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Confocal laser scanning microscopy of an aquatic biofilm sample. Adapted from doi: 10.1264/jsme2.ME12095.


We employ genomics, machine learning, and theories to study microbes as sensors of the urban environment. Our ultimate goal is to discover the principles underlying the diversity, functioning, and resilience of microbial ecosystems and develop tools to enable ecologically informed designs. Below are several themes that we are actively pursuing.


Rethink wastewater as samples containing information about a population


Wastewater-based monitoring studies large, mixed samples of raw sewage to track biological contents that affect public health. This novel approach collects anonymous data from large groups rather than single people. It can avoid data collection problems created by unequal access to health care services. WBE is highly attractive for monitoring diseases that spread silently. To utilize wastewater-based health data more accurately, we develop new methods to decipher the wastewater samples and synthesize results across studies. 

Read more about our NSF-funded project at the Source.

Our study to develop a new method for population size estimation is available as a preprint.

Our meta-analysis of SARS-CoV-2 WBE  is available as an article in Environmental Science: Water Research and Technology. 

The microorganisms that are found in potable water and its treatment and supply systems are collectively considered as the drinking water microbiome. As part of the built environment, potable water can play a role in seeding the human commensal microbiomes. At the same time, certain opportunistic pathogens are enriched in the water plumbing systems and could lead to public health concerns. Despite its importance, very little is known about the diversity and functions of the drinking water microbiome, nor the forces that shape their variations. We look at the potable water system and aquatic biofilms in built environments from the perspectives of both biogeographical exploration and public health.  Equally important, we translate the exploration of microbial biogeography in household water into an educational experience for K-12 students. 

Read more about our ongoing community-engaged science project on our Outreach page. 


Map microbes in household water supplies


Photo credit: Whitney Curtis



Integrate microorganisms into the wildlife conservation toolbox

turtle and fish.png

Photo credit: Tom Malkowicz

Human activity is recognized as the dominant driver of changes in the Earth’s environment, resulting in dramatic losses of biodiversity worldwide. Maintaining and restoring the earth’s biodiversity requires concerted efforts from various fields. We hypothesize that host-associated microbes play a large yet under-studied role in the success of conservation efforts, making their characterization and exploration of their responses to host and environmental conditions an urgent task. We work with experts in conservation medicine, freshwater ecology, and fish biology to together integrate microbes into the wildlife conservation toolbox. 

We are working with Dr. Sharon Deem and her group at the Institute for Conservation Medicine in the St. Louis Zoo to study the box turtle population in Forest Park. Read more about this LEC-funded project

We are working with Dr. Jason Knouft and his group at St. Louis University to study the freshwater biomes. Read more about this LEC-funded project

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