Microbiomes in Animal Ecology: Advances, Assumptions, and Opportunities

The study of animal microbiomes has revolutionized our understanding of host physiology, behavior, and ecology. However, many studies focus on correlations rather than causal functional interaction, and critical caps persist in linking microbial dynamics to ecological and fitness-relevant outcomes. Advances in multi-omics approaches, combined with stable isotope microbiomics, offer promising tools for linking microbial community dynamics to host function in ecologically relevant conditions. Here, we highlight the importance of longitudinal studies, controlled physiological comparisons, and integrative methodological approaches for microbe-host interactions beyond laboratory models. We emphasize the integration of multi-omics approaches and stable isotope probing to track microbial metabolites and their effects on hosts. Examples from African herbivores, geladas, and amphibians illustrate how longitudinal sampling and isotopic labeling can reveal microbiome plasticity in response to environmental variability. Furthermore, experimental systems such as larval amphibians, fish models, and dietary specialists like koalas demonstrate the potential of combining microbiome manipulations with multi-omics to disentangle host-microbe interactions in ecologically relevant contexts. We argue that advancing this field requires moving beyond disease-focused study of model organisms to explore microbiome contributions to life-history traits, nutrient provisioning, and resilience in wild populations. Coupling stable isotope probing with multi-omics in field experiments that compare dichotomous physiological and/or ecological states can be a powerful approach for providing insight into microbiome functional effects on hosts in fitness-relevant contexts.