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 269 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 a) a standard protocol using QIIME closed-reference picking resulting in 39,543 Operational Taxonomic Units (OTU) at 97% sequence identity, b) a de novo protocol using Mothur resulting in 518,246 OTUs, and c) 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.

Additional details

Read the peer-reviewed publication(s):

Moitinho-Silva, L., Nielsen, S., Amir, A., Gonzalez, A., Ackermann, G. L., Cerrano, C., … Thomas, T. (2017). The sponge microbiome project. GigaScience, 6(10), 1–7. doi:10.1093/gigascience/gix077

Accessions (data included in GigaDB):

BioProject: PRJEB18736

Projects:






Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
10533.222408172marine metagenomemarine metagenome Description:Metagenome sequences from seawater iso...
Alternative accession-BioSample:SAMEA37977418
Alternative names:10793.10533.222
...
+
10533.225408172marine metagenomemarine metagenome Description:Metagenome sequences from seawater iso...
Alternative accession-BioSample:SAMEA37979668
Alternative names:10793.10533.225
...
+
10533.22408172marine metagenomemarine metagenome Description:Metagenome sequences from seawater iso...
Alternative accession-BioSample:SAMEA37975918
Alternative names:10793.10533.22
...
+
10533.221408172marine metagenomemarine metagenome Description:Metagenome sequences from seawater iso...
Alternative accession-BioSample:SAMEA37976668
Alternative names:10793.10533.221
...
+
10533.223408172marine metagenomemarine metagenome Description:Metagenome sequences from seawater iso...
Alternative accession-BioSample:SAMEA37978168
Alternative names:10793.10533.223
...
+
10533.224408172marine metagenomemarine metagenome Description:Metagenome sequences from seawater iso...
Alternative accession-BioSample:SAMEA37978918
Alternative names:10793.10533.224
...
+
10533.1c408172marine metagenomemarine metagenome Description:Metagenome sequences from seawater iso...
Alternative accession-BioSample:SAMEA44623918
Alternative names:10793.10533.1c
...
+
10533.219408172marine metagenomemarine metagenome Description:Metagenome sequences from seawater iso...
Alternative accession-BioSample:SAMEA37975168
Alternative names:10793.10533.219
...
+
10533.227408172marine metagenomemarine metagenome Description:Metagenome sequences from seawater iso...
Alternative accession-BioSample:SAMEA37981168
Alternative names:10793.10533.227
...
+
10533.226408172marine metagenomemarine metagenome Description:Metagenome sequences from seawater iso...
Alternative accession-BioSample:SAMEA37980418
Alternative names:10793.10533.226
...
+
Displaying 1-10 of 4033 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Textbiom36.03 MB2017-08-10
otherUNKNOWN50.97 MB2017-07-30
Tabular DataUNKNOWN29.02 MB2017-07-30
Tabular DataUNKNOWN29.82 MB2017-07-30
Genome sequenceFASTA12.36 MB2017-07-30
HTMLHTML7.64 MB2017-07-30
Phylogenetic treeUNKNOWN2.42 MB2017-07-30
Textbiom27.25 MB2017-07-30
ReadmeTEXT3.95 KB2017-07-30
Tabular DataTSV1.7 MB2017-07-30
Displaying 1-10 of 11 File(s).
Funding body Awardee Award ID Comments
Australian Research Council Torsten Thomas FT140100197
Australian Research Council Dr NS Webster FT120100480
W.M. Keck Foundation Dr R Knight
John Templeton Foundation Dr R Knight
Date Action
August 9, 2017 Dataset publish
August 10, 2017 Description updated from : 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=3568 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 269 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 a) a standard protocol using QIIME closed-reference picking resulting in 39,543 Operational Taxonomic Units (OTU) at 97% sequence identity, b) a de novo protocol using Mothur resulting in 518,246 OTUs, and c) 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.
August 10, 2017 Additional file Deblur.final.withtax.biom added
August 10, 2017 File Deblur.final.withtax.biom updated
August 10, 2017 File QIIME-output.biom updated
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix077