The sponge microbiome project
Citations
333 citations
Cites background from "The sponge microbiome project"
...Marine sponges (phylum Porifera) perfectly illustrate the idea of holobionts as ecosystems, given the exceptionally diverse microbial communities housed within them [23, 24]....
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...The most dominant bacterial symbiont groups belong to the phyla Proteobacteria (mainly Gamma- and Alphaproteobacteria), Actinobacteria, Chloroflexi, Nitrospirae, Cyanobacteria, and candidatus phylum Poribacteria, while Thaumarchaea represents the dominant archaeal group [23, 24]....
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..., the Global Sponge Microbiome Project) [23, 24]....
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...A recent publication made use of the Global Sponge Microbiome Project data to further investigate the microbial diversity features of HMA and LMA sponges at large scale by way of a machine learning [227]....
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...The Global Sponge Microbiome Project, under the umbrella of the Earth Microbiome Project, is a recent collaborative initiative to assess the microbial diversity in sponges from around the world, following standardized protocols [23, 24]....
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314 citations
259 citations
Cites background from "The sponge microbiome project"
...The first data set is a subset of the Sponge Microbiome Project (sponges) (21), where...
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166 citations
103 citations
References
28,911 citations
"The sponge microbiome project" refers methods in this paper
...Taxonomywas added to the resulting biom table using QIIME [28], RDP classifier [29], and Greengenes v. 13.8 [21]....
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...Clustering using the EMP standard protocols in QIIME Raw sequences were demultiplexed and quality controlled following the recommendations of Bokulich et al. [16]....
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...Project name: The Sponge Microbiome Project Project home page: www.spongeemp.com; https://github. com/amnona/SpongeEMP Operating system(s): Unix Programming language: Python and R Other requirements: Python v. 2.7, Biopython v. 1.65, Python 3.5, R v. 3.2.2, Mothur v. 1.37.6, QIIME v. 1.9.1, Deblur License: MIT Any restrictions to use by non-academics: none...
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...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....
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...The additional datasets that support the results of this article are available in the GigaScience repository, GigaDB [32] and include an OTU abundance matrix (the output “.shared” file from Mothur, which is tab delimited), an OTU taxonomic classification table (tab delimited text file), an OTU representative sequence FASTA file, a table of samples’ metadata, the biom files from QIIME and Deblur analyses, and the QIIME-generated tree file....
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18,256 citations
Additional excerpts
...123 database (SILVA, RRID:SCR 006423) [20]....
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17,350 citations
Additional excerpts
...6 (Mothur, RRID:SCR 011947) [18] and Python v....
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16,048 citations
"The sponge microbiome project" refers methods in this paper
...Taxonomywas added to the resulting biom table using QIIME [28], RDP classifier [29], and Greengenes v....
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11,904 citations
"The sponge microbiome project" refers methods in this paper
...Chimeras were identified with UCHIME (UCHIME, RRID:SCR 008057) [23] and removed....
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