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Gigascience. 2017 Oct 1;6(10):1-7. doi: 10.1093/gigascience/gix077.

The sponge microbiome project.

Author information

1
Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia.
2
Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA.
3
Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy.
4
School of Biological Sciences, University of Auckland, Auckland, New Zealand.
5
Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL 33004, USA.
6
Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
7
State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China.
8
Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece.
9
Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland.
10
School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
11
Hawaii Institute of Marine Biology, 46-007 Lilipuna Road, Kaneohe, HI 96744-1346.
12
Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA.
13
Ecological Networks and Global Change Group, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, Moulis, France.
14
Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA.
15
INRA, UMR1309 CMAEE; Cirad, UMR15 CMAEE, 34398 Montpellier, France.
16
Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.
17
Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia.
18
Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
19
Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA.
20
Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky and University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany.
21
Department of Microbiology and Immunology, University of British Columbia, Canada, V6T 1Z3.
22
Department of Computer Science and Engineering, and Center for Microbiome Innovation, University of California - San Diego, La Jolla, CA 92093, USA.
23
Department of Ecology and Evolution, Stony Brook University, Stony Brook NY 11794, USA.
24
Institute for Bioengineering and Biosciences (IBB), Department of Bioengineering, IST, Universidade de Lisboa, Lisbon, Portugal.
25
Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt Street, Baltimore, MD 21202, USA.
26
KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
27
RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, and Christian-Albrechts-University of Kiel, Germany.
28
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.

Erratum in

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.

KEYWORDS:

16S rRNA gene; archaea; bacteria; marine sponges; microbial diversity; microbiome; symbiosis

PMID:
29020741
PMCID:
PMC5632291
DOI:
10.1093/gigascience/gix077
[Indexed for MEDLINE]
Free PMC Article

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