Post-defecation exposure alters gut microbiota of forest musk deer with implications for conservation metagenomics

In the context of the ongoing global decline in biodiversity, the conservation of endangered species represents a critical component of global biodiversity preservation, ecosystem restoration, and sustainable development (Pereira et al. 2024 ; Maxwell et al. 2020 ). Fecal sampling enables the collection of biological information from endangered species when invasive sampling of tissues such as muscle, blood, or stomach contents is often unfeasible due to small population sizes and elusive behavior, providing a non-invasive approach to investigate host genetics, health status, and host and gut microbiota interactions (Grieneisen et al. 2021 ; Turjeman et al. 2023 ). Fecal sampling not only serves as an effective non-invasive method but also represents a crucial tool in conservation biology, enabling the collection of biological information from endangered species without direct contact or disruption to their health and behavior, thereby providing a low-disturbance alternative particularly suited for rare, dispersed, or highly vigilant taxa (Zhou et al. 2020a , b ). Additionally, fecal samples contain abundant biological information, including host DNA, gut microbial communities, hormone levels, parasite species, and metabolic products, which make them uniquely valuable for research in genetics, nutrition, behavioral ecology, and pathology (Hu et al. 2024 ). The unique value of fecal samples in the conservation of endangered species has been validated in numerous studies (Huang et al. 2023 ). By extracting host DNA genetic information from feces, the genetic diversity, population dynamics, and potential recovery mechanisms of endangered species can be tracked (Wang et al. 2024 ). DNA metabarcoding of fecal samples can quantify the dietary characteristics, ecological niche differentiation, and predator-prey food web structure of coexisting endangered species (Shao et al. 2021 ). Analyzing residual metabolic products and gut microbiota composition in feces can not only assess individual health status, adaptive response mechanisms (Wang et al. 2021 ), and the microbial response mechanisms to seasonal dietary changes at the species and functional level (Li et al. 2023a , b , c ), but also serve as a key indicator for evaluating the success of wild reintroduction programs for captive endangered species (Huang et al. 2024 ). Hormonal analysis in feces can provide insights into the physiological state, acute and chronic stress levels, and reproductive potential of individuals (Yan et al. 2024 ; Nie et al. 2015 ). It is evident that the importance of fecal samples in the conservation of endangered species cannot be overlooked. Therefore, under the current urgent circumstances of endangered species research and conservation, fully exploring and utilizing the research potential of fecal samples will contribute significantly to global biodiversity conservation efforts.