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The sponge microbiome project.

Identifieur interne : 000382 ( PubMed/Corpus ); précédent : 000381; suivant : 000383

The sponge microbiome project.

Auteurs : Lucas Moitinho-Silva ; Shaun Nielsen ; Amnon Amir ; Antonio Gonzalez ; Gail L. Ackermann ; Carlo Cerrano ; Carmen Astudillo-Garcia ; Cole Easson ; Detmer Sipkema ; Fang Liu ; Georg Steinert ; Giorgos Kotoulas ; Grace P. Mccormack ; Guofang Feng ; James J. Bell ; Jan Vicente ; Johannes R. Björk ; Jose M. Montoya ; Julie B. Olson ; Julie Reveillaud ; Laura Steindler ; Mari-Carmen Pineda ; Maria V. Marra ; Micha Ilan ; Michael W. Taylor ; Paraskevi Polymenakou ; Patrick M. Erwin ; Peter J. Schupp ; Rachel L. Simister ; Rob Knight ; Robert W. Thacker ; Rodrigo Costa ; Russell T. Hill ; Susanna Lopez-Legentil ; Thanos Dailianis ; Timothy Ravasi ; Ute Hentschel ; Zhiyong Li ; Nicole S. Webster ; Torsten Thomas

Source :

RBID : pubmed:29020741

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.

DOI: 10.1093/gigascience/gix077
PubMed: 29020741

Links to Exploration step

pubmed:29020741

Le document en format XML

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<nlm:affiliation>Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia.</nlm:affiliation>
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<name sortKey="Cerrano, Carlo" sort="Cerrano, Carlo" uniqKey="Cerrano C" first="Carlo" last="Cerrano">Carlo Cerrano</name>
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<nlm:affiliation>Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy.</nlm:affiliation>
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<name sortKey="Astudillo Garcia, Carmen" sort="Astudillo Garcia, Carmen" uniqKey="Astudillo Garcia C" first="Carmen" last="Astudillo-Garcia">Carmen Astudillo-Garcia</name>
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<nlm:affiliation>School of Biological Sciences, University of Auckland, Auckland, New Zealand.</nlm:affiliation>
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<name sortKey="Easson, Cole" sort="Easson, Cole" uniqKey="Easson C" first="Cole" last="Easson">Cole Easson</name>
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<nlm:affiliation>Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL 33004, USA.</nlm:affiliation>
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<name sortKey="Sipkema, Detmer" sort="Sipkema, Detmer" uniqKey="Sipkema D" first="Detmer" last="Sipkema">Detmer Sipkema</name>
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<nlm:affiliation>Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands.</nlm:affiliation>
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<name sortKey="Liu, Fang" sort="Liu, Fang" uniqKey="Liu F" first="Fang" last="Liu">Fang Liu</name>
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<name sortKey="Steinert, Georg" sort="Steinert, Georg" uniqKey="Steinert G" first="Georg" last="Steinert">Georg Steinert</name>
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<nlm:affiliation>Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands.</nlm:affiliation>
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<name sortKey="Kotoulas, Giorgos" sort="Kotoulas, Giorgos" uniqKey="Kotoulas G" first="Giorgos" last="Kotoulas">Giorgos Kotoulas</name>
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<nlm:affiliation>Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece.</nlm:affiliation>
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<name sortKey="Mccormack, Grace P" sort="Mccormack, Grace P" uniqKey="Mccormack G" first="Grace P" last="Mccormack">Grace P. Mccormack</name>
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<nlm:affiliation>Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland.</nlm:affiliation>
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<name sortKey="Feng, Guofang" sort="Feng, Guofang" uniqKey="Feng G" first="Guofang" last="Feng">Guofang Feng</name>
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<nlm:affiliation>State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.</nlm:affiliation>
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<name sortKey="Bell, James J" sort="Bell, James J" uniqKey="Bell J" first="James J" last="Bell">James J. Bell</name>
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<nlm:affiliation>School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.</nlm:affiliation>
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<name sortKey="Vicente, Jan" sort="Vicente, Jan" uniqKey="Vicente J" first="Jan" last="Vicente">Jan Vicente</name>
