Abstract
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 (pā<ā0.05). 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.
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Data availability
Sequence data that support the findings of this study have been deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) with the primary accession code [PRJNA1270017](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1270017) .
References
DOF. Yearbook of Fisheries Statistics of Bangladesh, 2022ā23. 40, 138 (Fisheries Resource Survey System, Ministry of Fisheries and Livestock, 2023).
Ferdous, M., Karim, M., Hossain, M., Rahman, M. & Iqbal, M. Fin fish assemblage and biodiversity status of carps on Halda River. Bangladesh. Ann. Vet. Anim. Sci. 2, 151ā161 (2015).
Arshad-Ul-Alam, M. & Azadi, M. Fisheries exploitation of the Halda River, Bangladesh. J. Fish. 4, 361ā370 (2016).
Nath, R. K. et al. Assessment of heavy metal concentration in the water of major carp breeding River Halda Bangladesh. Sustain. Chem. One World. 3, 100018 (2024). https://doi.org/10.1016/j.scowo.2024.100018.
Patra, R. & Azadi, M. Hydrological conditions influencing the spawning of major carps in the Halda River, Chittagong, Bangladesh. Bangladesh J. Zool. 13, 63ā72 (1985).
Shampa, M. T. A., Shimu, N. J., Chowdhury, K. M. A., Islam, M. M. & Ahmed, M. K. A comprehensive review on sustainable coastal zone management in Bangladesh: present status and the way forward. Heliyon 9, 18190. https://doi.org/10.1016/j.heliyon.2023.e18190 (2023).
Boyd, C. E. et al. Achieving sustainable aquaculture: historical and current perspectives and future needs and challenges. J. World Aquac. Soc. 51, 578ā633 (2020).
Lima, R. et al. An overview on hydro-biology and management of Kaptai Lake fisheries. Bangladesh. Int. J. Aquac. Fish. Sci. 9, 29ā39 (2023).
Karmakar, S., Haque, S. S., Hossain, M. & Shafiq, M. Water quality of Kaptai reservoir in Chittagong Hill tracts of Bangladesh. J. For. Res. 22, 87ā92 (2011).
Ahmed, K., Rahman, S. & Ahammed, S. Managing fisheries resources in Kaptai Reservoir, Bangladesh. Outlook Agric. 35, 281ā289 (2006).
Naher, S. & Galib, S. Fishes of Kaptai Lake: management and conservation perspectives. J. Life Earth Sci. 15, 53ā58 (2020).
Arafeen, M. et al. Present status of fish diversity of the Kaptai Lake. J. Bangladesh Agric. Univ. 22, 506ā516 (2024).
Bakar, M. & Bhuyan, M. Assessment of water quality in Halda River (the major carp breeding ground) of Bangladesh. J. Pollut. 3, 429ā444 (2017).
Talwar, C., Nagar, S., Lal, R. & Negi, R. K. Fish gut microbiome: Current approaches and future perspectives. Indian J. Microbiol. 58, 397ā414 (2018).
Kanika, N. H. et al. Fish gut microbiome and its application in aquaculture and biological conservation. Front. Microbiol. 15, 1521048. https://doi.org/10.3389/fmicb.2024.1521048 (2025).
See, M. S. et al. Aquatic microbiomes under stress: The role of gut microbiota in detoxification and adaptation to environmental exposures. J. Hazard. Mater. Adv. 17, 100612. https://doi.org/10.1016/j.hazadv.2025.100612 (2025).
Stephens, W. Z. et al. The composition of the zebrafish intestinal microbial community varies across development. ISME J. 10, 644ā654 (2016).
Li, X. et al. Gut microbiota contributes to the growth of fast-growing transgenic common carp (Cyprinus carpio L.). PLoS ONE 8, 64577. https://doi.org/10.1371/journal.pone.0064577 (2013).
Giatsis, C. et al. Probiotic legacy effects on gut microbial assembly in tilapia larvae. Sci. Rep. 6, 33965. https://doi.org/10.1038/srep33965 (2016).
Nayak, S. K. Role of gastrointestinal microbiota in fish. Aquac. Res. 41, 1553ā1573 (2010).
