Signatures of landscape and captivity in the gut microbiota of Southern Hairy-nosed Wombats (Lasiorhinus latifrons)

Raphael Eisenhofer,David Taggart,Kristofer M Helgen

doi:10.1186/s42523-020-00068-y

Raphael Eisenhofer, David Taggart + Show 1 more

Open Access

https://doi.org/10.1186/s42523-020-00068-y

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Abstract

BackgroundHerbivorous mammals co-opt microbes to derive energy and nutrients from diets that are recalcitrant to host enzymes. Recent research has found that captive management—an important conservation tool for many species—can alter the gut microbiota of mammals. Such changes could negatively impact the ability of herbivorous mammals to derive energy from their native diets, and ultimately reduce host fitness. To date, nothing is known of how captivity influences the gut microbiota of the Southern Hairy-nosed Wombat (SHNW), a large herbivorous marsupial that inhabits South Australia. Here, using 16S rRNA gene sequencing, we characterized the faecal microbiota of SHNWs in captivity and from three wild populations, two from degraded habitats and one from an intact native grass habitat.ResultsWe found that captive SHNWs had gut microbiota that were compositionally different and less diverse compared to wild SHNWs. There were major differences in gut microbiota community membership between captive and wild animals, both in statistically significant changes in relative abundance of microbes, and in the presence/absence of microbes. We also observed differences in microbial composition between wild populations, with the largest difference associated with native vs. degraded habitat.ConclusionsThese results suggest that captivity has a major impact on the gut microbiota of SHNWs, and that different wild populations harbour distinct microbial compositions. Such findings warrant further work to determine what impacts these changes have on the fitness of SHNWs, and whether they could be manipulated to improve future management of the species.

Highlights

Herbivorous mammals co-opt microbes to derive energy and nutrients from diets that are recalcitrant to host enzymes
Captivity influences Southern Hairy-nosed Wombat (SHNW) gut microbiota diversity and composition Microbial diversity was higher in wombat scats collected from wild populations compared to those sourced from captivity (Fig. 2a & b)
The most abundant 90% core Amplicon Sequence Variant (ASV) in the wild samples was the most abundant ASV in the entire dataset, accounting for 5.8% of the total sequences in wild samples. This ASV was classified only to the order Bacteroidales, with only 86.7% nucleotide identity to the nearest reference. These results suggest that captivity has a major influence on SHNW gut microbiota diversity and composition, and that the SHNW gut contains bacteria that are highly divergent from current database references

Summary

Introduction

Herbivorous mammals co-opt microbes to derive energy and nutrients from diets that are recalcitrant to host enzymes. Recent research has found that captive management—an important conservation tool for many species—can alter the gut microbiota of mammals Such changes could negatively impact the ability of herbivorous mammals to derive energy from their native diets, and reduce host fitness. Sonnenburg et al [12] demonstrated that a change in diet can shift gut microbiota diversity and composition in laboratory mice (Mus musculus) and that, while these shifts were reversible in a single generation by dietary changes, they could not be restored by dietary intervention alone after multiple generations Such microbial ‘extinctions’ were only reversible by reintroduction of both the missing microbes and diet. Determining which mammals experience effects of captivity on their gut microbiota is an important first step in developing management practices to retain native gut microbial diversity

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