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<nlm:affiliation>Hawaii Institute of Marine Biology, 46-007 Lilipuna Road, Kaneohe, HI 96744-1346.</nlm:affiliation>
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<name sortKey="Bjork, Johannes R" sort="Bjork, Johannes R" uniqKey="Bjork J" first="Johannes R" last="Björk">Johannes R. Björk</name>
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<nlm:affiliation>Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA.</nlm:affiliation>
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<name sortKey="Montoya, Jose M" sort="Montoya, Jose M" uniqKey="Montoya J" first="Jose M" last="Montoya">Jose M. Montoya</name>
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<nlm:affiliation>Ecological Networks and Global Change Group, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, Moulis, France.</nlm:affiliation>
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<name sortKey="Olson, Julie B" sort="Olson, Julie B" uniqKey="Olson J" first="Julie B" last="Olson">Julie B. Olson</name>
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<nlm:affiliation>Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA.</nlm:affiliation>
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<author>
<name sortKey="Reveillaud, Julie" sort="Reveillaud, Julie" uniqKey="Reveillaud J" first="Julie" last="Reveillaud">Julie Reveillaud</name>
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<nlm:affiliation>INRA, UMR1309 CMAEE; Cirad, UMR15 CMAEE, 34398 Montpellier, France.</nlm:affiliation>
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<author>
<name sortKey="Steindler, Laura" sort="Steindler, Laura" uniqKey="Steindler L" first="Laura" last="Steindler">Laura Steindler</name>
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<nlm:affiliation>Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.</nlm:affiliation>
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<name sortKey="Pineda, Mari Carmen" sort="Pineda, Mari Carmen" uniqKey="Pineda M" first="Mari-Carmen" last="Pineda">Mari-Carmen Pineda</name>
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<nlm:affiliation>Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia.</nlm:affiliation>
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<name sortKey="Marra, Maria V" sort="Marra, Maria V" uniqKey="Marra M" first="Maria V" last="Marra">Maria V. Marra</name>
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<nlm:affiliation>Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland.</nlm:affiliation>
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<author>
<name sortKey="Ilan, Micha" sort="Ilan, Micha" uniqKey="Ilan M" first="Micha" last="Ilan">Micha Ilan</name>
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<nlm:affiliation>Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.</nlm:affiliation>
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<name sortKey="Taylor, Michael W" sort="Taylor, Michael W" uniqKey="Taylor M" first="Michael W" last="Taylor">Michael W. Taylor</name>
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<nlm:affiliation>School of Biological Sciences, University of Auckland, Auckland, New Zealand.</nlm:affiliation>
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<name sortKey="Polymenakou, Paraskevi" sort="Polymenakou, Paraskevi" uniqKey="Polymenakou P" first="Paraskevi" last="Polymenakou">Paraskevi Polymenakou</name>
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<nlm:affiliation>Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece.</nlm:affiliation>
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<author>
<name sortKey="Erwin, Patrick M" sort="Erwin, Patrick M" uniqKey="Erwin P" first="Patrick M" last="Erwin">Patrick M. Erwin</name>
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<nlm:affiliation>Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA.</nlm:affiliation>
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<name sortKey="Schupp, Peter J" sort="Schupp, Peter J" uniqKey="Schupp P" first="Peter J" last="Schupp">Peter J. Schupp</name>
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<nlm:affiliation>Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky and University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany.</nlm:affiliation>
</affiliation>
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<author>
<name sortKey="Simister, Rachel L" sort="Simister, Rachel L" uniqKey="Simister R" first="Rachel L" last="Simister">Rachel L. Simister</name>
<affiliation>
