Segata Lab - Computational Metagenomics (original) (raw)

The human microbiome harbors many unidentified species. By large-scale metagenomic assembly of 9,428 samples from diverse populations, we uncovered 154,723 microbial genomes that are recapitualed in 4,930 species-level genome bins (SGBs). Many species (77%) were never described before, increase the mappability (e.g., median mappability >95% in the gut) of metagenomes, and expand our understanding of global body-wide human microbiomes.

Data repository and supporting material

The 154,723 reconstructed genomes

• Sequences (fasta files; due to large size they are split into 5 parts): part 1 (main, alternative), part 2 (main, alternative), part 3 (main, alternative), part 4 (main, alternative), part 5 (main, alternative)
• UniRef90 functional profiles: download
• Mapping files linking contigs to UniRef90 functional profiles: working on

The 4,930 SGBs' representatives

• Sequences (fasta files): download
• eggNOG functional profiles: download

The 9,428 metagenomic samples

• Metagenomic assemblies (i.e. before binning): download bash script
• Accession numbers to download raw reads: download

Other

• Sequences of the SGB rRNAs predicted with Barrnap: download
• List of 644 additional reference genomes (available in NCBI as of Sept. 1st, 2018 from a total of 159,803 genomes) with the link to our uSGBs: download

These data types are also freely available at lifebit

For comments and questions please contact us

Citation

If you find the resource useful in your research, please cite our paper:

E. Pasolli1 F. Asnicar1,8 S. Manara1,8 M. Zolfo1,8 N. Karcher1 F. Armanini1 F. Beghini1 P. Manghi1 A. Tett1 P. Ghensi1 M. M. Collado2 B. L. Rice3 C. DuLong4 X. C. Morgan5 C. D. Golden4 C. Quince6 C. Huttenhower4,7 N. Segata1,9

Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle

Cell 201910.1016/j.cell.2019.01.001

1 CIBIO Department, University of Trento, Trento, Italy

2 Institute of Agrochemistry and Food Technology-National Research Council, Valencia, Spain

3 Harvard University, Cambridge, USA

4 Harvard T.H. Chan School of Public Health, Boston, USA

5 University of Otago, Otago, New Zealand

6 Warwick Medical School, University of Warwick, Warwick, UK

7 The Broad Institute, Cambridge, USA

8 These authors contributed equally

9 Lead contact