variation of gut microbiota biodiversity of captive herbivores, omnivores and carnivore species.  We performed 16S rRNA gene amplicon sequencing analysis using QIIME2 and R. Alpha diversity differed significantly (Faith’s phylogenetic distance p = 0.04; Pielou’s evenness p = 0.01) among herbivore groups primarily consuming fruits versus general plant materials, but not observed for the same diet grouping in omnivores. Captive carnivores with invertebrate-dominant diets had higher phylogenetic diversity (p = 0.005) compared to those primarily consuming mammals and birds. The most prevalent and abundant microbial taxa in the gut microbiota vary with the general diet types (carnivore, herbivore, and omnivore). Additionally, among the dominant food-type consumed, the key microbial taxa that significantly differ in abundance likely play functional roles in host digestion. These insights to bacterial biodiversity within captive species, ranging from herbivorous to carnivorous species, can potentially aid conservation management practices that aim to improve animal health and wellbeing in captivity.