Development of metagenomic methods for health monitoring of endangered species using fecal samples

Metagenomic analysis of fecal samples is emerging as a powerful tool for monitoring endangered species, particularly in assessing the burden of pathogens and parasites that can threaten population viability. However, accurate identification in non-model species remains challenging due to the frequent absence of host-specific pathogen reference genomes. In this study, we developed a robust computational framework for detecting potentially pathogenic bacteria from metagenomic sequences by mapping them to available reference genomes in databases. Several key parameters affecting the analysis, including mapping algorithm, database configuration, and identification parameters, were analyzed to optimize detection sensitivity and specificity. Applying this approach to fresh fecal samples of the Iberian desman (Galemys pyrenaicus), a critically endangered semi-aquatic mammal, we identified 26 potentially pathogenic bacterial species, with prevalences ranging from isolated cases to nearly half o..., , , # Development of metagenomic methods for health monitoring of endangered species using fecal samples

## Description of the data

The data consists of two parts:

Sequence reads in FASTQ format obtained from fresh fecal samples of 23 Iberian desmans. The endogenous reads, i.e., reads belonging to the Iberian desman, have been filtered out, so this set contains the exogenous DNA fraction of the fecal samples. For each individual, indicated by the first six letters of the filename, reads 1 and 2 are provided. The sequence reads filenames:

* BC2042.exogenous.1.fastq.gz, BC2042.exogenous.2.fastq.gz
* BC2045.exogenous.1.fastq.gz, BC2045.exogenous.2.fastq.gz
* BC2280.exogenous.1.fastq.gz, BC2280.exogenous.2.fastq.gz
* BC2360.exogenous.1.fastq.gz, BC2360.exogenous.2.fastq.gz
* BC2378.exogenous.1.fastq.gz, BC2378.exogenous.2.fastq.gz
* BC2381.exogenous.1.fastq.gz, BC2381.exogenous.2.fastq.gz
* BC2408.exogenous.1.fastq.gz, BC2408.exogenous.2.fastq.gz
* BC2416.exogenous.1.fastq.gz, BC2416.exo...,