Gut microbiomes of wild and domesticated mammals and birds in Slovenia, Europe: 16S rRNA sequencing data

TL;DR

This study provides a large dataset of gut microbiomes from wild and domesticated mammals and birds in Slovenia to better understand microbial spread and its health implications.

Contribution

The paper introduces a taxonomically diverse fecal microbiome dataset for microbial source tracking and broader microbiome research.

Findings

The dataset includes 715 samples from over 50 species, capturing microbial diversity across wild and domestic animals.

16S rRNA sequencing of the V3–V4 region was used to generate ZOTUs for bioinformatic analysis.

The dataset supports microbial source tracking and comparative studies across host species and ecological contexts.

Abstract

From a One Health perspective, the gut microbiota of animals acts as a major driver of microbial exchange between animals and the environment. Animals continuously release gut microbes into their surroundings, shaping environmental and human microbial communities and potentially dispersing pathogens. Characterizing gut microbiota across diverse animal hosts is therefore critical for understanding the patterns of microbial spread through ecosystems and their impact on animal, human and environmental health.

Here, we introduce a large, taxonomically diverse dataset of fecal microbiomes from 715 individual animals representing over 50 mammalian and avian species. We collected samples from both wild and domestic animals with an emphasis on capturing microbial diversity across a wide range of taxa and ecological contexts. The samples were subjected to 16S rRNA gene sequencing, targeting the V3–V4 hypervariable region. Bioinformatic analysis was performed using Usearch to generate zero-radius operational taxonomic units (ZOTUs).

This dataset was generated primarily for the development of microbial source tracking (MST) assays used for identifying the sources of fecal pollution in contaminated water. However, it provides a valuable resource for broader microbiome research. It enables comparative studies across host species, trophic guilds, and environmental contexts such as domestication.

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