Diversity and functional landscapes in the microbiota of animals in the wild

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Mining wild animal microbiomes

We have only just begun to examine the multitude of bacteria associated with other organisms. Levin et al. sampled the feces of 184 wild animals, including fish, birds, and mammals, from four different continents to survey the diversity of gut bacteria (see the Perspective by Lind and Pollard). They discovered more than 1000 previously undescribed bacterial species and identified factors that correlate with the composition, diversity, and functional content of the microbiota. Supporting the association of specific bacteria with animal lifestyle, they identified proteases, some previously undescribed, from the gut of griffon vultures that can break down toxins that may be present in their carrion diet.

Science, this issue p. eabb5352; see also p. 238

Structured Abstract

INTRODUCTION

Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These characteristics may be contributed largely by the animals’ microbiota. However, compared with the human microbiota, which has been extensively studied, the microbiota of animals in the wild has received less focus. In this study, we aimed to construct and functionally annotate a comprehensive database of microbiota sampled from wild animals in their natural habitats. Several considerations guided our sample collection and analysis strategy. First, we focused on sampling of animals from the wild, despite the many challenges that such sampling poses, because captivity was shown to alter the microbiome of several animal species. Second, to obtain a broad representation of wild animals, we sampled in four continents and from a diversity of animals with varied traits and feeding patterns. We hand-curated traits for each species, including dietary adaptations, activity hours, and social structures, allowing us to systematically study the relationships between microbiota composition and host phenotype. Finally, we adapted a metagenomic genome assembly pipeline and annotated the assembled genomes taxonomically and functionally, resulting in a broad collection of genomes that represents the microbial landscape of wildlife.

RATIONALE

It is becoming evident that animal microbiomes are a rich source of biological functions that may have biotechnological impact, including antibiotics, industrial enzymes, and immunomodulators. Moreover, animals in the wild exhibit adaptations such as the safe consumption of rotting, pathogen-infected meat and poisonous plants; production of highly potent toxins; bioluminescence; specific immunity to various diseases and microbial pathogens; regenerative capabilities; and, in some species, extreme longevity. Some of these adaptations, such as toxin production and bioluminescence, are conferred, at least in part, by microbial symbionts living in and on the animal. However, despite these examples, a comprehensive view of the association between an animal’s traits and its microbiota is still…



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