<nlm:affiliation>Department of Microbiology and Immunology, University of British Columbia, Canada, V6T 1Z3.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Knight, Rob" sort="Knight, Rob" uniqKey="Knight R" first="Rob" last="Knight">Rob Knight</name>
<affiliation>
<nlm:affiliation>Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Thacker, Robert W" sort="Thacker, Robert W" uniqKey="Thacker R" first="Robert W" last="Thacker">Robert W. Thacker</name>
<affiliation>
<nlm:affiliation>Department of Ecology and Evolution, Stony Brook University, Stony Brook NY 11794, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Costa, Rodrigo" sort="Costa, Rodrigo" uniqKey="Costa R" first="Rodrigo" last="Costa">Rodrigo Costa</name>
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<nlm:affiliation>Institute for Bioengineering and Biosciences (IBB), Department of Bioengineering, IST, Universidade de Lisboa, Lisbon, Portugal.</nlm:affiliation>
</affiliation>
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<author>
<name sortKey="Hill, Russell T" sort="Hill, Russell T" uniqKey="Hill R" first="Russell T" last="Hill">Russell T. Hill</name>
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<nlm:affiliation>Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt Street, Baltimore, MD 21202, USA.</nlm:affiliation>
</affiliation>
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<author>
<name sortKey="Lopez Legentil, Susanna" sort="Lopez Legentil, Susanna" uniqKey="Lopez Legentil S" first="Susanna" last="Lopez-Legentil">Susanna Lopez-Legentil</name>
<affiliation>
<nlm:affiliation>Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Dailianis, Thanos" sort="Dailianis, Thanos" uniqKey="Dailianis T" first="Thanos" last="Dailianis">Thanos Dailianis</name>
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<nlm:affiliation>Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece.</nlm:affiliation>
</affiliation>
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<author>
<name sortKey="Ravasi, Timothy" sort="Ravasi, Timothy" uniqKey="Ravasi T" first="Timothy" last="Ravasi">Timothy Ravasi</name>
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<nlm:affiliation>KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.</nlm:affiliation>
</affiliation>
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<author>
<name sortKey="Hentschel, Ute" sort="Hentschel, Ute" uniqKey="Hentschel U" first="Ute" last="Hentschel">Ute Hentschel</name>
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<nlm:affiliation>RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, and Christian-Albrechts-University of Kiel, Germany.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Li, Zhiyong" sort="Li, Zhiyong" uniqKey="Li Z" first="Zhiyong" last="Li">Zhiyong Li</name>
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<nlm:affiliation>State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Webster, Nicole S" sort="Webster, Nicole S" uniqKey="Webster N" first="Nicole S" last="Webster">Nicole S. Webster</name>
<affiliation>
<nlm:affiliation>Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Thomas, Torsten" sort="Thomas, Torsten" uniqKey="Thomas T" first="Torsten" last="Thomas">Torsten Thomas</name>
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<nlm:affiliation>Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia.</nlm:affiliation>
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<title xml:lang="en">The sponge microbiome project.</title>
<author>
<name sortKey="Moitinho Silva, Lucas" sort="Moitinho Silva, Lucas" uniqKey="Moitinho Silva L" first="Lucas" last="Moitinho-Silva">Lucas Moitinho-Silva</name>
<affiliation>
<nlm:affiliation>Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Nielsen, Shaun" sort="Nielsen, Shaun" uniqKey="Nielsen S" first="Shaun" last="Nielsen">Shaun Nielsen</name>
<affiliation>
<nlm:affiliation>Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Amir, Amnon" sort="Amir, Amnon" uniqKey="Amir A" first="Amnon" last="Amir">Amnon Amir</name>
<affiliation>
<nlm:affiliation>Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Gonzalez, Antonio" sort="Gonzalez, Antonio" uniqKey="Gonzalez A" first="Antonio" last="Gonzalez">Antonio Gonzalez</name>
<affiliation>
<nlm:affiliation>Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Ackermann, Gail L" sort="Ackermann, Gail L" uniqKey="Ackermann G" first="Gail L" last="Ackermann">Gail L. Ackermann</name>
<affiliation>
<nlm:affiliation>Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Cerrano, Carlo" sort="Cerrano, Carlo" uniqKey="Cerrano C" first="Carlo" last="Cerrano">Carlo Cerrano</name>
<affiliation>
