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.
Highlights
From more than 100,000 free-ranging African black rhinos in the 1960s, this critically endangered species has declined by more than 90% to approximately 5,000 animals today[1]
Wild rhinos had over a 2,000-fold increase over captive rhinos in reads that mapped to the rhino reference genome
The bacterial population in the gut is involved in the breakdown of fibrous plant material into various metabolites including small chain fatty acids (SCFA) that exert a significant impact on host health
Summary
From more than 100,000 free-ranging African black rhinos in the 1960s, this critically endangered species has declined by more than 90% to approximately 5,000 animals today[1]. McKenzie et al.[4] took a broader taxonomic approach and examined gut microbiome diversity across wild versus captive populations of a variety of mammals They investigated trends across six mammalian orders and found alpha diversity between wild and captive populations consistent across some mammalian hosts, decreased in captive populations in some hosts, and increased in one host – namely, the rhinoceros[4]. It provides for greater functional assignments as the data survey across the genome, not a single ribosomal gene[9] Given these advantages of metagenomics and the lack of consensus on the impact of captivity on gut microbiome coupled with our focus on black rhino health in captivity for conservation options, we applied metagenomic sequencing to wild and captive black rhino fecal material to characterize microbiome diversity as well as test for differences between wild and captive animals from both taxonomic and functional perspectives. We make recommendations based on this collective information for adjusting diet to create a normative gut microbiome, which in turn may promote better black rhino health
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