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      Fine Flounder ( Paralichthys adspersus) Microbiome Showed Important Differences between Wild and Reared Specimens

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          Abstract

          The intestinal microbiota is involved in a wide range of biological processes that benefit the host, including providing nutrition and modulating the immune system. Fine flounder ( Paralichthys adspersus) is a flatfish of commercial interest that is native to the Chilean coast. The high value of this flatfish has prompted the development of stock enhancement and aquaculture activities. Knowledge of microbiota may help to improve the cultivation of this species; however, few comparative studies have evaluated the intestinal microbiota composition in farmed versus wild fishes. Intestinal contents from wild and aquaculture fish were collected, and DNA was extracted. Subsequently, the V3-region of 16S rRNA was PCR amplified and sequenced using the Ion Torrent platform. The comparison between wild and aquaculture specimens revealed important differences in the composition of the microbiota. The most abundant phylum in wild flounder was Proteobacteria, with an average relative abundance of 68.1 ± 15.4%; in contrast, in aquaculture flounder, this phylum had an average relative abundance of 30.8 ± 24.1%. Reciprocally, the most abundant phylum in flounder aquaculture was Firmicutes, averaging 61.2 ± 28.4%; in contrast, this phylum showed low abundance in wild flounder, in which it averaged 4.7 ± 4%. The phylum Actinobacteria showed greater abundance in wild flounder, ranging from 21.7 ± 18.8%, whereas, it averaged only 2.7 ± 3.8% in aquaculture fish. Specific taxa that were differentially distributed between wild and aquaculture flounder were identified using a statistical approach. At the genus level, a total of four genera were differentially represented between the two conditions. Bacillus and Pseudomonas were more highly represented in aquaculture flounder, whereas Arthrobacter and Psychrobacter were observed in wild flounder. Furthermore, in both cases, predicted functions (metabolic pathways) indicated that those microbiota might provide beneficial effects for the host, but wild flounder showed more noteworthy pathways (EPA/DHA, SCFA, biotin). Our results highlight the differences in the microbiota composition between wild and reared fish. Knowing the composition of the intestinal microbiota of P. adspersus is the first step toward exploring the proper management of this species, as well as toward the development of probiotics and functional foods based on their requirements.

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          Most cited references 54

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          QIIME allows analysis of high-throughput community sequencing data.

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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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              Metagenomic biomarker discovery and explanation

              This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.
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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
                24 February 2017
                2017
                : 8
                Affiliations
                Unidad de Alimentos, Laboratorio de Biotecnología de los Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
                Author notes

                Edited by: Hongyue Dang, Xiamen University, China

                Reviewed by: Biswapriya Biswavas Misra, Texas Biomedical Research Institute, USA; Sigmund Jensen, University of Bergen, Norway

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

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

                Article
                10.3389/fmicb.2017.00271
                5324718
                28286497
                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: 0, Equations: 0, References: 58, Pages: 12, Words: 0
                Funding
                Funded by: Fondo Nacional de Desarrollo Científico y Tecnológico 10.13039/501100002850
                Award ID: 1140734
                Funded by: Comisión Nacional de Investigación Científica y Tecnológica 10.13039/501100002848
                Award ID: 21140856
                Categories
                Microbiology
                Original Research

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