From Scat to Sequencing: Non-Invasive Methods for Wildlife Microbiome Research and Conservation

Abstract

The gut microbiome, a complex community of microorganisms in the gastrointestinal tract, plays a vital role in host health, nutrition and adaptability. Advances in next-generation sequencing and metagenomics have deepened our understanding of how diet and environmental factors shape microbial diversity. In wild animals, microbiome analysis enables rapid and comprehensive profiling of microbial communities, identifying diverse taxa and exploring their phylogeny and functional potential. Direct genetic examination of environmental samples reveals the collective genome of the microbiota, offering insights into disease susceptibility and supporting wildlife conservation. However, invasive sampling methods pose risks to wild animals, highlighting the need for reliable non-invasive sampling approaches. Scat analysis provides an effective alternative, allowing detection of microbial DNA, metabolites and biomarkers to assess microbiome composition and its implications for survival. Non-invasive techniques are cost-effective, time-efficient, suitable for large cohorts and reduce harms associated with traditional sampling. This review discusses current non-invasive sampling methods and advanced molecular tools for microbial profiling, emphasizing the integration of microbiome research into conservation strategies to strengthen biodiversity preservation amid ongoing environmental challenges.