Genome, Methylome, Resistome – When the Same Sequence Produces a Different Phenotype

Advances in high-throughput sequencing technologies have not only significantly expanded capacity and reduced cost but also now allow an organism’s entire methylome to be captured as rapidly as its genome. Over the past few years, we have produced and annotated complete genomes for thousands of bacterial strains within the ATCC collection. To better understand how genes influence phenotype, we sought to determine whether methylation contributes to organism-specific phenotypic differences. In addition to generating annotated genomes for more than 5,500 bacterial strains, we produced methylomics data for a subset of these organisms and made the datasets available to the scientific community. To date, this represents the most diverse collection of microbial methylomics data available.

Here, we describe the process used to generate the resistome and methylome for more than 3,700 bacterial organisms. We then selected three species from the WHO bacterial priority pathogen list and conducted an in-depth analysis of ten strains from each species. For each strain, we analyzed the genome, methylome, and resistome, and compared these profiles to their corresponding phenotypes to identify potential patterns that may support targeted microbial control. We detail the methods used to process, curate, and analyze the resulting datasets, all of which were generated using established, documented workflows to ensure consistency and reproducibility. Additionally, the genome, resistome, methylome, and phenotype data described here are available through the ATCC Genome Portal. Together, these resources highlight the broad utility of the genomic data within the ATCC Genome Portal and provide a valuable asset for the scientific community.