Metagenomic ventures into outer sequence space

Dutilh, Bas E

To summarize, unknowns are genetic sequences that are difficult to identify using standard methods, such as by alignment to an annotated reference database. Unknowns remain a persistent elephant in the room in most metagenomics research projects, and exist for technical, biological, methodological, and logistical reasons. The most promising option to resolve the unknowns is by creating improved reference databases that chart biological sequence space, including the outer realms that remain unexplored by science (also known as dark matter). Besides sequencing reference strains or single cells, it may be expected that metagenomic sequencing, assembly, and binning will greatly add to improving these reference databases, for example by identifying common sequences in many metagenomes, and prioritizing them for targeted characterization. Characterizing unknowns will be vital to fully exploit the increasingly available metagenomic data sets from all ecosystems, toward understanding the roles of microbes and viruses in the biosphere. It remains an open question what is the actual size of biological sequence space, but the untargeted, shotgun nature of metagenomics makes it the most powerful tool to address this question.