Mobile Gene Content
Bacteria may acquire new DNA from other bacteria in their environment through the process of horizontal gene transfer. This transferred DNA often encodes new functions that expand an organism’s niche, change its relationships with its host, or provide a competitive edge against other organisms within its environment. Antibiotic resistance genes, for example, are frequently transferred between organisms. Despite the importance of this process, few methods exist to distinguish, in the vast sequencing data available, genes that are inherited versus those genes which have been mobilized and transferred between organisms.
Ilana L. Brito, Biomedical Engineering, and her team are developing a suite of computational tools for examining the mobile gene content in multiple data sets—to identify those genes that may shape the response of microbial communities to stress.
New high-throughput DNA sequencing technologies now allow researchers to simultaneously sequence data from millions of different bacterial species in a single sample, called metagenome sequencing. Thousands of metagenomic sequence data sets are publicly available for samples from diverse ecologies, including gut microbiomes from humans, animals, and insects; soil and root communities; surfaces in built environments; hydrothermal mats and vents; wastewater treatment plants; freshwater sources; and marine ecosystems. By providing new computational methods for reconstructing mobile genetic elements in this type of data set, Brito is tapping into the huge resource of existing metagenomic data to examine the role of horizontal gene transfer in shaping the functions of natural microbial communities. This research will be transformative for all fields of microbiology, including clinical microbiology, microbiome research, environmental microbiology, and microbial engineering.