---
layout: page
title: Data
---

<h3 class="section-heading  text-primary">Metagenomic data</h3>

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]](#1)
The Global Ocean Sampling Expedition (GOS) [[2]](#2), the Tara Oceans expedition (TARA) [[3]](#3), Malaspina [Council SNRC (CSIC). Malaspina expedition. Available at: http://www.expedicionmalaspina.es/, 2010] and Ocean Sampling Day (OSD) [[4]](#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.

<div class="img_container" style="width:50%; margin:2em auto;">

**Metagenomic data sets**

| Data set  | Samples | Sites |
|:---------:|:-------:|:-----:|
| TARA      |   242   |  141  |
| Malaspina |   116   |   30  |
| OSD       |   145   |  139  |
| GOS       |    80   |   70  |
| HMP       | 1,249   |   18  |

</div>

<br>

<div class="img_container" style="width:90%; margin:2em auto;">

<img alt="Metag_world_map.png" src="/img/Metag_world_map.png" width="800" height="">

*Ocean distribution of the metagenomic samples*

</div>

<br>

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]](#5) (GOS Sanger data have an average read length of ~800 nucleotides [[2]](#2)). TARA, OSD, Malaspina and the HMP data are, instead, metagenomic assemblies of Illumina pair-end reads. TARA reads were assembled using MOCAT [[6]](#6), Malaspina with RAY-Meta [[7]](#7), OSD using SPAdes [[8]](#8) and the HMP with SOAPdenovo (V 1.04 28) [[9]](#9).

<!---
DATA SOURCES:

TARA Oceans (https://www.embl.de/tara-oceans and https://oceans.taraexpeditions.org/en) Data distribution explained here: https://www.ebi.ac.uk/services/tara-oceans-data
Contextual: PANGAEA https://doi.pangaea.de/10.1594/PANGAEA.842197
Raw data: ENA https://www.ebi.ac.uk/ena/data/view/PRJEB402 and EBI metagenomics (MGnify) https://www.ebi.ac.uk/metagenomics/studies/ERP001736#overview
GOS (https://www.jcvi.org/gos)
Contextual: https://www.imicrobe.us/#/search/GOS (originally CAMERA, now iMICROBE)
Raw data: https://www.ncbi.nlm.nih.gov/bioproject/208472
OSD (https://www.microb3.eu/osd.html)
Contextual: PANGAEA http://store.pangaea.de/Projects/OSD_2014/
Raw data: ENA http://www.ebi.ac.uk/ena/data/view/PRJEB8682
Malaspina (http://www.expedicionmalaspina.es/Malaspina/Main.do#content:Home)
Contextual: Public? We got them directly from the Malaspina group.
Raw data: ENA, but I can find only these https://www.ebi.ac.uk/ena/data/view/PRJNA330770
HMP (https://portal.hmpdacc.org/)
Contextual : HMP portal https://hmpdacc.org/hmp/catalog/grid.php?dataset=metagenomic
Raw data: HMP portal https://portal.hmpdacc.org/

--->

<br>

<h2 class="section-heading  text-primary">Data sets integration via incremental clustering</h2>

<br>

<h3 class="section-heading  text-primary">Genomic data</h3>

**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

<div class="img_container" style="width:50%; margin:2em auto;">

**GTDB dataset**

|           | Genomes |  Proteins  |
|:---------:|:-------:|:----------:|
| Bacterial | 27,372  | 90,621,864 |
| Archaeal  |  1,569  | 3,101,326  |
|   Total   | 28,941  | 93,723,190 |

</div>

<br>

<h3 class="section-heading  text-primary">TARA gene catalog (version 2)</h3>

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.

<br>
<br>

* * *

<h4 class="section-heading  text-primary">References</h4>

<!---
Find a way to link also tables and figures
--->
<a name="1"></a>[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.

<a name="2"></a>[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.

<a name="3"></a>[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.

<a name="4"></a>[4]	A. Kopf et al., “The ocean sampling day consortium.,” GigaScience, vol. 4, p. 27, Jun. 2015.

<a name="5"></a>[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.

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

<a name="7"></a>[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.

<a name="8"></a>[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.

<a name="9"></a>[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.