Functional traits shape gut microbial assembly beyond phylogeny in estuarine fish

Host-specific patterns of symbiotic microbiomes are ubiquitous in nature, yet the intricate interplay among host phylogeny, functional traits, and gut microbiota remains insufficiently explored and debated. In this study, the gut microbiota of 61 fish species inhabiting the sympatric Pearl River Estuary, China, was examined by integrating host phylogeny and functional traits to elucidate the mechanisms underlying microbiota assembly. While substantial interspecies differences in gut microbiota composition were evident, the influence of phylosymbiosis was minimal. Instead, functional traits emerged as pivotal mediators of gut microbiota differentiation, emphasizing their roles in adaptive and ecological functions, such as habitat preferences, feeding strategies, and digestive efficiencies. Clustering and machine learning analyses identified three distinct enterotypes within the fish gut microbiota strongly associated with feeding habits and migratory behaviors. Gut microbiota diverged among fishes differing in estuarine use, feeding strategies, and resilience traits. Functional profiling of the gut microbiota unveiled enterotype-specific metabolic adaptations, encompassing pathways related to nutrient utilization and stress resistance. Notably, redundancy analysis indicated that functional traits—such as eye size, oral gape shape, and gut length—played significant roles in influencing enterotype clustering. Our findings introduce the concept of “functsymbiosis”, defined as the functional-trait-driven congruence between hosts and their symbiotic microbiota, indicating that host functional traits, rather than phylogenetic lineage, predominantly govern gut microbiota assembly. This study highlights the complex interactions between host traits and gut microbiota in fish, providing novel insights into the adaptive mechanisms underpinning host-microbiota dynamics and the ecological significance of gut microbiota in shaping host fitness and niche differentiation.