– What’s really in the microbiome I study?
Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. Therefore, we have developed a method for identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes (Nature biotechnology, 2014).
Using this metagenomics species (MGS) concept, we can capture up to 80% of the diversity in the samples while reference-based approaches only capture around 25%. This allows for studying the very large unknown part of the microbiome as we can assign it to distinctive species and investigate their functional and metabolic potential.
To date, we have identified more than 1500 metagenomic species from deep-sequenced shotgun sequencing data of the human and mouse gut microbiome, ocean water, soil etc.
Figure: A schematic overview of the pipeline for identifying and assembling metagenomic species