One Health probiotics refer to beneficial bacterial strains that confer positive health effects across animals, humans and the environment. Comparative metagenomic analysis of the fish gut microbiome under healthy and diseased conditions can reveal critical host–microbe interactions and facilitate the discovery of novel, universal probiotic strains with One Health applications. In this study, the gut microbial communities of Pangasianodon hypophthalmus and Labeo catla fingerlings were analysed under control and Aeromonas hydrophila-challenged conditions using 16S rRNA amplicon metagenomic sequencing. The results showed a significant difference in the microbial composition as well as the relative abundance between treatments. Comparative post-challenge microbiome profiling identified Proteobacteria, Firmicutes and Bacteroidetes as the dominant phyla constituting the core microbiome of farmed freshwater fishes. Interestingly, Lactobacillus constituted only 0.08% of the microbiota in control P. hypophthalmus, whereas the abundance of Aeromonas increased by 459-fold (to 4.59%) in challenged fish compared to control. Similarly, the abundance of Bacillus was higher in control L. catla group and Aeromonas sp. was higher in the challenged group.
Several promising indigenous strains were also identified i.e. Lactobacillus helveticus, Kocuria palustris, Rubrivivax gelatinosus, Reyranella massiliensis, Roseburia faecis etc. In addition, Next-generation probiotic taxa such as Akkermansia muciniphila, Faecalibacterium, Bacteroides and Odoribacter were identified for the first time in farmed P. hypophthalmus and L. catla. These bacterial taxa have already been known to exert beneficial effects in human and animal health. The discovery of these NGPs in farmed freshwater fishes highlights their potential as universal probiotics, supporting a sustainable, One Health-driven strategy for disease prevention and health management in aquaculture.
Keywords: Fish gut microbiome, Freshwater fishes, One Health probiotics, Metagenomics and Next Generation Probiotics.