Species-level genome bins (SGBs) from the human microbiome
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
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:
Cell 2019 10.1016/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