Are known bacterial strains really present?

Known strains are widely used to study bacterial genomes in shotgun metagenomic samples and to understand drug resistance to bacterial infection. However, bacterial genomes constantly evolve, with mutations accumulated in the genomes over time. It is thus unclear whether the previously identified known bacterial strains are still helpful or even valid for understanding a current shotgun metagenomic sample. To address this question, here we revisited the known strains of the bacterial species S. aureus and S. epidermis identified in 68 atopic dermatitis shotgun metagenomic samples. We find that even the same tools cannot predict the previously reported known strains on the same samples, and most known strains identified by different tools are different. Moreover, the coverage in the pooled and individual samples supports none of the inferred known strain. Our study thus indicates the limitation of the known-strain-based studies, especially those on rapidly evolving bacterial species. Our study also called for de novo bacterial strain identification directly from shotgun metagenomic reads.