The sponge microbiome project

Handle URI:
http://hdl.handle.net/10754/626161
Title:
The sponge microbiome project
Authors:
Moitinho-Silva, Lucas; Nielsen, Shaun; Amir, Amnon; Gonzalez, Antonio; Ackermann, Gail L.; Cerrano, Carlo; Astudillo-Garcia, Carmen; Easson, Cole; Sipkema, Detmer; Liu, Fang; Steinert, Georg; Kotoulas, Giorgos; McCormack, Grace P.; Feng, Guofang; Bell, James J.; Vicente, Jan; Björk, Johannes R.; Montoya, Jose M.; Olson, Julie B.; Reveillaud, Julie; Steindler, Laura; Pineda, Mari-Carmen; Marra, Maria V.; Ilan, Micha; Taylor, Michael W.; Polymenakou, Paraskevi; Erwin, Patrick M.; Schupp, Peter J.; Simister, Rachel L.; Knight, Rob; Thacker, Robert W.; Costa, Rodrigo; Hill, Russell T.; Lopez-Legentil, Susanna; Dailianis, Thanos; Ravasi, Timothy ( 0000-0002-9950-465X ) ; Hentschel, Ute; Li, Zhiyong; Webster, Nicole S.; Thomas, Torsten
Abstract:
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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; KAUST Environmental Epigenetics Research Program (KEEP)
Citation:
Moitinho-Silva L, Nielsen S, Amir A, Gonzalez A, Ackermann GL, et al. (2017) The sponge microbiome project. GigaScience 6: 1–7. Available: http://dx.doi.org/10.1093/gigascience/gix077.
Publisher:
Oxford University Press (OUP)
Journal:
GigaScience
Issue Date:
16-Aug-2017
DOI:
10.1093/gigascience/gix077
Type:
Article
ISSN:
2047-217X
Sponsors:
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.
Additional Links:
https://academic.oup.com/gigascience/article/6/10/1/4082886
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorMoitinho-Silva, Lucasen
dc.contributor.authorNielsen, Shaunen
dc.contributor.authorAmir, Amnonen
dc.contributor.authorGonzalez, Antonioen
dc.contributor.authorAckermann, Gail L.en
dc.contributor.authorCerrano, Carloen
dc.contributor.authorAstudillo-Garcia, Carmenen
dc.contributor.authorEasson, Coleen
dc.contributor.authorSipkema, Detmeren
dc.contributor.authorLiu, Fangen
dc.contributor.authorSteinert, Georgen
dc.contributor.authorKotoulas, Giorgosen
dc.contributor.authorMcCormack, Grace P.en
dc.contributor.authorFeng, Guofangen
dc.contributor.authorBell, James J.en
dc.contributor.authorVicente, Janen
dc.contributor.authorBjörk, Johannes R.en
dc.contributor.authorMontoya, Jose M.en
dc.contributor.authorOlson, Julie B.en
dc.contributor.authorReveillaud, Julieen
dc.contributor.authorSteindler, Lauraen
dc.contributor.authorPineda, Mari-Carmenen
dc.contributor.authorMarra, Maria V.en
dc.contributor.authorIlan, Michaen
dc.contributor.authorTaylor, Michael W.en
dc.contributor.authorPolymenakou, Paraskevien
dc.contributor.authorErwin, Patrick M.en
dc.contributor.authorSchupp, Peter J.en
dc.contributor.authorSimister, Rachel L.en
dc.contributor.authorKnight, Roben
dc.contributor.authorThacker, Robert W.en
dc.contributor.authorCosta, Rodrigoen
dc.contributor.authorHill, Russell T.en
dc.contributor.authorLopez-Legentil, Susannaen
dc.contributor.authorDailianis, Thanosen
dc.contributor.authorRavasi, Timothyen
dc.contributor.authorHentschel, Uteen
dc.contributor.authorLi, Zhiyongen
dc.contributor.authorWebster, Nicole S.en
dc.contributor.authorThomas, Torstenen
dc.date.accessioned2017-11-14T12:46:06Z-
dc.date.available2017-11-14T12:46:06Z-
dc.date.issued2017-08-16en
dc.identifier.citationMoitinho-Silva L, Nielsen S, Amir A, Gonzalez A, Ackermann GL, et al. (2017) The sponge microbiome project. GigaScience 6: 1–7. Available: http://dx.doi.org/10.1093/gigascience/gix077.en
dc.identifier.issn2047-217Xen
dc.identifier.doi10.1093/gigascience/gix077en
dc.identifier.urihttp://hdl.handle.net/10754/626161-
dc.description.abstractMarine 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.en
dc.description.sponsorshipT.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.en
dc.publisherOxford University Press (OUP)en
