We base our shotgun metagenomics analyses on the metagenomic species (MGS) concept, which facilitates high-resolution metagenomics analysis, far beyond classical reference-based approaches.
While classical reference-based methods rely on comparisons to the limited number of available reference genomes, the MGS approach allows identification and profiling of microbial species independent of reference sequences. The technique was published by our CSO, Dr. H. Bjørn Nielsen et al. in Nature Biotechnology (2014) and utilizes co-abundant binning of genes across a large collection of deep sequenced metagenomic samples to identify species.
At Clinical Microbiomics, we offer our clients microbiome analyses that take advantage of our MGS catalogues. The MGS catalogues have been extensively annotated for taxonomy and functional potential using both EggNOG and KEGG. In the typical human gut microbiome sample our gene catalogue accounts for more than 90% of the microbiome sequence reads, which greatly supersedes the typical 25-40% representation seen for reference-based approaches. Moreover, the MGS profiling provides substantially increased detection sensitivity and abundance accuracy.