<nlm:affiliation>Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Astudillo Garcia, Carmen" sort="Astudillo Garcia, Carmen" uniqKey="Astudillo Garcia C" first="Carmen" last="Astudillo-Garcia">Carmen Astudillo-Garcia</name>
<affiliation>
<nlm:affiliation>School of Biological Sciences, University of Auckland, Auckland, New Zealand.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Easson, Cole" sort="Easson, Cole" uniqKey="Easson C" first="Cole" last="Easson">Cole Easson</name>
<affiliation>
<nlm:affiliation>Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL 33004, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Sipkema, Detmer" sort="Sipkema, Detmer" uniqKey="Sipkema D" first="Detmer" last="Sipkema">Detmer Sipkema</name>
<affiliation>
<nlm:affiliation>Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Liu, Fang" sort="Liu, Fang" uniqKey="Liu F" first="Fang" last="Liu">Fang Liu</name>
<affiliation>
<nlm:affiliation>State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Steinert, Georg" sort="Steinert, Georg" uniqKey="Steinert G" first="Georg" last="Steinert">Georg Steinert</name>
<affiliation>
<nlm:affiliation>Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Kotoulas, Giorgos" sort="Kotoulas, Giorgos" uniqKey="Kotoulas G" first="Giorgos" last="Kotoulas">Giorgos Kotoulas</name>
<affiliation>
<nlm:affiliation>Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Mccormack, Grace P" sort="Mccormack, Grace P" uniqKey="Mccormack G" first="Grace P" last="Mccormack">Grace P. Mccormack</name>
<affiliation>
<nlm:affiliation>Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Feng, Guofang" sort="Feng, Guofang" uniqKey="Feng G" first="Guofang" last="Feng">Guofang Feng</name>
<affiliation>
<nlm:affiliation>State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Bell, James J" sort="Bell, James J" uniqKey="Bell J" first="James J" last="Bell">James J. Bell</name>
<affiliation>
<nlm:affiliation>School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Vicente, Jan" sort="Vicente, Jan" uniqKey="Vicente J" first="Jan" last="Vicente">Jan Vicente</name>
<affiliation>
<nlm:affiliation>Hawaii Institute of Marine Biology, 46-007 Lilipuna Road, Kaneohe, HI 96744-1346.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Bjork, Johannes R" sort="Bjork, Johannes R" uniqKey="Bjork J" first="Johannes R" last="Björk">Johannes R. Björk</name>
<affiliation>
<nlm:affiliation>Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Montoya, Jose M" sort="Montoya, Jose M" uniqKey="Montoya J" first="Jose M" last="Montoya">Jose M. Montoya</name>
<affiliation>
<nlm:affiliation>Ecological Networks and Global Change Group, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, Moulis, France.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Olson, Julie B" sort="Olson, Julie B" uniqKey="Olson J" first="Julie B" last="Olson">Julie B. Olson</name>
<affiliation>
<nlm:affiliation>Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Reveillaud, Julie" sort="Reveillaud, Julie" uniqKey="Reveillaud J" first="Julie" last="Reveillaud">Julie Reveillaud</name>
<affiliation>
<nlm:affiliation>INRA, UMR1309 CMAEE; Cirad, UMR15 CMAEE, 34398 Montpellier, France.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Steindler, Laura" sort="Steindler, Laura" uniqKey="Steindler L" first="Laura" last="Steindler">Laura Steindler</name>
<affiliation>
<nlm:affiliation>Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Pineda, Mari Carmen" sort="Pineda, Mari Carmen" uniqKey="Pineda M" first="Mari-Carmen" last="Pineda">Mari-Carmen Pineda</name>
<affiliation>
<nlm:affiliation>Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Marra, Maria V" sort="Marra, Maria V" uniqKey="Marra M" first="Maria V" last="Marra">Maria V. Marra</name>
<affiliation>
<nlm:affiliation>Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Ilan, Micha" sort="Ilan, Micha" uniqKey="Ilan M" first="Micha" last="Ilan">Micha Ilan</name>
<affiliation>
<nlm:affiliation>Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Taylor, Michael W" sort="Taylor, Michael W" uniqKey="Taylor M" first="Michael W" last="Taylor">Michael W. Taylor</name>
<affiliation>
<nlm:affiliation>School of Biological Sciences, University of Auckland, Auckland, New Zealand.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Polymenakou, Paraskevi" sort="Polymenakou, Paraskevi" uniqKey="Polymenakou P" first="Paraskevi" last="Polymenakou">Paraskevi Polymenakou</name>
<affiliation>
<nlm:affiliation>Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Erwin, Patrick M" sort="Erwin, Patrick M" uniqKey="Erwin P" first="Patrick M" last="Erwin">Patrick M. Erwin</name>
<affiliation>
