Comparative evaluation of fish larval preservation methods on microbiome profiles to aid in metagenomics research

Sumithra, T G and Sharma, S R Krupesha and Gayathri, S and Ebeneezar, Sanal and Reshma, K J and Anikuttan, K K and Iyapparajanarasimapallavan, G and Ramesh Kumar, P and Sakthivel, M and Linga Prabu, D and Tamilmani, G and Vijayagopal, P and Gopalakrishnan, A (2022) Comparative evaluation of fish larval preservation methods on microbiome profiles to aid in metagenomics research. Applied Microbiology and Biotechnology, 106 (11). pp. 1-17.

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Official URL: https://link.springer.com/article/10.1007/s00253-0...
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    Abstract

    Applications of microbiome research through metagenomics promise to generate microbiome manipulation strategies for improved larval survival in aquaculture. However, existing lacunae on the effects of sample preservation methods in metagenome profiles hinder the successful application of this technique. In this context, four preservation methods were scrutinized to identify reliable methods for fish larval microbiome research. The results showed that a total of ten metagenomics metrics, including DNA yield, taxonomic and functional microbiome profiles, and diversity measures, were significantly (P < 0.05) influenced by the preservation method. Activity ranking based on the performance and reproducibility showed that three methods, namely immediate direct freezing, room temperature preservation in absolute ethanol, and preservation at − 20 °C in lysis, storage, and transportation buffer, could be recommended for larval microbiome research. Furthermore, as there was an apparent deviation of the microbiome profiles of ethanol preserved samples at room temperature, the other methods are preferred. Detailed analysis showed that this deviation was due to the bias towards Vibrionales and Rhodobacterales. The microbial taxa responsible for the dissimilarity across different methods were identified. Altogether, the paper sheds light on the preservation protocols of fish larval microbiome research for the first time. The results can help in cross-comparison of future and past larval microbiome studies. Furthermore, this is the first report on the activity ranking of preservation methods based on metagenomics metrics. Apart from methodological perspectives, the paper provides for the first time certain insights into larval microbial profiles of Rachycentron canadum, a potential marine aquaculture species.

    Item Type: Article
    Uncontrolled Keywords: Cobia; Larvae; Metagenomics; Preservation; Absolute ethanol
    Subjects: Fish and Fisheries > Fish Genetics
    Divisions: CMFRI-Kochi > Marine Biotechnology
    Subject Area > CMFRI > CMFRI-Kochi > Marine Biotechnology
    CMFRI-Kochi > Marine Biotechnology
    Subject Area > CMFRI-Kochi > Marine Biotechnology
    Depositing User: Arun Surendran
    Date Deposited: 24 Jun 2022 04:51
    Last Modified: 24 Jun 2022 04:51
    URI: http://eprints.cmfri.org.in/id/eprint/16004

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