Taxonomic classification based on k-mers

DNA sequencing provides the possibility to obtain complete genomic DNA from environmental samples without the need for laboratory microbiological cultures. To this end, metagenomics, the direct DNA sequencing from microbial communities, has changed radically the field of microbiology, by unearthing a broad space of the planet’s microbial diversity, much of which remains unknown. Metagenomic approaches have become standard methods for identifying the biodiversity and the gene or metabolomic functionalities of bacterial and archaeal communities, with many applications not only in microbial ecology but also in public health as in clinical diagnostics and detection of pathogens. Yet, the decrease in the cost of high throughput sequencing and the great amount of microbial data produced every day, highlight one of the main biological questions: the taxonomic classification of metagenomic short reads. Which organisms are contained in a sample? Are there any features that can be used to identify them? To this end, many algorithms have been developed that achieve high speed, by counting k-mers, short sequence substrings of fixed-length k. In this way for the provided input sequences, a list of features can be computed that describes each one of them. Subsequently, the question now reforms to how can the produced k-mers be used for the taxonomic classification of the input sequences. Sample processing, sequencing, and core amplicon data analysis were performed by the Earth Microbiome Project (www.earthmicrobiome.org), and all amplicon sequence data and metadata have been made public through the EMP data portal (qiita.microbio.me/emp): Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., …, Jansson, J. K., Gilbert, J. A., Knight, R., & The Earth Microbiome Project Consortium. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551:457-463. doi:10.1038/nature24621.