| Strain level identification of bacteria is critical to active areas of research like infectious disease and metagenomics due to the varied human responses to different bacterial strains belonging to the same species. Popular methods for taxonomic assignment like 16S rRNA sequencing are unable to provide this degree of resolution, while methods like whole genome sequencing and shotgun metagenomic sequencing are resource intensive due to high depth requirements and computational complexity. We demonstrate that microbial double digested restriction-site associated DNA sequencing (mddRAD-seq) is a feasible and more efficient alternative for taxonomic assignment at the strain level. In both in silico and in vitro experiments, we found mddRAD-seq generates a reduced, reproducible and tunable set of unique markers that capture enough information for differentiating between two bacterial strains. Furthermore, this method is potentially scalable to complex communities. |
