Comparative gut microbiome analysis of Rohu fish from Halda River and Kaptai Lake using 16S rRNA sequencing

Freshwater ecosystems are vital for biodiversity and livelihoods in Bangladesh, where interest in fish gut microbiota is growing to aid aquaculture sustainability through microbial interventions. Therefore, this research investigated the bacteriomes of the gut of Rohu from the Halda River and Kaptai Lake, using Oxford Nanopore long-read 16S rRNA sequencing. The evaluation of diversity demonstrated notable variations in both alpha and beta diversity indices (p < 0.05). The fish in the Halda River had a varied bacteriome, mostly composed of Pirellulaceae_uncultured (9.26%), with environmentally tolerant taxa such as Exiguobacterium (5.48%). In contrast, the Kaptai Lake fish have a bacteriome that is abundant in probiotics, including Lactiplantibacillus (48.84%) and Pediococcus (8.82%). Water samples exhibited unique microbiological signatures: Halda River water was mostly characterized by Exiguobacterium (41.93%), while Kaptai Lake water was primarily composed of Acinetobacter (71.24%). Furthermore, functional analysis indicated that fish from the Halda River comprised metabolically diverse communities involved in nitrogen cycling, whereas the Kaptai Lake fish demonstrated a strong capacity for ammonia oxidation and pollutant breakdown. The research offers significant insights into the relationship between the host, microbiome, and environment, with implications for enhancing fish health and promoting sustainable aquaculture practices.