More Data is Not Always Better: The Influence of RefSeq Database Grows on Metagenomic Taxonomic Classification

Current technologies allow for the sequencing of microbial communities directly from the environment without prior culturing. One of the major problems when analyzing a microbial sample is to taxonomically annotate its reads to identify the species it contains. In order to determine the role of the reference database in taxonomic sequence classification, we examine the influence of the database over time on the performance of Kraken 2 a widely used taxonomic classification and profiling method. We reported that changes in reference database over time influenced the accuracy of metagenomic taxonomic classification, and training the classifier with more data, e.g. new species, worsen the results.