A human gut bacterial genome and culture collection for improved metagenomic analyses.
Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y, Pike LJ, Louie T, Browne HP, Mitchell AL, Neville BA, Finn RD, Lawley TD
Nat Biotechnol. Feb 2019. doi: 10.1038/s41587-018-0009-7
COMMENT: The authors present the Human Gastrointestinal Bacteria Culture Collection (HBC). A collection of 737 bacterial genomes from 273 species from human gastrointestinal microbiome and the corresponding isolates. Both the sequence data and the isolates are publicly available at the ENA database and the following culture collections respectively.
Sequence data is deposited in the ENA under project numbers ERP105624 and ERP012217. Bacterial isolates have been deposited at the Leibniz Institute DSMZ-German Collection of Microorganims and Cell Cultures (http://www.dsmz.de), the CCUG-Culture Collection, University of Gothenburg, Sweden (http://www.ccug.se), the Belgian Co-ordinated Collection of Microorganisms hosted by the Laboratory of Microbiology (BCCM/LMG) at Ghent University (http://bccm.belspo.be/) and at the Japan Collection of Microorganisms (JCM; http://jcm.brc.riken.jp/en/).
It is highlighted the importance of this kind of publicly available datasets in functional analysis of the human gut microbiome
In addition to improved species classification, access to comprehensive genome sequenced isolates fundamentally alters the methods, resolution and accuracy of functional analysis. Genome-sequenced isolates enable functional capacity to be inferred from the genetic repertoire of the reference genomes. This eliminates the need to perform ultra-deep metagenomic sequencing and ensures that complete functional pathways are contained within individual bacterium. In addition to improved accuracy, this method also has the capacity to improve sensitivity for functional analysis, allowing detection of functions that, although not prevalent, may represent fundamental differences between study cohorts.