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

Autor: Sumithra TG; Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India., Sharma SRK; Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India. krupeshsharma@gmail.com., Gayathri S; Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India., Ebeneezar S; Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India., Reshma KJ; Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India., Anikuttan KK; Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India., Narasimapallavan GI; Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India., Rameshkumar P; Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India., Sakthivel M; Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India., Prabu DL; Tuticorin Regional Station of ICAR-CMFRI, South Beach Road, 628 001, Tuticorin, India., Tamilmani G; Mandapam Regional Centre of ICAR-CMFRI, Marine Fisheries P.O, 623 520, Mandapam Camp, India., Vijayagopal P; Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India., Gopalakrishnan A; Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Post Box No. 1603, Ernakulam North P.O, Kochi, 682 018, India.
Jazyk: angličtina
Zdroj: Applied microbiology and biotechnology [Appl Microbiol Biotechnol] 2022 Jun; Vol. 106 (12), pp. 4719-4735. Date of Electronic Publication: 2022 Jun 24.
DOI: 10.1007/s00253-022-12026-6
Abstrakt: 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. KEY POINTS: • First report on effects of preservation methods on fish larval microbiome profiles. • First report on activity ranking of preservation methods based on metagenomics metrics. • Storage methods influenced DNA yield, taxonomic and functional microbiome profiles.
(© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
Databáze: MEDLINE
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