Jyoti, & Dey, P. Mechanisms and implications of the gut microbial modulation of intestinal metabolic processes. Npj Metab. Health Dis. 3, 24 (2025).
Pham, V. T., Dold, S., Rehman, A., Bird, J. K. & Steinert, R. E. Vitamins, the gut microbiome and gastrointestinal health in humans. Nutr. Res. 95, 35ā53 (2021).
Llewellyn, M. S., Boutin, S., Hoseinifar, S. H. & Derome, N. Teleost microbiomes: The state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Front. Microbiol. 5, 207 (2014).
Lee, P.-T., Yamamoto, F. Y., Low, C.-F., Loh, J.-Y. & Chong, C.-M. Gut immune system and the implications of oral-administered immunoprophylaxis in finfish aquaculture. Front. Immunol. 12, 773193. https://doi.org/10.3389/fimmu.2021.773193 (2021).
Linda, S. S. et al. Synbiotic supplementation boosts growth, gut health, and immunity in Asian fossil catfish (Heteropneustes fossilis). Aquac. Res. 2025, 4542077. https://doi.org/10.1155/are/4542077 (2025).
RingĆø, E. et al. Effect of dietary components on the gut microbiota of aquatic animals: A never-ending story?. Anim. Nutr. 22, 219ā282 (2016).
El-Saadony, M. T. et al. The functionality of probiotics in aquaculture: an overview. Fish Shellfish Immunol. 117, 36ā52 (2021).
Sullam, K. E. et al. Environmental and ecological factors that shape the gut bacterial communities of fish: A meta-analysis. Mol. Ecol. 21, 3363ā3378 (2012).
Egerton, S., Culloty, S., Whooley, J., Stanton, C. & Ross, R. P. The gut microbiota of marine fish. Front. Microbiol. 9, 873 (2018).
Maji, U. et al. Exploring the gut microbiota composition of Indian major carp, rohu (Labeo rohita), under diverse culture conditions. Genomics 114, 110354. https://doi.org/10.1016/j.ygeno.2022.110354 (2022).
Cardona, E. et al. Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system. BMC Microbiol. 16, 157 (2016).
Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621ā1624 (2012).
Percie du Sert, N. et al. The arrive guidelines 20: Updated guidelines for reporting animal research. PLoS Biol. 18, 3000410. https://doi.org/10.1371/journal.pbio.3000410 (2020).
Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41, e1. https://doi.org/10.1093/nar/gks808 (2013).
Bonenfant, Q., NoƩ, L. & Touzet, H. Porechop_ABI: Discovering unknown adapters in Oxford Nanopore technology sequencing reads for downstream trimming. Bioinform. Adv. 3, 085. https://doi.org/10.1093/bioadv/vbac085 (2022).
De Coster, W., DāHert, S., Schultz, D. T., Cruts, M. & Van Broeckhoven, C. NanoPack: Visualizing and processing long-read sequencing data. Bioinformatics 34, 2666ā2669 (2018).
Tyler, A. D. et al. Evaluation of Oxford Nanoporeās MinION sequencing device for microbial whole genome sequencing applications. Sci. Rep. 8, 10931. https://doi.org/10.1038/s41598-018-29334-5 (2018).
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, 590ā596 (2013).
Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 257. https://doi.org/10.1186/s13059-019-1891-0 (2019).
McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, 61217. https://doi.org/10.1371/journal.pone.0061217 (2013).
Oksanen, J. et al. Vegan: community ecology package. R Package Version 2.2ā1, 1ā2 https://cran.r-project.org/web/packages/vegan/vegan.pdf (2015).
Arndt, D. et al. METAGENassist: A comprehensive web server for comparative metagenomics. Nucleic Acids Res. 40, 88ā95 (2012).
RingĆø, E. et al. Lactic acid bacteria in finfishāAn update. Front. Microbiol. 9, 1818. https://doi.org/10.3389/fmicb.2018.01818 (2018).
Salma, U. et al. Occurrence, risks, and mitigation of antibiotic pollution in Bangladeshi aquaculture systems. Environ. Chem. Ecotoxicol. 7, 351ā363 (2025).
Okeke, E. S. et al. Antibiotic resistance in aquaculture and aquatic organisms: a review of current nanotechnology applications for sustainable management. Environ. Sci. Pollut. Res. Int. 29, 69241ā69274 (2022).
