Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health

Abstract

A number of recent studies have shown the importance of the mammalian gut microbiome in host health. In the context of endangered species, a few studies have examined the relationship between the gut microbiome in wild versus captive populations due to digestive and other health issues. Unfortunately, the results seem to vary across taxa in terms of captive animals having higher, lower, or equivalent microbiome diversity relative to their wild counterparts. Here, we focus on the black rhinoceros as captive animals suffer from a number of potentially dietary related health effects. We compared gut microbiomes of wild and captive black rhinos to test for differences in taxonomic diversity (alpha and beta) and in functional diversity of the microbiome. We incorporated a more powerful metagenomic shotgun sequencing approach rather than a targeted amplification of the 16S gene for taxonomic assignment of the microbiome. Our results showed no significant differences in the alpha diversity levels between wild and captive black rhinos, but significant differences in beta diversity. We found that bacterial taxa traditionally associated with ruminant guts of domesticated animals had higher relative abundances in captive rhinos. Our metagenomic sequencing results suggest that unknown gut microbes of wild rhinos are being replaced by those found in conventional human-domesticated livestock. Wild rhinos have significantly different functional bacterial communities compared to their captive counterparts. Functional profiling results showed greater abundance of glycolysis and amino acid synthesis pathways in captive rhino microbiomes, representing an animal receiving sub-optimal nutrition with a readily available source of glucose but possibly an imbalance of necessary macro and micronutrients. Given the differences observed between wild and captive rhino gut microbiomes, we make a number of recommendations for potentially modifying captive gut microbiome to better reflect their wild counterparts and thereby hopefully improve overall rhino health in captivity.

Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun

“…There was no significant difference in the alpha diversity measures between wild, captive, and domestic populations. Numerous, previous studies have also observed no difference in the alpha diversity between wild and captive populations of rhinoceros, musk deer, bovid, giraffes, aardvarks, and anteaters (Li et al, 2017;McKenzie et al, 2017;Gibson et al, 2019). In contrast, beta diversity significantly varied between populations, suggesting that distinct group of microbes inhabits the gut of wild, captive, and domestic populations.…”

Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity

“…However, such large-scale metagenome assembly-based approaches have not been as extensively applied to most non-human vertebrates. The low amount of metagenome reads classified in some recent studies of the rhinoceros, chicken, cod, and cow gut/rumen microbiome suggests that databases lack much of the genomic diversity in less-studied vertebrates [8][9][10][11] . Indeed, the limited number of studies incorporating metagenome assembly hint at the extensive amounts of as-of-yet novel microbial diversity across the >66,000 vertebrate species on our planet.…”

Wild environment and diet structure shape gut microbiome and functional composition in semi-feral Tibetan goats

“…In addition, a previous study compared the gut microbial communities of wild and captive black rhinos, and found that there was no signi cant difference in alpha diversity levels between wild and captive black rhinos, but signi cant differences in beta diversity, this study also found that bacterial groups traditionally associated with the ruminant gut of domestic animals have a higher relative abundance in captive rhinos. Functional pro ling results showed greater abundance of glycolysis and amino acid synthesis pathways in captive rhino microbiomes, representing an animal receiving sub-optimal nutrition with a readily available source of glucose but possibly an imbalance of necessary macro and micronutrients [22]. The phenotypic differences between the feeding systems examined here were primarily affected by the GIT lumen microbial structure.…”