Identification and characterization of accessory genomes in bacterial species based on genome comparison and metagenomic recruitment

Accessory genomes in bacterial species carry important genetic elements that are frequently related to antibiotic resistance, virulence factors, and the biotransformation of xenobiotics. Facilitated by the recent advances in sequencing technology, bacterial genomes and metagenomes are accumulating at an unprecedented pace, providing opportunities for studies of accessory genomes. Comparison of closely related genomes reveals potential (and static) accessory genomes, and metagenomic recruitment (i.e., mapping metagenomic sequences onto reference genomes) provides insights into the nature and the dynamics of the accessory portion of the genomes. Recent metagenomic recruitment approaches focus on the identification of `metagenomic islands' (MIs), segments in reference genomes that are under-recruiting in metagenomic samples and therefore likely to be mobile genetic elements (MGEs) in accessory genomes. However, the discovery of MIs often relies on manual inspection of the read recruitment plots. Here we introduce a method that integrates comparison of closely related genomes using A-Bruijn graph, metagenomic recruitment, and recurrent analysis for the identification and characterization of accessory genomes. In addition to metage-nomic islands (valleys), our method reveals `metagenomic peaks' (MPs), segments in a reference genome that disproportionally recruit more metagenomic sequencing reads as compared to the remaining of the reference genome, indicating an enrichment of those segments in specific environments. Our method facilitates automated detection and characterization of accessory genomes at a large scale, and leads to the observation that MGEs are largely specific to environments, as demonstrated in the discovery of MGEs related to Streptococcus mitis in human microbiomes.