Popoola, B. M., Adeyemi, O. A. & Samson, O. J. Antibiotic-resistant bacteria in tropical freshwater ecosystems: A review of occurrence, distribution and environmental implications. Microbe https://doi.org/10.1016/j.microb.2025.100457 (2025).
Buckland, S. T., Magurran, A. E., Green, R. E. & Fewster, R. M. Monitoring change in biodiversity through composite indices. Phil. Trans. R. Soc. 360, 243ā254 (2005).
Yasmin, Z. et al. Comparison of fecal bacteriome of diarrhoeic and non-diarrhoeic calves revealed diversified community structures. Microbe 6, 100251. https://doi.org/10.1016/j.microb.2025.100251 (2025).
Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14ā49 (2011).
Liu, T.-T. & Yang, H. Comparative analysis of the total and active bacterial communities in the surface sediment of Lake Taihu. FEMS Microbiol. Ecol. 96, 059. https://doi.org/10.1093/femsec/fiaa059 (2020).
Vitorino, I. R., Gambardella, N., Semedo, M., MagalhĆ£es, C. & Lage, O. M. Diversity and vertical distribution of Planctomycetota in the water column of the remote North Pacific. Environ. Microbiol. Rep. 17, 70063. https://doi.org/10.1111/1758-2229.70063 (2025).
KaborƩ, O. D., Godreuil, S. & Drancourt, M. Planctomycetes as host-associated bacteria: a perspective that holds promise for their future isolations, by mimicking their native environmental niches in clinical microbiology laboratories. Front. Cell. Infect. Microbiol. 10, 519301. https://doi.org/10.3389/fcimb.2020.519301 (2020).
Katiku, M. M., Matofari, J. W. & Nduko, J. M. Preliminary evaluation of probiotic properties and safety profile of Lactiplantibacillus plantarum isolated from spontaneously fermented milk, Amabere amaruranu. Heliyon 8, 10342. https://doi.org/10.1016/j.heliyon.2022.e10342 (2022).
Kumari, V. B. et al. Characterization of Lactobacillus spp. as probiotic and antidiabetic potential isolated from Boza, traditional fermented beverage in Turkey. Adv. Biol. 2024, 2148676. https://doi.org/10.1155/2024/2148676 (2024).
Xie, G. et al. Functional genomic characterization reveals the probiotic tendency and safety assessment of Exiguobacterium acetylicum G1ā33 isolated from the gut of the hybrid grouper (Epinephelus fuscoguttatusā Ć E. lanceolatusā). Aquac. Rep. 36, 102127; https://doi.org/10.1016/j.aqrep.2024.102127 (2024).
Bai, J. et al. Different lactic acid bacteria and their combinations regulated the fermentation process of ensiled alfalfa: ensiling characteristics, dynamics of bacterial community and their functional shifts. Microb. Biotechnol. 14, 1171ā1182 (2021).
Xiong, J. B., Nie, L. & Chen, J. Current understanding on the roles of gut microbiota in fish disease and immunity. Zool. Res. 40, 70ā76 (2019).
Luan, Y. et al. The fish microbiota: Research progress and potential applications. Engineering 29, 137ā146 (2023).
Mohammed, E. A. H., Ahmed, A. E. M., KovƔcs, B. & PƔl, K. The significance of probiotics in aquaculture: A review of research trend and latest scientific findings. Antibiotics 14, 302. https://doi.org/10.3390/antibiotics14030242 (2025).
Zhang, Y., Shi, P. & Ma, J. Exiguobacterium spp. and their applications in environmental remediation. Chin. J. Appl. Environ. Biol. 19, 898ā904 (2013).
Delegan, Y. et al. Characterization and genomic analysis of Exiguobacterium alkaliphilum B-3531D, an efficient crude oil degrading strain. Biotechnol. Rep. 32, 00678. https://doi.org/10.1016/j.btre.2021.e00678 (2021).
Howard, A., OāDonoghue, M., Feeney, A. & Sleator, R. D. Acinetobacter baumannii: An emerging opportunistic pathogen. Virulence 3, 243ā250 (2012).
