Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus)

Abstract

Vertebrate gastrointestinal tracts have co-existed with microbes over millennia. These microbial communities provide their host with numerous benefits. However, the extent to which different environmental factors contribute to the assemblage of gut microbial communities is not fully understood. The purpose of this study was to determine how the external environment influences the development of gut microbiome communities (GMCs). Faecal samples were collected from deer mice (Peromyscus maniculatus) born and raised in captivity and the wild at approximately 3-5 weeks of age. Additional samples were collected 2 weeks later, with a subset of individuals being translocated between captive and wild environments. Microbial data were analysed using 16S rRNA next-generation Illumina HiSeq sequencing methods. GMCs of deer mice were more similar between neighbours who shared the same environment, regardless of where an individual was born, demonstrating that GMCs are significantly influenced by the surrounding environment and can rapidly change over time. Mice in natural environments contained more diverse GMCs with higher relative abundances of Ruminoccocaceae, Helicobacteraceae and Lachnospiraceae spp. Future studies should examine the fitness consequences associated with the presence/absence of microbes that are characteristic of GMCs of wild populations to gain a better understanding of environment-microbe-host evolutionary and ecological relationships.

Effects of captivity, diet, and relocation on the gut bacterial communities of white‐footed mice

“…The structure of the microbiota in terms of evenness is more uniform in wild‐born mice than captive‐born mice that have more disparate microbial communities. Similar results were found in studies including the place of birth as a factor of variation in gut microbiota for horses and deer mice (Metcalf et al, 2017; Schmidt et al, 2019). Kohl and Dearing (2014) also observed that evenness decreased with time spent in captivity in desert woodrats.…”

“…The external environment of a host (Schmidt, Mykytczuk, & Schulte‐hostedde, 2019), its diet, and genetics (Campbell et al, 2012; Spor, Koren, & Ley, 2011) are all known to modify the gut microbiota. Housing facilities such as zoos where captive breeding programs are held provide intense veterinary care, sanitized enclosures, a standardized diet, and reduced sexual selection.…”

“…Few studies have shown how host‐associated microbiota vary between captivity and relocation into a natural habitat and mainly focused on the impacts of place of birth and the immediate environmental exposure (Chong et al, 2019; Metcalf et al, 2017; Schmidt et al, 2019; Yao et al, 2019). Even less studies looked at the effect of captive diet on the gut microbiome during animal relocation (Martinez‐Mota, Kohl, Orr, & Dearing, 2019).…”

“…Overall, animals born in captivity have lower α‐diversity and more differences in microbial communities compared to animals born in nature reserves or in the wild (Metcalf et al, 2017). Furthermore, deer mice ( Peromyscus maniculatus ) born in captivity and later released had gut microbial communities closer to their wild counterparts compared to animals that stayed in captivity (Schmidt et al, 2019). Since the literature gap of the effects on gut bacteria of captive diet during relocation remains unaddressed, we focused on the impact of captive diet for the gut bacteria during the relocation process in a generalist species with an omnivorous diet.…”

Gut Microbiome Composition and Metabolomic Profiles of Wild and Captive Chinese Monals (Lophophorus Lhuysii)

“…It performs numerous bene cial functions for the host, such as nutrient acquisition, immunomodulation and physiogenesis in response to profound lifestyle changes [7,8]. Numerous factors in uence the unique and variable community of gut microbiota present in each individual, such as host's age [9], diet composition (Guan et al 2017), social interactions [11], gut morphology [9] and health status [12]. Thus, the study of intestinal microbial activity is helpful to understand the health and nutritional status of the host.…”