Assessing of the gut microbiome effects from captivity in Crocidura russula and Apodemus sylvaticus

As continued growth in gut microbiome studies in captive and model animals elucidates the importance of their role in host biology, further pursuit of how to retain a wild-like microbial community is becoming increasingly important to obtain representative results. In this study, we assessed how captivity housing conditions altered the gut microbiome of two wild-caught small mammals, namely Crocidura russula (Eulypotyphla, insectivore) and Apodemus sylvaticus (Rodentia, omnivore). We analysed the gut microbiota of 15 A. sylvaticus and 20 C. russula, immediately after bringing them into captivity and five weeks later, under two housing treatments: 'natural', 'and laboratory'. Natural which consisted of fresh bedding and enrichment elements directly obtained from nature; and 'laboratory', which consisted of physically analogous bedding and enrichment elements, yet artificially manufactured and sterilised. Through sequencing of the V3-V4 region of the 16S rRNA gene, we found that captivity significantly reduced microbial alpha diversity and induced significant compositional variation in both species. However, the use of natural elements enriched with environmental microbes did not significantly mediate alpha diversity loss, neither did it alter community assemblage when compared to conventional laboratory conditions. Additionally, by utilising different diversity metrics, incorporating both phylogenetic and phylogenetically neutral metrics, we were able to demonstrate that while we saw significant declines in diversity, these mostly shared a phylogenetic structure and that bacterial replacement occurred within related ASVs. While the results of this experiment do not support the use of microbially enriched environments to retain wild-like microbial communities when using adult animals, it may be of interest when rearing juvenile study organisms without a well-established microbiota.