Gut microbiomes of mammals and birds from Slovenia: 16S rRNA sequencing data

A large dataset of fecal microbiomes from 715 individual animals representing over 50 mammalian and avian species from Slovenia. 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.

The Mendeley Data repository contains both raw and processed versions of the ZOTU table, ZOTU sequences in FASTA format, taxonomy table and sample metadata. The raw data is located in the "Raw" folder, while the processed data (filtered to remove non-bacterial sequences and rarefied) can be found in the "Filtered and rarefied" folder. All scripts used for data processing, analysis, and figure generation are provided in the “Code” folder.