Studies on spatial and interannual variation in fish community structure, diet composition, and gut microbiome remain limited in Afrotropical river systems. As a result, little is known about the diet composition and gut microbiomes of Labeobarbus altianalis and Labeo victorianus, two dominant and ecologically important species in the Mara River. This study addresses this gap by examining the relationships among fish community structure, diet composition, and gut microbiome of the two dominant fish species along a longitudinal gradient in the Mara River Basin in East Africa.
We compared historical (2013–2016) and recent (2021–2022) datasets and found no significant differences in species diversity and fish biomass between the two sampling periods. Stable isotope values (δ¹³C and δ¹⁵N) revealed clear spatial and species-specific patterns across sites. Where both species co-occurred (M4, M5, M6, M7, and M9), Labeobarbus altianalis consistently occupied a slightly higher trophic position than Labeo victorianus, as indicated by enriched δ¹⁵N values. Gut content analyses showed that both species were primarily supported by amorphous detritus and non-algal biofilm. However, the relative contribution of these resources varied markedly among sites, particularly at M4, M7, and M9. PERMANOVA indicated no significant main effect of species on overall gut composition (p = 0.468), suggesting broadly similar diets when averaged across the river system. A significant species-site interaction (p = 0.015) further showed that the two species did not respond uniformly to these spatial differences; instead, each species altered its diet in distinct ways across sites. The two fish species were dominated by Clostridia, Gammaproteobacteria, Bacteroidia, Bacilli, Fusobacteria, and Planctomycetes. Overall, Labeo victorianus exhibited higher microbiome diversity. Consequently, microbiome diversity declined along the longitudinal gradient across the three sites (M4, M7, M9).
Collectively, these findings demonstrate that while fish community structure in the Mara River has remained relatively stable over time, underlying trophic pathways, feeding strategies, and host-associated microbiomes vary strongly across space. This study highlights the importance of integrating multiple ecological compartments to better understand how tropical river ecosystems function and respond to environmental gradients, and provides a valuable baseline for future assessments of ecological change in Afrotropical rivers.