Bacterial Taxonomic Profiling of Freshwater Fish Across Hydrographic Basins of Kazakhstan

Bacterial taxonomic profiles associated with freshwater fish in Kazakhstan remain poorly characterized. We characterized bacterial sequence profiles from 193 apparently healthy wild freshwater fish representing six families and six major hydrographic basins. Gill, kidney, spleen, and liver tissues were combined into 20 pooled samples, and RNA-derived double-stranded cDNA libraries were analyzed for bacterial taxonomic assignments. Pseudomonadota (51.9%) and Actinomycetota (29.5%) showed the highest mean relative sequence abundances, followed by Bacillota (8.3%), Bacteroidota (4.9%), and Fusobacteriota (2.7%). Alpha diversity did not differ significantly among basins. In separate PERMANOVA models, basin accounted for 33.6% of variation in genus-level profiles but was not significant (R2 = 0.336, p = 0.0555), while fish family accounted for 25.3% (R2 = 0.253, p = 0.5472). In the joint model, basin showed a significant marginal effect after accounting for fish family (R2 = 0.346, p = 0.0338), whereas fish family remained nonsignificant. Seventeen genera met the operational core criteria. Selected potentially health-relevant sequence assignments included Escherichia coli, Salmonella enterica, Aeromonas spp., and Stenotrophomonas maltophilia. These sequence-based detections do not establish organism viability or active infection. Overall, these findings provide baseline information on fish-associated bacterial taxonomic profiles across Kazakhstan’s major freshwater systems.