Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level
Motivation: An accurate and reliable distance (or dissimilarity) among shotgun metagenomes is fundamental to deducing the beta-diversity of microbiomes. To compute the distance at the species level, current methods either ignore the evolutionary relationship among species or fail to account for unclassified organisms that cannot be mapped to definite tip nodes in the phylogenic tree, thus can produce erroneous beta-diversity pattern. Results: To solve these problems, we propose the Dynamic Meta-Storms (DMS) algorithm to enable the comprehensive comparison of metagenomes on the species level with both taxonomy and phylogeny profiles. It compares the identified species of metagenomes with phylogeny, and then dynamically places the unclassified species to the virtual nodes of the phylogeny tree via their higher-level taxonomy information. Its high speed and low memory consumption enable pairwise comparison of 100 000 metagenomes (synthesized from 3688 bacteria) within 6.4 h on a single computing node.
Jing, G., Zhang, Y., Yang, M., Liu, L., Xu, J., & Su, X. (2020). Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level. Bioinformatics, 36 (7), 2308-2310. https://doi.org/10.1093/bioinformatics/btz910