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Microbiome pattern and diversity of an anadromous fish, hilsa shad (Tenualosa ilisha)

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Abstract

Background

The host-microbe interactions are complex, dynamic and context-dependent. In this regard, migratory fish species like hilsa shad (Tenualosa ilisha), which migrates from seawater to freshwater for spawning, provides a unique system for investigating the microbiome under an additional change in fish’s habitat. This work was undertaken to detect taxonomic variation of microbiome and their function in the migration of hilsa.

Methods and results

The study employed 16S rRNA amplicon-based metagenomic analysis to scrutinize bacterial diversity in hilsa gut, skin mucus and water. Thus, a total of 284 operational taxonomic units (OTUs), 9 phyla, 35 orders and 121 genera were identified in all samples. More than 60% of the identified bacteria were Proteobacteria with modest abundance (> 5%) of Firmicutes, Bacteroidetes and Actinobacteria. Leucobacter in gut and Serratia in skin mucus were the core bacterial genera, while Acinetobacter, Pseudomonas and Psychrobacter exhibited differential compositions in gut, skin mucus and water.

Conclusions

Representative fresh-, brackish- and seawater samples of hilsa habitats were primarily composed of Vibrio, Serratia and Psychrobacter, and their diversity in seawater was significantly higher (P < 0.05) than freshwater. Overall, salinity and water microbiota had an influence on the microbial composition of hilsa shad, contributing to host metabolism and adaptation processes. This pioneer exploration of hilsa gut and skin mucus bacteria across habitats will advance our insights into microbiome assembly in migratory fish populations.

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Data availability

The data that support the findings of the current work are included in this article and its supplementary material. The raw sequence data can be found in NCBI under the BioProject accession number PRJNA861733. All data will be made available from the corresponding author on request.

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Acknowledgements

The authors would like to express appreciation to the Next-generation Sequencing, Research and Innovation Laboratory Chattogram (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Dept. of Genetic Engineering and Biotechnology; Institute of Marine Sciences, University of Chittagong; Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia; and Curtin University, Perth, Australia for their constant support throughout the study. This research was partially supported and funded by the Research and Publication Cell, University of Chittagong, and the Ministry of Science and Technology, Bangladesh.

Funding

This work received partial funds from the Ministry of Science and Technology (MoST: SRG-221193), Bangladesh and the Research and Publication Cell (RPC: 727/2022–23/1st Call/27/2022), University of Chittagong. The authors declare that no grants were received during the preparation of this manuscript.

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Authors and Affiliations

  1. Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh

    Sabuj Biswas, Adnan Mannan, Afsana Yeasmin Tanzina, Afroza Akter Tanni, Farjana Sharmen, Md. Mobarok Hossain & S. M. Rafiqul Islam

  2. Next-generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Disease Biology and Molecular Epidemiology (dBme) Research Group, Biotechnology Research and Innovation Centre (BRIC), Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh

    Sabuj Biswas, Adnan Mannan, Afsana Yeasmin Tanzina, Afroza Akter Tanni, Farjana Sharmen, Md. Mobarok Hossain & S. M. Rafiqul Islam

  3. School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia

    Md Javed Foysal

  4. Institute of Marine Sciences, University of Chittagong, Chattogram, Bangladesh

    SM Sharifuzzaman & M. Shah Nawaz Chowdhury

  5. Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia

    Alfred Chin-Yen Tay

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Contributions

S.M.R.I., A.M. and SM.S.: Conceptualization, study design, funding acquisition, supervision, methodology, result interpretation, manuscript review and editing. S.B.: Sample collection, laboratory experiments, data analysis, result interpretation, drafting original manuscript and editing. A.Y.T. and M.M.H.: Laboratory support, data analysis, manuscript editing. M.J.F. and A.T.: Data analysis, visualization, manuscript revision. F.S., A.A.T., and M.S.N.C.: Investigation, visualization, manuscript review and editing. A.M., SM.S., A.T. and S.M.R.I.: Preparation of revised and final manuscript. All authors have read and agreed to the submitted version of the manuscript.

Corresponding author

Correspondence to S. M. Rafiqul Islam.

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Conflict of interest

The authors have no relevant financial or non-financial interests to disclose.

Ethics approval

This study was conducted while carefully adhering to the ethical guidelines and recommendations outlined by the Faculty of Life Sciences at the University of Chittagong, Chattogram, Bangladesh. The research procedures were designed and executed to ensure full compliance with these ethical standards and to uphold the principles of responsible research. It is noteworthy that the samples used in this study were exclusively obtained from deceased fish. This approach was adopted deliberately, as it eliminated the requirement for animal ethics approval, aligning with ethical considerations and responsible research practices.

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Biswas, S., Foysal, M.J., Mannan, A. et al. Microbiome pattern and diversity of an anadromous fish, hilsa shad (Tenualosa ilisha). Mol Biol Rep 51, 38 (2024). https://doi.org/10.1007/s11033-023-08965-6

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