Diet diversity and environment determine the intestinal microbiome and bacterial pathogen load of fire salamanders

Yu Wang,Luc Lens,Miguel Vences,An Martel,Dries Bonte,Hannah K Smith,Lionel Hertzog,Frank Pasmans,Molly C Bletz,Evy Goossens,Kris Verheyen

doi:10.1038/s41598-021-98995-6

Yu Wang, Luc Lens + Show 9 more

Open Access

https://doi.org/10.1038/s41598-021-98995-6

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Abstract

Diverse communities of symbiotic microbes inhabit the digestive systems of vertebrates and play a crucial role in animal health, and host diet plays a major role in shaping the composition and diversity of these communities. Here, we characterized diet and gut microbiome of fire salamander populations from three Belgian forests. We carried out DNA metabarcoding on fecal samples, targeting eukaryotic 18S rRNA of potential dietary prey items, and bacterial 16S rRNA of the concomitant gut microbiome. Our results demonstrated an abundance of soft-bodied prey in the diet of fire salamanders, and a significant difference in the diet composition between males and females. This sex-dependent effect on diet was also reflected in the gut microbiome diversity, which is higher in males than female animals. Proximity to human activities was associated with increased intestinal pathogen loads. Collectively, the data supports a relationship between diet, environment and intestinal microbiome in fire salamanders, with potential health implications.

Highlights

Diverse communities of symbiotic microbes inhabit the digestive systems of vertebrates and play a crucial role in animal health, and host diet plays a major role in shaping the composition and diversity of these communities
Fire salamander ingested prey biomass was determined by the relative number of sub-OTU reads for each prey category
More than 70% of the sub-OTU reads were identified as gastropods, followed by millipedes at 10.8%, centipedes at 5.8%, and soil mites at 4.4%

Summary

Introduction

Diverse communities of symbiotic microbes inhabit the digestive systems of vertebrates and play a crucial role in animal health, and host diet plays a major role in shaping the composition and diversity of these communities. For fish10,11, birds[12,13], myrmecophagous mammals14, mice[15] and a mphibians[16,17], host diet has been found to be one of the primary determinants in shaping microbial communities Other factors, such as c limate18, habitat[19,20], and the host immune s ystem[21] drive internal microbiome diversity of certain animal clades to some extent. Frogs and salamanders influence leaf litter decomposition as well as nutrient cycling, by preying upon omnivore and detritivore invertebrate populations[38,39,40,41] This applies to fire salamanders (Salamandra salamandra), a species occurring throughout most of temperate deciduous forests in central and southern E urope[42]. The aim is to provide detailed information on the diversity, relative abundance and prevalence of prey taxa found within fecal samples of fire salamanders, as well as the impact of diet, sex and geographical location on the gut microbiome

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