Research

Evolution of Antagonistic Interactions

Antagonistic interactions, such as the production of bacteriocins and antibiotics, are common in bacteria. In Streptococcus pneumoniae, the genes responsible for competence and bacteriocin production are controlled by quorum sensing. In quorum sensing, cells constantly release low levels of a small signal molecule; when concentrations of the signal molecule reach a high enough concentration, then all cells up-regulate genes in a coordinated manner.

One key bacteriocin system in S. pneumoniae is the blp (bacteriocin-like peptides) operon, which controls at least 12 different bacteriocin molecules. The method of action of these bacteriocins is unknown; as these bacteriocins specifically kill other S. pneumoniae cells, it is also unknown how a cell producing bacteriocins prevents unintentional suicide. We aim to understand the blp operon on a mechanistic level (how do the proteins interact with each other?) as well as on the evolutionary level (which evolutionary forces create and maintain this diversity?) and on the ecological level (how does this operon affect interactions between other S. pneumoniae strains and other species?).

Antagonistic interactions also may act to maintain diversity if there is no best strategy for outcompeting neighbours, exactly like how there is no best strategy in a paper-rock-scissors game. Using agent-based computer simulations, what are the conditions required to maintain, or even create, diversity through these antagonistic interactions?

Evolution and Impact of Competence

Competence systems (i.e. the ability to pick up DNA outside of the cell) are common within the Streptococcus viridans group, which are a set of related species that range from free-living to opportunistic pathogens of mammals. Horizontal gene transfer is rampant between these species, as one of these related operons is the com operon, which controls bacteriocin production followed by DNA uptake. Competence systems are also controlled through quorum sensing in the Streptococcus viridians group.

How do the unique quorum sensing signals in S. suis affect their competence, (i.e. their ability to pick up DNA outside of the cell)? These patterns will then be compared to S. pneumoniae, which has a different quorum sensing pathway that activates the same genes.

Most species in the Streptococcus genus can pick up DNA from the environment (i.e. competence) and recombine it into their own genome. Through bioinformatic analysis of recombination across species, we can examine which types of genes are more likely to be carried across species. Additionally, are species more likely to recombine with evolutionarily-distant species found in the same ecological habitat, or closely related species in which genes are more likely to maintain their function?

Investigating the Phyllosphere

What are the microbes that live on leaf surfaces (i.e. the phyllosphere)? How do these microbes interact with each other and the host plant? Working with Jon Wilson’s group and using culture-based and culture-independent methods, we explore this environment and look at the challenges of living in close association with a host. Previous Superlabs at Haverford College cultured hundreds of microbes from the phyllosphere, some of which appear to be new species (and therefore need to be described properly!).

Speciation in Microbes

What differentiates species of bacteria? The standard definition of species — organisms reproductively isolated from each other — fails when describing bacteria species. Likewise, bacteria are given species designations based on pairwise percent identity, which has little evolutionary (and no ecological) basis. Genomic analysis allows us to examine the similarities and differences between organisms to better understand species in terms of unique clusters of genes that always co-occur. Through examining core genes (i.e. genes present in all members of a species), can we discover what makes a species unique when compared to closely-related species?

Surveillance of Animal Infections in Malawi

There is the possibility to work with researchers in Malawi to survey infectious agents of wildlife and livestock diseases. This involves laboratory screening of samples at Haverford, as well as potential travel to Malawi with Eric. This work would involve collaborations with veterinarians and veterinary students, and it would focus on collecting samples to detect microbes in tick-bourne and blood-bourne diseases once back at Haverford. This is a new project for the Microbial Evolution and Ecology lab at Haverford; any travel plans would require acquiring additional funding for the trip and as well as extensive planning. If you are interested, please discuss with Eric.