<nlm:affiliation>Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Schupp, Peter J" sort="Schupp, Peter J" uniqKey="Schupp P" first="Peter J" last="Schupp">Peter J. Schupp</name>
<affiliation>
<nlm:affiliation>Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky and University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Simister, Rachel L" sort="Simister, Rachel L" uniqKey="Simister R" first="Rachel L" last="Simister">Rachel L. Simister</name>
<affiliation>
<nlm:affiliation>Department of Microbiology and Immunology, University of British Columbia, Canada, V6T 1Z3.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Knight, Rob" sort="Knight, Rob" uniqKey="Knight R" first="Rob" last="Knight">Rob Knight</name>
<affiliation>
<nlm:affiliation>Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Thacker, Robert W" sort="Thacker, Robert W" uniqKey="Thacker R" first="Robert W" last="Thacker">Robert W. Thacker</name>
<affiliation>
<nlm:affiliation>Department of Ecology and Evolution, Stony Brook University, Stony Brook NY 11794, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Costa, Rodrigo" sort="Costa, Rodrigo" uniqKey="Costa R" first="Rodrigo" last="Costa">Rodrigo Costa</name>
<affiliation>
<nlm:affiliation>Institute for Bioengineering and Biosciences (IBB), Department of Bioengineering, IST, Universidade de Lisboa, Lisbon, Portugal.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Hill, Russell T" sort="Hill, Russell T" uniqKey="Hill R" first="Russell T" last="Hill">Russell T. Hill</name>
<affiliation>
<nlm:affiliation>Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt Street, Baltimore, MD 21202, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Lopez Legentil, Susanna" sort="Lopez Legentil, Susanna" uniqKey="Lopez Legentil S" first="Susanna" last="Lopez-Legentil">Susanna Lopez-Legentil</name>
<affiliation>
<nlm:affiliation>Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Dailianis, Thanos" sort="Dailianis, Thanos" uniqKey="Dailianis T" first="Thanos" last="Dailianis">Thanos Dailianis</name>
<affiliation>
<nlm:affiliation>Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Ravasi, Timothy" sort="Ravasi, Timothy" uniqKey="Ravasi T" first="Timothy" last="Ravasi">Timothy Ravasi</name>
<affiliation>
<nlm:affiliation>KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Hentschel, Ute" sort="Hentschel, Ute" uniqKey="Hentschel U" first="Ute" last="Hentschel">Ute Hentschel</name>
<affiliation>
<nlm:affiliation>RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, and Christian-Albrechts-University of Kiel, Germany.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Li, Zhiyong" sort="Li, Zhiyong" uniqKey="Li Z" first="Zhiyong" last="Li">Zhiyong Li</name>
<affiliation>
<nlm:affiliation>State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Webster, Nicole S" sort="Webster, Nicole S" uniqKey="Webster N" first="Nicole S" last="Webster">Nicole S. Webster</name>
<affiliation>
<nlm:affiliation>Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia.</nlm:affiliation>
</affiliation>
</author>
<author>
<name sortKey="Thomas, Torsten" sort="Thomas, Torsten" uniqKey="Thomas T" first="Torsten" last="Thomas">Torsten Thomas</name>
<affiliation>
<nlm:affiliation>Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia.</nlm:affiliation>
</affiliation>
</author>
</analytic>
<series>
<title level="j">GigaScience</title>
<idno type="eISSN">2047-217X</idno>
<imprint>
<date when="2017" type="published">2017</date>
</imprint>
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<front>
<div type="abstract" xml:lang="en">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.</div>
</front>
</TEI>
<pubmed>
<MedlineCitation Status="In-Process" Owner="NLM">
<PMID Version="1">29020741</PMID>
<DateCreated>
<Year>2017</Year>
<Month>10</Month>
<Day>12</Day>
</DateCreated>
<DateRevised>
<Year>2017</Year>
<Month>10</Month>
<Day>15</Day>
</DateRevised>
<Article PubModel="Print">
<Journal>
<ISSN IssnType="Electronic">2047-217X</ISSN>
<JournalIssue CitedMedium="Internet">
<Volume>6</Volume>
<Issue>10</Issue>
<PubDate>
<Year>2017</Year>
<Month>Oct</Month>
<Day>01</Day>
</PubDate>
</JournalIssue>
<Title>GigaScience</Title>
<ISOAbbreviation>Gigascience</ISOAbbreviation>
</Journal>
<ArticleTitle>The sponge microbiome project.</ArticleTitle>
<Pagination>
<MedlinePgn>1-7</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1093/gigascience/gix077</ELocationID>
<Abstract>
<AbstractText>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.</AbstractText>
<CopyrightInformation>© The Authors 2017. Published by Oxford University Press.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Moitinho-Silva</LastName>
