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      The Microbiome of Seriola lalandi of Wild and Aquaculture Origin Reveals Differences in Composition and Potential Function

      1 , 2 , 1

      Frontiers in Microbiology

      Frontiers Media S.A.

      microbiota, high-throughput sequencing, yellowtail, Seriola

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          Abstract

          Seriola lalandi is an economically important species that is globally distributed in temperate and subtropical marine waters. Aquaculture production of this species has had problems associated with intensive fish farming, such as disease outbreaks or nutritional deficiencies causing high mortalities. Intestinal microbiota has been involved in many processes that benefit the host, such as disease control, stimulation of the immune response, and the promotion of nutrient metabolism, among others. However, little is known about the potential functionality of the microbiota and the differences in the composition between wild and aquacultured fish. Here, we assayed the V4-region of the 16S rRNA gene using high-throughput sequencing. Our results showed that there are significant differences between S. lalandi of wild and aquaculture origin (ANOSIM and PERMANOVA, P < 0.05). At the genus level, a total of 13 genera were differentially represented between the two groups, all of which have been described as beneficial microorganisms that have an antagonistic effect against pathogenic bacteria, improve immunological parameters and growth performance, and contribute to nutrition. Additionally, the changes in the presumptive functions of the intestinal microbiota of yellowtail were examined by predicting the metagenomes using PICRUSt. The most abundant functional categories were those corresponding to the metabolism of cofactors and vitamins, amino acid metabolism and carbohydrate metabolism, revealing differences in the contribution of the microbiota depending on the origin of the animals. To our knowledge, this is the first study to characterize and compare the intestinal microbiota of S. lalandi of wild and aquaculture origin using high-throughput sequencing.

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          Most cited references 68

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          QIIME allows analysis of high-throughput community sequencing data.

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            Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

            In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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              UPARSE: highly accurate OTU sequences from microbial amplicon reads.

               Robert Edgar (2013)
              Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                26 September 2017
                2017
                : 8
                Affiliations
                1Laboratorio de Biotecnología de los Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile , Santiago, Chile
                2Doctorado en Acuicultura, Programa Cooperativo Universidad de Chile, Universidad Católica del Norte, Pontificia Universidad Católica de Valparaíso , Santiago, Chile
                Author notes

                Edited by: Télesphore Sime-Ngando, Centre National de la Recherche Scientifique (CNRS), France

                Reviewed by: José Manuel Mazón-Suástegui, Centro de Investigaciones Biológicas del Noroeste, Mexico; Eric E. Allen, Scripps Institution of Oceanography, United States; Miguel Ignacio Uyaguari-Diaz, University of British Columbia, Canada

                *Correspondence: Jaime Romero jromero@ 123456inta.uchile.cl

                This article was submitted to Aquatic Microbiology, a section of the journal Frontiers in Microbiology

                10.3389/fmicb.2017.01844
                5622978
                Copyright © 2017 Ramírez and Romero.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Counts
                Figures: 5, Tables: 3, Equations: 0, References: 68, Pages: 10, Words: 7613
                Funding
                Funded by: Fondo Nacional de Desarrollo Científico y Tecnológico 10.13039/501100002850
                Award ID: FONDECYT 1140734
                Award ID: FONDECYT 1171129
                Categories
                Microbiology
                Original Research

                Microbiology & Virology

                seriola, yellowtail, high-throughput sequencing, microbiota

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