Spatial variation shapes gut microbiome composition and functional potential in an Afrotropical fish

Abstract Host-associated microbiomes are shaped by environmental heterogeneity across spatial gradients. However, the extent to which site-level variation structures gut microbial communities in Afrotropical fishes remains poorly resolved. In this study, we employed high-throughput 16S rRNA gene sequencing to characterize the gut microbiome of the African forktail catfish ( Chrysichthys nigrodigitatus ) encompassing two contrasting habitat types, with the aim of assessing spatial patterns in microbial composition and predicted functional potential. Across all sites, gut microbial communities were dominated by Firmicutes, Proteobacteria, Bacteroidota, and Fusobacteriota, with a conserved core microbiome shared among populations. Alpha diversity metrics (Observed richness, Shannon, Simpson, and Chao1 indices) did not differ significantly among sites, indicating comparable levels of microbial richness and evenness. In contrast, beta diversity analysis based on Bray–Curtis dissimilarity revealed pronounced site-specific structuring and clear differentiation between habitat types. Differential abundance and indicator taxa analyses identified distinct bacterial assemblages associated with specific habitats, reflecting localized environmental influences. Functional predictions indicated enrichment of pathways related to xenobiotic degradation, oxidative stress response, and aromatic compound metabolism in lagoon habitat. The concordance between taxonomic composition and predicted functional profiles underscores the role of site variation in shaping gut microbiome structure. Collectively, these findings demonstrate that spatial variation is a key determinant of gut microbiome composition and predicted functional capacity in this widely distributed Afrotropical fish species, providing new insights into host-microbiome-environment interactions in tropical aquatic systems.