How Host Phylogeny and Diet Shape the Specificity and Specificity Diversity of Animal Gut Microbiomes

ABSTRACT The forces shaping host specificity in the animal gastrointestinal microbiome (AGM) are often studied through separate lenses: community‐level patterns (phylosymbiosis) or lineage‐level histories (cophylogeny). Furthermore, traditional diversity metrics fail to capture compositional heterogeneity from host‐specific distributions. We bridge these gaps using our SSD (Species Specificity and Specificity Diversity) framework, a recent conceptual and computational advance that quantifies host specificity across scales via: (i) Species Specificity (SS), locating species on the specialist‐generalist continuum; (ii) Specificity Diversity (SD), quantifying community compositional heterogeneity; and (iii) statistical tests for identifying unique/enriched species. Applying SSD to 4903 AGM samples from 318 species, we identified unique and enriched microbial species in specific host taxa and diets, demonstrating that host phylogeny and diet jointly shape these patterns. A PTSD (Phylogenetic Timeline–Specificity Diversity) power‐law model reveals the evolution of more complex microbiome structures in modern species. One surprising finding is the high similarity amongst animal AGMs, with only 252 microbial species being exclusively unique at the animal class level—somewhat analogous to the high genomic similarity between humans and primates. Our findings demonstrate a unified quantitative approach to dissecting the eco‐evolutionary forces that shape microbial specificity and specificity heterogeneity, with potential synthesis with established phylosymbiosis and cophylogeny frameworks.