Stability of fecal microbiota during degradation in ex situ cheetahs in the USA

Abstract

Objective Gut health and its relationship to gut microbiota is an important consideration in the care and well-being of managed endangered species, such as the cheetah (Acinonyx jubatus). Non-invasive fecal sampling as a proxy for gut microbiota is preferred and collecting fresh fecal samples is the current gold standard. Unfortunately, even in managed facilities, collecting fresh samples from difficult to observe or dangerous animals is challenging. Therefore, we conducted a study to determine the terminal collection timepoint for fecal microbial studies in the cheetah. Methods We longitudinally sampled eight freshly deposited fecals every 24 h for 5 days and assessed bacterial relative abundance, diversity, and composition changes over time. Results Our data indicated that fecal samples up to 24 h post defecation provided accurate representations of the fresh fecal microbiome. After 24 h, major changes in community composition began to occur. By 72 h, individual cheetah fecal microbiota signatures were lost. Conclusion Our findings suggest that cheetah fecal samples should be collected within 24 h of defecation in humid environments, especially if precipitation occurs, in order to provide a more biologically accurate representation of the gut microbiome, and we provide visual characteristics that can aid researchers in approximating time since defecation. Significance statement Data from this study provides guidelines for researchers investigating cheetah and other large felids and carnivores where the ability to collect fresh fecal deposits is limited.