Microbiome-based tracking of diet shifts in ectotherms: a new approach to monitor effects of global changes on food webs?

Background Global warming and other human-driven impacts are reshaping food webs, compromising both food quality and availability. Ectotherms are particularly challenged under these conditions because they simultaneously face elevated energetic demands and unstable food supply. Their gut microbiomes respond strongly to diet and may either enhance host adaptive potential or undergo dysbiosis, contributing to adaptive failure. Understanding how diet affects ectotherm microbiomes is therefore fundamental for predicting the consequences of environmentally driven dietary change. However, studies on ectotherm diet-microbiome interactions remain relatively scarce, taxonomically biased, and methodologically heterogeneous. Results Here, we present a systematic literature review and meta-analysis quantifying diet-driven changes in gut microbiome diversity in ectothermic vertebrates while accounting for taxonomic/phylogenetic, ecological, and methodological sources of variation. Methodological heterogeneity hampered robust comparisons of microbiome alpha and phylogenetic diversity across gradients of diet nutritional composition. Across studies, however, we identified several bacterial genera and families that increased in relative abundance with higher insect consumption. These taxa are known to degrade chitin and other complex insect-derived compounds, generating metabolites that act as signaling molecules along hypothalamic–pituitary and related neuroendocrine axes to modulate host growth, development, reproduction, and senescence. Conclusions Our findings highlight the potential of diet-sensitive microbial groups as microbiome-based indicators and as agents that may promote ectotherm resilience to environmental change through physiological regulation of host metabolism. We outline priorities for improving data collection, reducing methodological heterogeneity, and ensuring open availability of sequence data.