Quantifying mobile genetic element interactions in bacteria

Bacteria are foundational to the function of all biomes. Many bacteria carry plasmids: extrachromosomal replicons that can transfer between cells. The cargo genes carried by plasmids enable their bacterial hosts to adapt to different niches. In plants, plasmids can carry genes which degrade pesticides, and in the human gut, they can carry antimicrobial resistance genes. Genes can also be transferred within cells via genetic structures known as transposons and integrons, which shuttle genes between the chromosome and plasmids. This can impact the cell as it affects dosage (plasmids can have higher copy number), and has evolutionary effects due to differences in inheritance. Understanding the spread of bacterial genes poses a significant challenge due to the potential for shared genes to undergo multiple rounds of transfer through multiple routes. This research aims to improve our understanding of bacterial gene spread, illuminating the movement of key adaptive traits in all biomes. To achieve this, computational methods will be used to compare bacterial genomes. The decreasing cost of sequencing in recent years has resulted in a wealth of available data. Work on this scale, however, presents its own set of challenges. This work will unlock the potential of big sequence data.