Academic Journal
The sponge microbiome project
| العنوان: | The sponge microbiome project |
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| المؤلفون: | Moitinho-Silva, Lucas, Nielsen, Shaun, Amir, Amnon, Gonzalez, Antonio, Ackermann, Gail L., Cerrano, Carlo, Astudillo-García, Carmen, Easson, Cole, Sipkema, Detmer, Liu, Fang, Steinert, Georg, Kotoulas, Giorgos, Mccormack, Grace P., Feng, Guofang, Bell, James J., Vicente, Jan, Bjork, Johannes R., Montoya, Jose M., Olson, Julie B., Reveillaud, Julie, Steindler, Laura, Pineda, Mari Carmen, Marra, Maria V., Ilan, Micha, Taylor, M. W., Polymenakou, P., Erwin, Patrick M., Schupp, Peter J., Simister, Rachel L., Knight, Rob, Thacker, Robert W., Costa, Rodrogo, Hill, Russell T., Lopez-Legentil, Susanna, Dailianis, Thanos, Ravasi, Timothy, Hentschel, Ute, Li, Zhiyong Y., Webster, Nicole S., Thomas, Torsten |
| المساهمون: | University of New South Wales Sydney (UNSW), University of California San Diego (UC San Diego), University of California (UC), Polytechnic University of Marche / Università Politecnica delle Marche (UNIVPM), School of Biological Sciences, University of Auckland Auckland, Nova Southeastern University (NSU), Laboratory of Microbiology, Wageningen University and Research Wageningen (WUR), Shanghai Jiao Tong University Shanghai, Hellenic Centre for Marine Research (HCMR), National University of Ireland (NUI), School of Biological Sciences Wellington, New Zealand, Victoria University of Wellington, Hawaii Institute of Marine Biology, University of Hawai‘i Mānoa (UHM), University of Notre Dame, Partenaires INRAE, Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales Toulouse (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales Toulouse (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France-Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, University of Alabama Tuscaloosa (UA), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), University of Haifa Haifa, Australian Institute of Marine Science (AIMS), Tel Aviv University (TAU), Department of Biology and Marine Biology, University of North Carolina Wilmington (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), University of Oldenburg, University of British Columbia (UBC), State University of New York (SUNY), Universidade de Lisboa = University of Lisbon = Université de Lisbonne (ULISBOA), University of Maryland Center for Environmental Science (UMCES), University of Maryland System, King Abdullah University of Science and Technology Saudi Arabia (KAUST), Helmholtz Centre for Ocean Research Kiel (GEOMAR), Christian-Albrechts-Universität zu Kiel = Christian-Albrechts University of Kiel = Université Christian-Albrechts de Kiel (CAU), The University of Queensland (UQ All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations ), T.T. and N.S.W were funded by Australian Research Council Future Fellowships FT140100197 and FT120100480, respectively. T.T. received funds from the Gordon and Betty Moore Foundation. This work was also supported in part by the W.M. Keck Foundation and the John Templeton Foundation. R.K. received funding as a Howard Hughes Medical Institute Early Career Scientist. |
| المصدر: | EISSN: 2047-217X ; GigaScience ; https://hal.inrae.fr/hal-02628845 ; GigaScience, 2017, 6 (10), 7 p. ⟨10.1093/gigascience/gix077⟩ |
| بيانات النشر: | HAL CCSD Oxford Univ Press |
| سنة النشر: | 2017 |
| المجموعة: | Institut national des sciences de l'Univers: HAL-INSU |
| مصطلحات موضوعية: | bacteria, 16S rRNA gene, microbial diversity, marine sponges, archaea, symbiosis, microbiome, [SDV]Life Sciences [q-bio] |
| الوصف: | correction :10.1093/gigascience/giy145 ; International audience ; Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| Relation: | PRODINRA: 410875; WOS: 000412397500002 |
| DOI: | 10.1093/gigascience/gix077 |
| الاتاحة: | https://hal.inrae.fr/hal-02628845 https://hal.inrae.fr/hal-02628845v1/document https://hal.inrae.fr/hal-02628845v1/file/Moitinho-Silva_gigascience_2017_1.pdf https://doi.org/10.1093/gigascience/gix077 |
| Rights: | info:eu-repo/semantics/OpenAccess |
| رقم الانضمام: | edsbas.9479AA6B |
| قاعدة البيانات: | BASE |
| DOI: | 10.1093/gigascience/gix077 |
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