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      Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish

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          Abstract

          Background

          Recent increases in understanding the ecological and evolutionary roles of microbial communities have underscored the importance of their hosts’ biology. Yet, little is known about gut microbiota dynamics during the early stages of ecological diversification and speciation. We sequenced the V4 region of the 16s rRNA gene to study the gut microbiota of Nicaraguan Midas cichlid fish ( Amphilophus cf. citrinellus). Specifically, we tested the hypothesis that parallel divergence in trophic ecology in extremely young adaptive radiations from two crater lakes is associated with parallel changes of their gut microbiota.

          Results

          Bacterial communities of fish guts and lake water were highly distinct, indicating that the gut microbiota is shaped by host-specific factors. Among individuals of the same crater lake, differentiation in trophic ecology was weakly associated with gut microbiota differentiation, suggesting that diet, to some extent, affects the gut microbiota. However, differences in trophic ecology were much more pronounced across than within species whereas similar patterns were not observed for taxonomic and functional differences of the gut microbiota. Across the two crater lakes, we could not detect conclusive evidence for parallel changes of the gut microbiota associated with trophic ecology.

          Conclusions

          A lack of clearly differentiated niches during the early stages of ecological diversification might result in non-parallel changes of gut microbial communities, as observed in our study system as well as in other recently diverged fish species.

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          Most cited references69

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

            SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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              Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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                Author and article information

                Contributors
                ahaerer@ucsd.edu
                julian.torres-dowdall@uni-konstanz.de
                sina.rometsch@uni-konstanz.de
                elizabeth.yohannes@uni-konstanz.de
                machadogonzalo@uniovi.es
                axel.meyer@uni-konstanz.de
                Journal
                Microbiome
                Microbiome
                Microbiome
                BioMed Central (London )
                2049-2618
                29 October 2020
                29 October 2020
                2020
                : 8
                : 149
                Affiliations
                [1 ]GRID grid.9811.1, ISNI 0000 0001 0658 7699, Department of Biology, , University of Konstanz, ; Universitätsstrasse 10, 78457 Konstanz, Germany
                [2 ]GRID grid.266100.3, ISNI 0000 0001 2107 4242, Current address: Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, , University of California San Diego, ; La Jolla, California USA
                [3 ]GRID grid.10863.3c, ISNI 0000 0001 2164 6351, Current address: Department of Functional Biology, , University of Oviedo, ; Oviedo, Spain
                Author information
                http://orcid.org/0000-0002-0888-8193
                Article
                897
                10.1186/s40168-020-00897-8
                7597055
                33121541
                72daf291-827c-4aaa-8b22-89a4d0d8d017
                © The Author(s) 2020

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 1 April 2020
                : 21 July 2020
                Funding
                Funded by: European Research Council
                Award ID: 293700-GenAdap
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100009052, Hector Fellow Academy;
                Categories
                Research
                Custom metadata
                © The Author(s) 2020

                amphilophus citrinellus,trophic ecology,stable isotopes,neotropical cichlids,rapid adaptation,16s rrna gene sequencing,parallel evolution,nicaragua

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