Abstract
Although water recirculates through fish tanks, plant beds and filters in an aquaponic unit, each compartment supports a microbial community shaped by its local conditions. This distinction is especially important for major carps, including rohu (Labeo rohita), catla (Catla catla) and mrigal (Cirrhinus mrigala), because these major South Asian food fishes occupy contrasting feeding niches and provide a useful comparison of shared environmental exposure and host-associated selection. This focused narrative review examines major-carp gut microbiota, aquaponic water and biofilter communities, gut-water connectivity, and the strengths and limitations of 16S rRNA amplicon sequencing and shotgun metagenomics. Literature screening started with the reference collection assembled for the initial research synopsis. Titles, abstracts and available full texts were reviewed, targeted PubMed searches were used to check coverage, and bibliographic details were cross-checked against publisher, DOI and indexing records. Literature available up to 10 September 2026 was considered. Studies of aquaponic systems consistently show that water, biofilters, roots, biofilms and fish-associated habitats support distinct microbial assemblages despite continuous recirculation. Major-carp studies likewise report variation among host species, gut regions and culture conditions. Overlap between gut and environmental taxa should therefore be treated as evidence of ecological connectivity rather than direct proof of colonization or transmission. Common limitations include inconsistent sampling designs, insufficient tank replication, reliance on relative abundance, limited temporal sampling, low-biomass contamination in water samples and weak functional validation. Future studies would benefit from replicated carp culture, synchronized sampling of gut and aquaponic compartments, water-quality measurements, 16S profiling for community structure and selected shotgun metagenomics for functional resolution. Nitrogen cycling, carbohydrate metabolism, antimicrobial-resistance determinants, mobile genetic elements and source-selection relationships deserve particular attention. Future work should move beyond cataloguing taxa and determine how host identity, aquaponic habitat and microbial function interact over time in a controlled production system.