E. scolopes is a species of small squids living off the coast of Hawaii. Early in its life cycle, it forms a life-long symbiosis with V. fischeri bacteria. The squids need the bioluminescent bacteria for counter-illumination, a form of camouflage that help the squid blend in with the moonlit ocean surface at night. Scientist also find that the bacteria is crucial in squid’s development – without the bacterial infection, squids do not develop mature light organs .
This simple symbiosis serves as a model system for studying host-microbe interactions. To study this system, there are many angles we can take. This project focuses on the bacterium, and in particular, when it is grown on a petri dish.
Some strains of V. fischeri have the ability to kill other bacteria using the Type VI secretion system (T6SS). Individuals with T6SS can assemble a molecular “syringe,” then use it to inject toxins into neighboring cells. The toxins can cause cell death, unless the cell is immune to it. Cells from the killing strain are typically immune to their own toxins. We typically call killers strains T6SS+ or lethal strains, and the non-killer strains T6SS- or nonlethal strains.
The lethal strains are sometimes present in the squid light organ. The light organ has 6 chambers, called crypts. In experiments, it has not been observed that lethal strains coexist with any other strain in the same crypt. But it is also not the case that lethal strains take over the entire light organ .
On a petri dish, when two nonlethal strains are grown together, they are well-mixed. Microcolonies are form around the initial seed bacterium (or an initial cluster of bacteria), but the sizes are small. However, when two lethal strains are grown together, the microcolonies become larger, the two strains are more separated .
Chris and I developed a multi-agent model for cell growth, division, and death in 2D. Though we use our model for V. fischeri, the model can be generalize to look at many other phenomena.
In our model, we simulate mechanical interactions and T6SS killing between cells. We also solve the diffusion equation for resource field, which the bacteria feed on (acting as sinks, in the math lingo).
I will be presenting at American Physical Society March meeting (2019) on the progress in this project. I’m cautiously optimistic to say that we see good agreements between simulation and experimental data, but more experiments (both numerical and physical) are underway!
 McFall-Ngai, M.(2014), Annu. Rev. Microbiol. 68, 177-94.
 Speare, L, et al.(2018), PNAS 115, E528-E537.