Enriching captivity conditions with natural elements does not prevent the loss of wild‐like gut microbiota but shapes its compositional variation in two small mammals

Abstract

As continued growth in gut microbiota 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 from captive animals. In this study, we assessed how the gut microbiota of two wild‐caught small mammals, namely Crocidura russula (Eulipotyphla, insectivore) and Apodemus sylvaticus (Rodentia, omnivore), changed when bringing them into captivity. We analyzed fecal samples of 15 A. sylvaticus and 21 C. russula , immediately after bringing them into captivity and 5 weeks later, spread over two housing treatments: a “natural” setup enriched with elements freshly collected from nature and a “laboratory” setup with sterile artificial elements. Through sequencing of the V3–V4 region of the 16S recombinant RNA gene, we found that the initial microbial diversity dropped during captivity in both species, regardless of treatment. Community composition underwent a change of similar magnitude in both species and under both treatments. However, we did observe that the temporal development of the gut microbiome took different trajectories (i.e., changed in different directions) under different treatments, particularly in C. russula , suggesting that C. russula may be more susceptible to environmental change. The results of this experiment do not support the use of microbially enriched environments to retain wild‐like microbial diversities and compositions, yet show that specific housing conditions can significantly affect the drift of microbial communities under captivity.

Captive and urban environments are associated with distinct gut microbiota in deer mice ( Peromyscus maniculatus )

“…Despite experiencing limited handling and a more natural diet, the microbiota of the captive zoo population was much more similar to those of laboratory populations than that of the urban population found on the grounds of the same zoo. This suggests that attempts to emulate the natural environment in captivity may not be sufficient to prevent a shift to a captive microbiota, consistent with another recent study [28]. The smaller differences found between the microbiota of captive populations parallel findings that laboratory mice from different vendors or at different facilities also have distinct microbiota [29].…”

Environmental change drives multi-generational shifts in the gut microbiome that mirror changing animal fitness

“…With our repeat sampling, we observed a reduction in dispersion in the gut microbiota, indicating that while the individual-level alpha diversity of the microbiota does not change, the population-level range of variation is reduced in captive pocket mice. This pattern has also been observed in other studies indicating that reduction in diversity may indeed be characteristic of captivity (35,66,67), though whether it manifests at the individual or population level may vary among species (24,68). Moreover, pocket mice in our ex situ population receive native seed enrichment and live in a facility with skylights that allow for natural photoperiod and enclosures that allow for the retention of many of their natural behaviors, such as burrowing in sandy-soil substrates and living solitarily but with visual and olfactory conspecific cues.…”

Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation

“…For the successful reintroduction processes of protected animal species, such as the Mediterranean monk seal (Monachus monachus), the final aim of any rehabilitation process is to have healthy animals prior to their release in the wild. Both detrimental and beneficial microorganisms associated with these animals are of central importance for the reintroduction to the wild, with housing and care conditions being at the frontline (83). The present study investigated for the first time the skin and fecal microbiota succession of two rescued female M. monachus) pups during their rehabilitation period.…”