Research

Dry work: former lab member Pekka Marttinen sketches out an idea on the whiteboard in lab meeting
Dry labwork: former lab member Pekka Marttinen sketches out an idea on the whiteboard in lab meeting

Thanks for your interest in our work! Our activities are divided between computational or ‘dry’ and laboratory or ‘wet’ work. The former makes use of bioinformatics methods, computer simulations and statistics. The latter is mostly centered around sequencing methods. An introduction follows below, and more detail is available from the menu at left.

 

It's not all equations and R.
Wet lab work: it’s not all equations and R.

General themes

We are often told that bacteria are clonal, meaning that they inherit only the mutations accumulated in their parent cell. But this is not the case. Bacteria have multiple means of transferring DNA from cell to cell, often among lineages and sometimes between ‘species’*. And some do it more than others, for reasons that are not known (but likely include opportunity, selective value of the acquired DNA, and variation in the mechanism of recombination). Much research in my lab deals more or less directly with the phenomenon of recombination in bacteria and its consequences.

While in the past bacterial evolution would have been studied using sequences at a fraction of loci in the genome, the availability of ‘next-gen’ sequencing methods means it is now possible to obtain data from almost the entire genome as routine. It should be noted that this is not always “whole genome sequence” because the methods involved do not necessarily completely close the genome. However it is possible to economically obtain data from hundreds or thousands of genomes. This is revealing extraordinary diversity, illustrated below. We are only beginning to realize the ways in which this technology can enhance our understanding of biology and leverage it to improve public health.

Zooming into bacterial diversity. The leftmost tree shows the relationships between streptococcal species. Note how every S. mitis is as different from every other on average as from the pneumococcus (the tight black dot). Zooming in to the greater resolution offered by MLST, we find many diverse lineages separated by long branches. The genome tree shows relationships among isolates in just one tip of the MLST tree. Genomic studies reveal gain and loss of major antigens as well as other important features of bacterial evolution.
Zooming into bacterial diversity. The leftmost tree shows the relationships between streptococcal species estimated from MLSA data. Note how every S. mitis (blue) is as different from every other on average as from the pneumococcus (the tight black dot). Zooming in to the greater resolution offered by concatenated MLST we find many diverse lineages separated by long branches, typical of a ‘fuzzy species’. The genome tree shows relationships among isolates in just one tip of the MLST tree. Genomic studies reveal gain and loss of major antigens as well as other important features of bacterial evolution.