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
100.11811021163772  sponge metagenome Description:Metagenome sequences from sponge tissu...
Alternative accession-BioSample:SAMEA40436668
Alternative names:10793.100.1181102
...
+
101.11810931163772  sponge metagenome Description:Metagenome sequences from sponge tissu...
Alternative accession-BioSample:SAMEA40437418
Alternative names:10793.101.1181093
...
+
10.11817981163772  sponge metagenome Description:Metagenome sequences from sponge tissu...
Alternative accession-BioSample:SAMEA40435168
Alternative names:10793.10.1181798
...
+
102.11814911163772  sponge metagenome Description:Metatranscriptome sequences from spong...
Alternative accession-BioSample:SAMEA40438168
Alternative names:10793.102.1181491
...
+
103.11812711163772  sponge metagenome Description:Metagenome sequences from sponge tissu...
Alternative accession-BioSample:SAMEA40438918
Alternative names:10793.103.1181271
...
+
104.11820331163772  sponge metagenome Description:Metatranscriptome sequences from spong...
Alternative accession-BioSample:SAMEA40439668
Alternative names:10793.104.1182033
...
+
105.11813791163772  sponge metagenome Description:Metagenome sequences from sponge tissu...
Alternative accession-BioSample:SAMEA40440418
Alternative names:10793.105.1181379
...
+
10533.1021163772  sponge metagenome Description:Metagenome sequences from sponge tissu...
Alternative accession-BioSample:SAMEA44557168
Alternative names:10793.10533.102
...
+
10533.1031163772  sponge metagenome Description:Metagenome sequences from sponge tissu...
Alternative accession-BioSample:SAMEA44557918
Alternative names:10793.10533.103
...
+
10533.1051163772  sponge metagenome Description:Metagenome sequences from sponge tissu...
Alternative accession-BioSample:SAMEA44558668
Alternative names:10793.10533.105
...
+
Displaying 1-10 of 4033 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Genome sequenceFASTA12.36 MB2017-07-30
Githubarchive23.41 MB2017-07-30
HTMLHTML7.64 MB2017-07-30
otherUNKNOWN50.97 MB2017-07-30
Phylogenetic treeUNKNOWN2.42 MB2017-07-30
ReadmeTEXT3.95 KB2017-07-30
Tabular DataUNKNOWN29.02 MB2017-07-30
Tabular DataUNKNOWN29.82 MB2017-07-30
Tabular DataTSV1.7 MB2017-07-30
Textbiom27.25 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