<ForeName>Lucas</ForeName>
<Initials>L</Initials>
<AffiliationInfo>
<Affiliation>Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Nielsen</LastName>
<ForeName>Shaun</ForeName>
<Initials>S</Initials>
<AffiliationInfo>
<Affiliation>Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Amir</LastName>
<ForeName>Amnon</ForeName>
<Initials>A</Initials>
<AffiliationInfo>
<Affiliation>Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA.</Affiliation>
</AffiliationInfo>
</Author>
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<LastName>Gonzalez</LastName>
<ForeName>Antonio</ForeName>
<Initials>A</Initials>
<AffiliationInfo>
<Affiliation>Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Ackermann</LastName>
<ForeName>Gail L</ForeName>
<Initials>GL</Initials>
<AffiliationInfo>
<Affiliation>Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Cerrano</LastName>
<ForeName>Carlo</ForeName>
<Initials>C</Initials>
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<Affiliation>Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Astudillo-Garcia</LastName>
<ForeName>Carmen</ForeName>
<Initials>C</Initials>
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<Affiliation>School of Biological Sciences, University of Auckland, Auckland, New Zealand.</Affiliation>
</AffiliationInfo>
</Author>
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<LastName>Easson</LastName>
<ForeName>Cole</ForeName>
<Initials>C</Initials>
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<Affiliation>Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL 33004, USA.</Affiliation>
</AffiliationInfo>
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<LastName>Sipkema</LastName>
<ForeName>Detmer</ForeName>
<Initials>D</Initials>
<AffiliationInfo>
<Affiliation>Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands.</Affiliation>
</AffiliationInfo>
</Author>
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<LastName>Liu</LastName>
<ForeName>Fang</ForeName>
<Initials>F</Initials>
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<Affiliation>State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Steinert</LastName>
<ForeName>Georg</ForeName>
<Initials>G</Initials>
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<Affiliation>Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands.</Affiliation>
</AffiliationInfo>
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<LastName>Kotoulas</LastName>
<ForeName>Giorgos</ForeName>
<Initials>G</Initials>
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<Affiliation>Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece.</Affiliation>
</AffiliationInfo>
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<LastName>McCormack</LastName>
<ForeName>Grace P</ForeName>
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<Affiliation>Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland.</Affiliation>
</AffiliationInfo>
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<LastName>Feng</LastName>
<ForeName>Guofang</ForeName>
<Initials>G</Initials>
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<Affiliation>State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Bell</LastName>
<ForeName>James J</ForeName>
<Initials>JJ</Initials>
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<Affiliation>School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Vicente</LastName>
<ForeName>Jan</ForeName>
<Initials>J</Initials>
<AffiliationInfo>
<Affiliation>Hawaii Institute of Marine Biology, 46-007 Lilipuna Road, Kaneohe, HI 96744-1346.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Björk</LastName>
<ForeName>Johannes R</ForeName>
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<Affiliation>Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Montoya</LastName>
<ForeName>Jose M</ForeName>
<Initials>JM</Initials>
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<Affiliation>Ecological Networks and Global Change Group, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, Moulis, France.</Affiliation>
</AffiliationInfo>
</Author>
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<LastName>Olson</LastName>
<ForeName>Julie B</ForeName>
<Initials>JB</Initials>
<AffiliationInfo>
<Affiliation>Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Reveillaud</LastName>
<ForeName>Julie</ForeName>
<Initials>J</Initials>
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<Affiliation>INRA, UMR1309 CMAEE; Cirad, UMR15 CMAEE, 34398 Montpellier, France.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Steindler</LastName>
<ForeName>Laura</ForeName>
<Initials>L</Initials>