Hossain, M. et al. Mixed dye degradation by Bacillus pseudomycoides and Acinetobacter haemolyticus isolated from industrial effluents: a combined affirmation with wetlab and in silico studies. Arab. J. Chem. 15, 104078. https://doi.org/10.1016/j.arabjc.2022.104078 (2022).
Jung, J. & Park, W. Acinetobacter species as model microorganisms in environmental microbiology: Current state and perspectives. Appl. Microbiol. Biotechnol. 99, 2533ā2548 (2015).
Benoit, T. et al. Acinetobacter calcoaceticus-baumannii complex prevalence, spatial-temporal distribution, and contamination sources in Canadian aquatic environments. Microbiol. Spectr. 12, 0150924. https://doi.org/10.1128/spectrum.01509-24 (2024).
Segura, A., HernĆ”ndez SĆ”nchez, V., MarquĆ©s, S. & Molina, L. Insights in the regulation of the degradation of PAHs in Novosphingobium sp HR1a and utilization of this regulatory system as a tool for the detection of PAHs. Sci. Total Environ. 590ā591, 381ā393 (2017).
Segura, A., Udaondo, Z. & Molina, L. PahT regulates carbon fluxes in Novosphingobium sp HR1a and influences its survival in soil and rhizospheres. Environ. Microbiol. 23, 2969ā2991 (2021).
Dong, Y. et al. Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats. Microbiol. Spectr. 11, 0207323. https://doi.org/10.1128/spectrum.02073-23 (2023).
Magnuson, E., Altshuler, I., Freyria, N. J., Leveille, R. J. & Whyte, L. G. Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring. Microbiome 11, 203. https://doi.org/10.1186/s40168-023-01628-5 (2023).
Hou, Y., Jia, R., Ji, P., Li, B. & Zhu, J. Organic matter degradation and bacterial communities in surface sediment influenced by Procambarus clarkia. Front. Microbiol. 13, 985555. https://doi.org/10.3389/fmicb.2022.985555 (2022).
Hayatsu, M., Tago, K. & Saito, M. Various players in the nitrogen cycle: Diversity and functions of the microorganisms involved in nitrification and denitrification. J. Plant Nutr. Soil Sci. 54, 33ā45 (2008).
Omori, T., Iwata, K., Yu, S. S. & Azlan, N. N. A. Ammonia Accumulation of Novel Nitrogen-Fixing Bacteria in BiotechnologyāMolecular Studies and Novel Applications for Improved Quality of Human Life (ed Sammour, R. H.) (IntechOpen, 2012).
Wang, X. et al. Adaptation and assembly of microbial communities under saline-alkaline stress in paddy ecosystems: implications for nitrogen and carbon cycling. Environ. Technol. Innov. 39, 104329. https://doi.org/10.1016/j.eti.2025.104329 (2025).
Zhang, K. et al. Fish growth enhances microbial sulfur cycling in aquaculture pond sediments. Microb. Biotechnol. 13, 1597ā1610 (2020).
Acknowledgements
We are thankful to the Research and Extension, and Department of Genomics and Bioinformatics, Chattogram Veterinary and Animal Sciences University.
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This research is funded by the Research and Extension (Grant ID: 830-75) Division of Chattogram Veterinary and Animal Sciences University, Chattogram.
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M. S. U., K. C. and M. H. U. M. Conceptualized and designed the study outline, performed all the analyses, prepared the figures, wrote and revised the manuscript; M. R. N., S. C., A. S. and I. H. performed the analyses, wrote the manuscript; M. S. U., M. H. U. M. and ASM. L. A. Supervised the study and revised the manuscript; All authors have agreed with the manuscript and provided their consent for publication.
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The Ethics Approval Committee (EAC) of Chattogram Veterinary and Animal Sciences University (CVASU) reviewed and authorized the study protocol (Approval no. CVASU/Dir (R&E) EC/2025/881/15).
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Uddin, M.S., Chamonara, K., Nayem, M.R. et al. Comparative gut microbiome analysis of Rohu fish from Halda River and Kaptai Lake using 16S rRNA sequencing. Sci Rep (2026). https://doi.org/10.1038/s41598-025-33754-5
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DOI: https://doi.org/10.1038/s41598-025-33754-5
