Dark Matter Database (Beta)

Users can query shotgun metagenomic samples against the Dark Matter Database (beta). This database includes public (1) metagenome-assembled genomes (MAGs) from non-culturable but viable microbes sometimes referred to as “dark matter”.

We recommend to primarily use Dark Matter (beta) results when looking for novel or non-culturable strains for which high quality genome assemblies are not available, or in order to further refine the taxonomic classification of taxa for which the validated CosmosID databases only provide nearest neighbor information.

Like for other CosmosID databases, a proprietary curation approach was used to identify and phylogenetically organize marker gene sequences (kmers) representing both coding and non-coding sequences uniquely identified by taxon and/or distinct nodes of the phylogenetic tree of MAGs. Basing the tree structure on genomic relatedness of organisms rather than e.g. phenotypically predetermined taxonomy allows CosmosID to offer a high degree of accuracy in identifying microorganisms based on their DNA in metagenomic samples. A distinct advantage of this approach is the identification of novel organisms through the determination of the closest match to genomes that do not have strain level references in the database (if, for example, they have never been sequenced before).

Please note that:

  1. Queries are free of additional charge during the beta period, but will cost additional credits thereafter.
  2. Genomes in this database are inferred from the de novo assembly of metagenomic data, which is an imperfect process. Therefore results from queries against the Dark Matter (beta) database may deviate from queries against the validated CosmosID databases for bacteria, virus, fungi, protists, and phages.

Almeida et al. (2019). A new genomic blueprint of the human gut microbiota. Nature 8 (7753), 1027 - 504. https://dx.doi.org/10.1038/s41586-019-0965-1