At some point in your life, you probably experienced “gut issues” that led to diarrhea, discomfort, and other unpleasant symptoms. In many cases, our gut microbiome—a complex ecosystem of trillions of bacteria—is responsible for gastrointestinal illnesses.

My research is motivated by “microbiome-based medicine:” personalized bacterial therapies that might one day heal suffering individuals by improving their gut microbiome. A contemporary example is fecal microbiota transplantation (FMT), a therapy that cures C. difficile infection by transplanting poo from a healthy donor into a sick person’s gut.

My research is driven by a practical concern:

How can fecal transplants be made more effective?

The human gut microbiome consists of thousands of bacterial species and trillions of individuals, and is extremely complex. To inform fecal transplants in humans, I study the much simpler assembly of microbiomes in fruit flies (tens of species and tens of thousands of individuals).

I look forward to extending principles of fruit fly microbiome assembly (e.g. stochastic colonization or establishment of bacteria in localized spatial niches) to more complex model organisms (with you?) in the future.

How do microbes colonize the gut in the first place?

Stochastically! For details see my paper “Stochastic microbiome assembly depends on context” (Jones et al., PNAS, 2022).

Where do microbes colonize in the gut?

In fruit flies, bacteria colonize furrows of the proventriculus. I characterized the spatial structure of these colonization patterns using metapopulation theory. Beautiful microscopy colonized bacteria and more can be found in the paper led by Ren Dodge, “A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota” (Dodge, Jones, et al., Nature Communications, 2023).

How should we quantify noisy population growth?

With the distribution of first-passage times at which populations reach a threshold abundance. See how noisy population growth is related to growth rate and inoculum size in my paper “Signal in the noise: temporal variation in exponentially growing populations” (Jones et al., submitted).


Recent posters summarize my theoretical and and experimental research.