DOI: 10.5061/dryad.p5hqbzm00
title: Development of metagenomic methods for health monitoring of endangered species using fecal samples

description: 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 of the individuals examined. Furthermore, our analysis revealed that
 some desmans had atypical compositions of potential pathogens, suggesting
 variations in environmental exposure or host genetic factors. This work
 demonstrates a novel application of fecal metagenomics for species-level
 detection of microorganisms implicated in disease, providing a powerful
 approach to gain essential insights into the health and epidemiology of
 endangered species and to support the development of more effective
 conservation strategies.
description: # 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.exogenous.2.fastq.gz * BC2765.exogenous.1.fastq.gz,
 BC2765.exogenous.2.fastq.gz * BC2856.exogenous.1.fastq.gz,
 BC2856.exogenous.2.fastq.gz * BC2865.exogenous.1.fastq.gz,
 BC2865.exogenous.2.fastq.gz * BC2876.exogenous.1.fastq.gz,
 BC2876.exogenous.2.fastq.gz * BC2934.exogenous.1.fastq.gz,
 BC2934.exogenous.2.fastq.gz * BC2989.exogenous.1.fastq.gz,
 BC2989.exogenous.2.fastq.gz * BC3015.exogenous.1.fastq.gz,
 BC3015.exogenous.2.fastq.gz * BC3267.exogenous.1.fastq.gz,
 BC3267.exogenous.2.fastq.gz * BC3343.exogenous.1.fastq.gz,
 BC3343.exogenous.2.fastq.gz * BC3345.exogenous.1.fastq.gz,
 BC3345.exogenous.2.fastq.gz * BC3876.exogenous.1.fastq.gz,
 BC3876.exogenous.2.fastq.gz * BC3895.exogenous.1.fastq.gz,
 BC3895.exogenous.2.fastq.gz * BC3899.exogenous.1.fastq.gz,
 BC3899.exogenous.2.fastq.gz * BC3903.exogenous.1.fastq.gz,
 BC3903.exogenous.2.fastq.gz * BC3906.exogenous.1.fastq.gz,
 BC3906.exogenous.2.fastq.gz Document detailing the main programs and
 commands used in the pipeline: Pipeline_evolutionary_applications.pdf