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Structure and predictive metabolic contribution of intestinal microbiota of Longfin yellowtail (Seriola rivoliana) juveniles in aquaculture systems

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Abstract

Seriola rivoliana intestinal microbiota (IM) was characterised under aquaculture conditions through 16S rRNA amplicon sequencing. Specimens of 30 days after hatching (DAH) were maintained in three tanks and fed under the same environmental conditions for characterisation 15 days prior to sampling. Three fish were randomly taken from each tank; total DNA extraction of the gut microbiota was performed to characterise microbial composition and its metabolic prediction. The V3 hypervariable region of the 16S rRNA was amplified and sequenced with Illumina pair-end technology. The prokaryotic components in the S. rivoliana intestine were dominated mainly by the phyla Proteobacteria, Firmicutes, Bacteroidetes, Cyanobacteria and Actinobacteria. No significant differences in beta diversity were detected in the three samples (tanks). However in alpha diversity, they were detected in juveniles of the same cohort within the same group, as exemplified by enrichment of certain bacterial groups, mainly of the Clostridia class, which were specific in each fish within the same tank. The metabolic prediction analyses suggested that S. rivoliana IM contribute to the metabolism of amino acids, carbohydrates, lipids, and immune system. This study provides the first IM characterisation under rearing conditions of S. rivoliana—a species with broad economic potential—and contributes to novel information for potential use of probiotics in future trials.

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Acknowledgements

To CIBNOR staff for their technical support: Patricia Hinojosa Baltazar, Ángel Hernández-Contreras, Marcos Quiñones and Milagro García. To Kampachi Farms for providing fertilized eggs for the study. The authors want to especially thank D.E. Salas-Leiva from the Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB), for her insightful recommendations for data analyses; D. Fischer for editorial services in English.

Funding

To Sectoral Fund for Research and Education of México, projects CB-CONACyT No. 258282 and No. 157763 under the academic responsibilities of J.M.S. and D.T.R., respectively. A.T. and J.S.L., received doctoral (CONACyT 335728) and post-doctoral (CIB-PRY-20256) fellowships, respectively.

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  1. Joan Salas-Leiva and José Manuel Mazón-Suástegui are equally contributing first co-author.

Authors and Affiliations

  1. Consejo Nacional de Ciencia y Tecnología (CONACyT), Centro de Investigación en Materiales Avanzados (CIMAV), Miguel de Cervantes 120, Complejo Industrial Chihuahua, C.P. 31136, Chihuahua, CHIH, Mexico

    Joan Salas-Leiva

  2. Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. IPN 195, Col Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, BCS, Mexico

    José Manuel Mazón-Suástegui, Andressa Teles & Dariel Tovar-Ramírez

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  1. Joan Salas-Leiva
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Contributions

JSL, JMS and DTR, conceived and designed research; JSL and AT, conducted experiments; JSL, performed bioinformatics analysis; JSL and DTR, contributed reagents or analytical tools; JSL, JMS and DTR, analysed data; JSL and DTR, wrote the manuscript; All authors read and approved the manuscript.

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Correspondence to Dariel Tovar-Ramírez.

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The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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The experiment complied with the Guidelines of the European Union Council (2010/63/EU) and the Mexican Government (NOM-062—ZOO-1999) for the production, care, and use of experimental animals, and with the ARRIVE guidelines.

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Salas-Leiva, J., Mazón-Suástegui, J.M., Teles, A. et al. Structure and predictive metabolic contribution of intestinal microbiota of Longfin yellowtail (Seriola rivoliana) juveniles in aquaculture systems. Mol Biol Rep 47, 9627–9636 (2020). https://doi.org/10.1007/s11033-020-05970-x

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