An expanded version of our Culturable Genome Reference (CGR), termed CGR2, providing 3,324 high-quality draft genomes from isolates selected from a large-scale cultivation of over 20,000 bacterial isolates from fecal samples of healthy Chinese individuals. The CGR2 classifies 527 species (222 novel species) from 8 phyla. This collection of bacterial genomes will constitute a valuable source for future studies on the gut microbiota, and further in-depth knowledge of the gut microbiota.
1. Backgroud
1.1 Reference catalog of genomes of cultivated species of the human gut microbiota
A reference catalog comprising 1,520 non-redundant high-quality genomes of human gut bacteria, generated from a culture-based isolation of >6,000 bacterial clones from fecal samples of healthy individuals, termed the culturable genome reference (CGR).
1.2 Expanded Cultivated Genome Reference (CGR2) of the human gut microbiota
The CGR2, an expanded version of CGR, providing 3,324 high-quality draft genomes from isolates selected from a large-scale cultivation of >20,00_x005f0 bacterial isolates from fecal samples of healthy Chinese individuals. The CGR2 classifies 527 species (179 novel species) from 8 phyla. This collection of bacterial genomes will constitute a valuable source for future studies on the gut microbiota, and further in-depth knowledge of the gut microbiota.
2. Data description
2.1 Strain
299 healthy human donors not taking any drugs during the last month before sampling were included for fecal collection. The selection of candidate donors only considered healthy donors who reported without any clearly diagnosed disease, regardless of their gender. The samples were immediately transferred to an anaerobic chamber (Bactron Anaerobic Chamber, Bactron IV-2, Shellab, USA), homogenized in pre-reduced phosphate buffered saline (PBS) supplemented with 0.1% cysteine, and then diluted and spread on agar plates with different growth media. Plates were incubated under anaerobic condition in an atmosphere of 90% N2, 5% CO2 and 5% H2 at 37 °C for 2–3 d. Single colonies were picked and streaked onto new plates to obtain single clones. All the strains were stored in a glycerol suspension (20%, v/v) containing 0.1% cysteine at –80 °C. The collection of the 299 samples was approved by the Institutional Review Board on Bioethics and Biosafety of BGI under the number BGI-IRB 20106. The study was conducted in accordance with the Declaration of Helsinki and informed consent was provided by all donors.
2.2 Genome
Genomes were sequenced on Illumina or MGI platform to obtain about 100 × clean data for each sample. The reads were assembled using SOAPdenovo 2.04 to form scaffolds. Genome quality was evaluated using CheckM (v1.1.2) ‘lineage_wf’ workflow to select genomes with > 90% completeness and <10% contamination as high-quality genomes. GTDB-Tk (v2.1.0, database release r207, ‘classify_wf ’ function and default parameters) was used to perform taxonomic annotation of each genome.
| Taxonomy Level | Total | Novel |
|---|---|---|
| Phylum | 8 | 0 |
| Class | 12 | 0 |
| Order | 32 | 1 |
| Family | 58 | 1 |
| Genus | 170 | 31 |
| Species | 527 | 179 |
2.3 Project
2.3.1 CGR
Project: https://db.cngb.org/search/project/CNP0000126/
All data are available in the CNP0000126.
2.3.2 CGR2 (New sequenced)
Project: https://db.cngb.org/search/project/CNP0001833/
All data are available in the CNP0001833.
3. Publication
[1]. Zou Y, Xue W, Luo G, et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses[J]. Nature biotechnology, 2019, 37(2): 179-185.
4. How to request strains of CGR2
Download "Strain Requirements Table"
5.How to analysis in CODEPLOT
To perform sequence alignment with the CGR2 database, you can clone the CGR dataset to your workspace, then change value of the "fname" parameter in blast to "/sfs/blastdb/CGR2/CGR2".