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The microbiome is critical for host survival and fitness, but gaps remain in our understanding of how this symbiotic community is structured. Despite evidence that related hosts often harbor similar bacterial communities, it is unclear whether this pattern is due to genetic similarities between hosts or to common ecological selection pressures. Here, using herbivorous rodents in the genusNeotoma, we quantify how geography, diet, and host genetics, alongside neutral processes, influence microbiome structure and stability under natural and captive conditions. Using bacterial and plant metabarcoding, we first characterized dietary and microbiome compositions for animals from 25 populations, representing seven species from 19 sites across the southwestern United States. We then brought wild animals into captivity, reducing the influence of environmental variation. In nature, geography, diet, and phylogeny collectively explained ∼50% of observed microbiome variation. Diet and microbiome diversity were correlated, with different toxin-enriched diets selecting for distinct microbial symbionts. Although diet and geography influenced natural microbiome structure, the effects of host phylogeny were stronger for both wild and captive animals. In captivity, gut microbiomes were altered; however, responses were species specific, indicating again that host genetic background is the most significant predictor of microbiome composition and stability. In captivity, diet effects declined and the effects of host genetic similarity increased. By bridging a critical divide between studies in wild and captive animals, this work underscores the extent to which genetics shape microbiome structure and stability in closely related hosts.
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Effects of Captivity and Captive-Breeding on the Cutaneous Microbiome of Lungless Salamanders
Abstract Captive breeding has become a critical tool for the restoration of amphibian populations decimated by diseases. However, much is unknown about effects of long-term captivity on amphibian health and particularly immune system function. Therefore, we have begun a project to understand the effects of captivity and captive breeding on the cutaneous microbiome of lungless salamanders. The community of microbes living in and on the skin of lungless salamanders (Plethodontidae) is an important predictor of the organisms’ ability to ward off diseases like chytridiomycosis. We compare the microbiome of wild and long-term (8 years) captive or captive-bred Ocoee and Blue Ridge two-lined salamanders (Desmognathus ocoee and Eurycea wilderae, respectively) all from the Charles H. Wharton Conservation Center in Union County, GA. Microbiome communities were estimated by amplifying the V4 region of the 16S rDNA gene and then comparing with sequences from the Greengenes database. We present our study design and preliminary results.
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- Award ID(s):
- 2027813
- PAR ID:
- 10348889
- Date Published:
- Journal Name:
- Georgia journal of science
- Volume:
- 80
- Issue:
- 1
- ISSN:
- 0147-9369
- Page Range / eLocation ID:
- 51
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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