Data

Metagenomic data

To obtain a comprehensive view of the microbial communities in different environments we combined four major/primary marine metagenomic datasets, which cover all the ocean regions at various depths and the Human Microbiome Project dataset [1] The Global Ocean Sampling Expedition (GOS) [2], the Tara Oceans expedition (TARA) [3], Malaspina [Council SNRC (CSIC). Malaspina expedition. Available at: http://www.expedicionmalaspina.es/, 2010] and Ocean Sampling Day (OSD) [4], form together one of the most extensive public marine data sets. The data from GOS originated from 80 samples at 70 different sampling sites; the Malaspina data set comprises data from 116 samples, taken at 30 different stations; the TARA data covers 141 different locations for a total 242 samples and OSD data belongs to 146 metagenomic samples taken at 139 different stations. We added to this dataset 1,249 HMP metagenomes, coming from 5 main body sites (“gastrointestinal tract”, “oral”, “airways”, “urogenital tract” and “skin”) and 18 specific sites. The numbers are shown in Table 1.

The data were collected in the form of single-reads from GOS and at the stage of metagenomic assemblies from the other four projects. Specifically, GOS single-reads came from shotgun sequencing performed with the Sanger sequencing techniques, which leads to sufficiently long reads [5] (GOS Sanger data have an average read length of ~800 nucleotides [2]). TARA, OSD, Malaspina and the HMP data are, instead, metagenomic assemblies of Illumina pair-end reads. TARA reads were assembled using MOCAT [6], Malaspina with RAY-Meta [7], OSD using SPAdes [8] and the HMP with SOAPdenovo (V 1.04 28) [9].

Data sets integration via incremental clustering

Genomic data

The Genome Taxonomy Database (GTDB): 127,318 genomes, BACTERIA (125,243), ARCHAEA (2,075), Release 03-RS86 (19th August 2018)

We downloaded the protein sequences for bacterial and archaeal genomes from the Annotree website at: https://data.ace.uq.edu.au/public/misc_downloads/annotree/r86/.

We collected 90,621,864 proteins from 27,372 bacterial genomes, and 3,101,326 from 1,569 archaeal genomes

TARA gene catalog (version 2)

OM-RGC-v2 reference paper: “Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome” https://www.sciencedirect.com/science/article/pii/S009286741931164X

OM-RGC.v2 contains 46,775,154 non-redundant genes.

It can be downloaded from the https://www.ocean-microbiome.org/ portal.

---

References

[1] J. Lloyd-Price et al., “Strains, functions and dynamics in the expanded Human Microbiome Project.,” Nature, vol. 550, no. 7674, pp. 61–66, Oct. 2017.

[2] D. B. Rusch et al., “The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific,” PLoS Biology, vol. no. 3, p. 77, 2007.

[3] S. Sunagawa et al., “Ocean plankton. Structure and function of the global ocean microbiome.,” Science (New York, N.Y.), vol. 348, no. 6237, p. 1261359, May 2015.

[4] A. Kopf et al., “The ocean sampling day consortium.,” GigaScience, vol. 4, p. 27, Jun. 2015.

[5] F. Sanger, S. Nicklen, and A. R. Coulson, “DNA sequencing with chain-terminating inhibitors.,” Proceedings of the National Academy of Sciences of the United States of America, vol. 74, no. 12, pp. 5463–5467, Dec. 1977.

[6] J. R. Kultima et al., “MOCAT: a metagenomics assembly and gene prediction toolkit.,” PloS one, vol. 7, no. 10, p. e47656, Oct. 2012.

[7] S. Boisvert, F. Raymond, E. Godzaridis, F. Laviolette, and J. Corbeil, “Ray Meta: scalable de novo metagenome assembly and profiling,” Genome biology, vol. 13, no. 12, p. 122, 2012.

[8] A. Bankevich et al., “SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.,” Journal of computational biology: a journal of computational molecular cell biology, vol. 19, no. 5, pp. 455–477, May 2012.

[9] R. Li et al., “De novo assembly of human genomes with massively parallel short read sequencing.,” Genome research, vol. 20, no. 2, pp. 265–272, Feb. 2010.