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Wild Animal Gut Microbiomes Reveal New Species, Ties to Host Traits

NEW YORK – The microbial communities found in the guts of wild animals are home to diverse species not described in the past, including organisms that may impact human health and disease, according to new research from a team in Israel and the US.

"The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and lifespan," co-senior and corresponding author Eran Segal, a researcher at the Weizmann Institute of Science, and colleagues wrote in Science on Thursday.

The researchers performed metagenomic sequencing on more than 400 fecal samples from captive and wild animals spanning 184 species from five parts of the world, including birds and bony fish, snakes, and mammals in Uganda, Madagascar, Australia, Israel, Hungary, and the Falkland Islands. From there, they put together de novo metagenome assemblies that encompassed thousands of genomes and more than 1,200 bacterial species — many not found in the past.

"We found that more than 75 [percent] of the genomes in our database represent previously undescribed bacterial species," the authors reported, calling wild animal gut microbial communities "a largely untapped resource for the discovery of therapeutics and biotechnology applications."

"Beyond its biotechnological potential," they explained, "studying animal microbiomes improves our understanding of host-microbe ecology and bidirectional interactions."

The team reasoned that gut microbes may contribute to important biological functions — including abilities that some wild animals have to withstand pathogens or foodborne poisons that can fell humans.

To explore gut microbial contributors more extensively, the investigators used shotgun metagenomic sequencing and a set de novo metagenome assembly pipeline to profile hundreds of fecal samples collected in a standardized way from 121 captive and 285 wild animals across 184 species — from the Asiatic wild ass, Burchell's zebra, King penguin, and common wombat to Madagascar's cat-like carnivore, the fossa.

"The animals that we profiled cover diverse animal classes, dietary patterns, activity hours, social structures, and lifespan," the authors reported, "and we uncover numerous associations between these traits and their microbiota composition and functional gene content."

The team mapped more than 7 percent of reads from each sample to reference genome sequences available in the GenBank database, while the metagenomic assemblies yielded some 1,209 species-level genomes and made it possible to map far more reads per sample.

With their gut microbial genome set, the investigators got a look at the species diversity differences across animal groups, along with the phylogenetic relationships represented by the gut bugs they found. The results suggested that gut microbial communities are typically more similar between closely related animal species, providing an opportunity to start teasing out ties between host traits and gut microbiome features.

Broadly speaking, they saw enhanced gut bacterial diversity in animals with herbivore diets compared to their carnivore or omnivore counterparts, for example, though some gut microbes appeared to coincide with specific host taxa. Other gut microbes appeared to vary in relation to their host animal's size or lifespan, particularly within mammals.

The sequence data also made it possible to dig into microbial gene collections and pathways present in the guts of wild animals, including metabolite biosynthesis pathways that may offer antibiotic or antitoxin activity against foodborne pathogens or toxic compounds they encounter.

"Mapping the microbiota of animals in the wild could shed light on the natural reservoir of microbial pathogens," the authors added, noting that the collection "could enable the surveillance and tracking of the movement of specific pathogens from their animal hosts into the human population, and enable early warning of potential outbreaks."