Development of Metagenomic Methods for Health Monitoring of Endangered Species Using Fecal Samples.

ABSTRACT: 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 I

SUBMITTER: Sapino R 

PROVIDER: S-EPMC12855166 | biostudies-literature | 2026 Feb

REPOSITORIES: biostudies-literature