<AffiliationInfo>
<Affiliation>Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Pineda</LastName>
<ForeName>Mari-Carmen</ForeName>
<Initials>MC</Initials>
<AffiliationInfo>
<Affiliation>Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia.</Affiliation>
</AffiliationInfo>
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<LastName>Marra</LastName>
<ForeName>Maria V</ForeName>
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<Affiliation>Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Ilan</LastName>
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<Initials>M</Initials>
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</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Taylor</LastName>
<ForeName>Michael W</ForeName>
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</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Polymenakou</LastName>
<ForeName>Paraskevi</ForeName>
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</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Erwin</LastName>
<ForeName>Patrick M</ForeName>
<Initials>PM</Initials>
<AffiliationInfo>
<Affiliation>Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Schupp</LastName>
<ForeName>Peter J</ForeName>
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<AffiliationInfo>
<Affiliation>Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky and University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Simister</LastName>
<ForeName>Rachel L</ForeName>
<Initials>RL</Initials>
<AffiliationInfo>
<Affiliation>Department of Microbiology and Immunology, University of British Columbia, Canada, V6T 1Z3.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Knight</LastName>
<ForeName>Rob</ForeName>
<Initials>R</Initials>
<AffiliationInfo>
<Affiliation>Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Department of Computer Science and Engineering, and Center for Microbiome Innovation, University of California - San Diego, La Jolla, CA 92093, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Thacker</LastName>
<ForeName>Robert W</ForeName>
<Initials>RW</Initials>
<AffiliationInfo>
<Affiliation>Department of Ecology and Evolution, Stony Brook University, Stony Brook NY 11794, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Costa</LastName>
<ForeName>Rodrigo</ForeName>
<Initials>R</Initials>
<AffiliationInfo>
<Affiliation>Institute for Bioengineering and Biosciences (IBB), Department of Bioengineering, IST, Universidade de Lisboa, Lisbon, Portugal.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Hill</LastName>
<ForeName>Russell T</ForeName>
<Initials>RT</Initials>
<AffiliationInfo>
<Affiliation>Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt Street, Baltimore, MD 21202, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Lopez-Legentil</LastName>
<ForeName>Susanna</ForeName>
<Initials>S</Initials>
<AffiliationInfo>
<Affiliation>Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Dailianis</LastName>
<ForeName>Thanos</ForeName>
<Initials>T</Initials>
<AffiliationInfo>
<Affiliation>Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Ravasi</LastName>
<ForeName>Timothy</ForeName>
<Initials>T</Initials>
<AffiliationInfo>
<Affiliation>KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Hentschel</LastName>
<ForeName>Ute</ForeName>
<Initials>U</Initials>
<AffiliationInfo>
<Affiliation>RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, and Christian-Albrechts-University of Kiel, Germany.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Li</LastName>
<ForeName>Zhiyong</ForeName>
<Initials>Z</Initials>
<AffiliationInfo>
<Affiliation>State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Webster</LastName>
<ForeName>Nicole S</ForeName>
<Initials>NS</Initials>
<AffiliationInfo>
<Affiliation>Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia.</Affiliation>
</AffiliationInfo>
<AffiliationInfo>
<Affiliation>Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y">
<LastName>Thomas</LastName>
<ForeName>Torsten</ForeName>
<Initials>T</Initials>
<AffiliationInfo>
<Affiliation>Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia.</Affiliation>
</AffiliationInfo>
</Author>
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<Keyword MajorTopicYN="N">16S rRNA gene</Keyword>
<Keyword MajorTopicYN="N">archaea</Keyword>
<Keyword MajorTopicYN="N">bacteria</Keyword>
<Keyword MajorTopicYN="N">marine sponges</Keyword>
<Keyword MajorTopicYN="N">microbial diversity</Keyword>
<Keyword MajorTopicYN="N">microbiome</Keyword>
<Keyword MajorTopicYN="N">symbiosis</Keyword>
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