dc.relation.urlhttps://academic.oup.com/gigascience/article/6/10/1/4082886en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectmarine spongesen
dc.subjectarchaeaen
dc.subjectbacteriaen
dc.subjectsymbiosisen
dc.subjectmicrobiomeen
dc.subject16S rRNA geneen
dc.subjectmicrobial diversityen
dc.titleThe sponge microbiome projecten
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentKAUST Environmental Epigenetics Research Program (KEEP)en
dc.identifier.journalGigaScienceen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCentre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, , Australiaen
dc.contributor.institutionDepartment of Pediatrics, University of California - San Diego, La Jolla, CA, 92093, , United Statesen
dc.contributor.institutionDepartment of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, , Italyen
dc.contributor.institutionSchool of Biological Sciences, University of Auckland, Auckland, , New Zealanden
dc.contributor.institutionHalmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, 33004, , United Statesen
dc.contributor.institutionWageningen University, Laboratory of Microbiology, Stippeneng 4, Wageningen, 6708 WE, , Netherlandsen
dc.contributor.institutionState Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, , Chinaen
dc.contributor.institutionHellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, Heraklion, 71500, , Greeceen
dc.contributor.institutionZoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, , Irelanden
dc.contributor.institutionSchool of Biological Sciences, Victoria University of Wellington, Wellington, , New Zealanden
dc.contributor.institutionHawaii Institute of Marine Biology, 46-007 Lilipuna Road, Kaneohe, HI, 96744-1346, , United Statesen
dc.contributor.institutionGalvin Life Science Center, University of Notre Dame, Notre Dame, IN, 46556, , United Statesen
dc.contributor.institutionEcological Networks and Global Change Group, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, Moulis, , Franceen
dc.contributor.institutionDepartment of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, , United Statesen
dc.contributor.institutionINRA, UMR1309 CMAEE; Cirad, UMR15 CMAEE, Montpellier, 34398, , , Franceen
dc.contributor.institutionDepartment of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, , Israelen
dc.contributor.institutionAustralian Institute of Marine Science (AIMS), Townsville, QLD, 4810, , Australiaen
dc.contributor.institutionDepartment of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, , , Israelen
dc.contributor.institutionDepartment of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, , United Statesen
dc.contributor.institutionInstitute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky and University Oldenburg, Schleusenstr. 1, Wilhelmshaven, 26382, , Germanyen
dc.contributor.institutionDepartment of Microbiology and Immunology, University of British Columbia, V6T 1Z3, , Canadaen
dc.contributor.institutionDepartment of Computer Science and Engineering and Center for Microbiome Innovation, University of California - San Diego, La Jolla, CA, 92093, , United Statesen
dc.contributor.institutionDepartment of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, , United Statesen
dc.contributor.institutionInstitute for Bioengineering and Biosciences (IBB), Department of Bioengineering, IST, Universidade de Lisboa, Lisbon, , , , Portugalen
dc.contributor.institutionInstitute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt Street, Baltimore, MD, 21202, , United Statesen
dc.contributor.institutionRD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Christian-Albrechts-University of Kiel, Kiel, , , Germanyen
dc.contributor.institutionAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, , Australiaen
kaust.authorRavasi, Timothyen
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