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      Characterization of ecto- and endoparasite communities of wild Mediterranean teleosts by a metabarcoding approach

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          Abstract

          Next‐generation sequencing methods are increasingly used to identify eukaryotic, unicellular and multicellular symbiont communities within hosts. In this study, we analyzed the non-specific reads obtained during a metabarcoding survey of the bacterial communities associated to three different tissues collected from 13 wild Mediterranean teleost fish species. In total, 30 eukaryotic genera were identified as putative parasites of teleosts, associated to skin mucus, gills mucus and intestine: 2 ascomycetes, 4 arthropods, 2 cnidarians, 7 nematodes, 10 platyhelminthes, 4 apicomplexans, 1 ciliate as well as one order in dinoflagellates (Syndiniales). These results highlighted that (1) the metabarcoding approach was able to uncover a large spectrum of symbiotic organisms associated to the fish species studied, (2) symbionts not yet identified in several teleost species were putatively present, (3) the parasitic diversity differed markedly across host species and (4) in most cases, the distribution of known parasitic genera within tissues is in accordance with the literature. The current work illustrates the large insights that can be gained by making maximum use of data from a metabarcoding approach.

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          Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

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            Parasites in food webs: the ultimate missing links

            Parasitism is the most common consumer strategy among organisms, yet only recently has there been a call for the inclusion of infectious disease agents in food webs. The value of this effort hinges on whether parasites affect food-web properties. Increasing evidence suggests that parasites have the potential to uniquely alter food-web topology in terms of chain length, connectance and robustness. In addition, parasites might affect food-web stability, interaction strength and energy flow. Food-web structure also affects infectious disease dynamics because parasites depend on the ecological networks in which they live. Empirically, incorporating parasites into food webs is straightforward. We may start with existing food webs and add parasites as nodes, or we may try to build food webs around systems for which we already have a good understanding of infectious processes. In the future, perhaps researchers will add parasites while they construct food webs. Less clear is how food-web theory can accommodate parasites. This is a deep and central problem in theoretical biology and applied mathematics. For instance, is representing parasites with complex life cycles as a single node equivalent to representing other species with ontogenetic niche shifts as a single node? Can parasitism fit into fundamental frameworks such as the niche model? Can we integrate infectious disease models into the emerging field of dynamic food-web modelling? Future progress will benefit from interdisciplinary collaborations between ecologists and infectious disease biologists.
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              SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare?

              Background A key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely SILVA, RDP, Greengenes or NCBI. It is unclear how similar these are and how to compare analysis results that are based on different taxonomies. Results We provide a method and software for mapping taxonomic entities from one taxonomy onto another. We use it to compare the four taxonomies and the Open Tree of life Taxonomy (OTT). Conclusions While we find that SILVA, RDP and Greengenes map well into NCBI, and all four map well into the OTT, mapping the two larger taxonomies on to the smaller ones is problematic. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3501-4) contains supplementary material, which is available to authorized users.
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                Author and article information

                Contributors
                Role: Formal analysisRole: InvestigationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: InvestigationRole: Writing – review & editing
                Role: Writing – review & editing
                Role: Writing – review & editing
                Role: Formal analysisRole: MethodologyRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                10 September 2019
                2019
                : 14
                : 9
                : e0221475
                Affiliations
                [1 ] Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Banyuls/Mer, France
                [2 ] Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM Observatoire Océanologique, Banyuls/Mer, France
                [3 ] Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls, Banyuls/Mer, France
                [4 ] CNRS, Muséum National d’Histoire Naturelle, Molécules de Communication et Adaptation des Micro-organismes, UMR7245 MCAM, Muséum National d’Histoire Naturelle, Paris, France
                Lund University, SWEDEN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-4419-0841
                http://orcid.org/0000-0003-3868-6362
                Article
                PONE-D-19-05177
                10.1371/journal.pone.0221475
                6736230
                31504055
                c906b802-f935-42b9-98c3-a869f8390aa2
                © 2019 Scheifler et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 21 February 2019
                : 7 August 2019
                Page count
                Figures: 3, Tables: 3, Pages: 21
                Funding
                This research was supported by Sorbonne Universités programme Emergence 2016, SU-16-R-EMR-22-MICROFISH to YD, SD. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Anatomy
                Body Fluids
                Mucus
                Medicine and Health Sciences
                Anatomy
                Body Fluids
                Mucus
                Biology and Life Sciences
                Physiology
                Body Fluids
                Mucus
                Medicine and Health Sciences
                Physiology
                Body Fluids
                Mucus
                Biology and Life Sciences
                Organisms
                Eukaryota
                Biology and Life Sciences
                Anatomy
                Animal Anatomy
                Aquatic Respiratory Anatomy
                Gills
                Medicine and Health Sciences
                Anatomy
                Animal Anatomy
                Aquatic Respiratory Anatomy
                Gills
                Biology and Life Sciences
                Zoology
                Animal Anatomy
                Aquatic Respiratory Anatomy
                Gills
                Biology and Life Sciences
                Anatomy
                Respiratory System
                Gills
                Medicine and Health Sciences
                Anatomy
                Respiratory System
                Gills
                Biology and Life Sciences
                Anatomy
                Digestive System
                Gastrointestinal Tract
                Medicine and Health Sciences
                Anatomy
                Digestive System
                Gastrointestinal Tract
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Invertebrates
                Flatworms
                Medicine and Health Sciences
                Parasitic Diseases
                Parasitic Intestinal Diseases
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Invertebrates
                Nematoda
                Biology and Life Sciences
                Parasitology
                Intestinal Parasites
                Custom metadata
                The data may be found on https://www.ncbi.nlm.nih.gov/sra (SRA accession: PRJNA531247).

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                Uncategorized

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