Research

Researchers in the Microbiomics Program study how microbial communities influence health across the body and how disruptions in the microbiome can contribute to disease. Research focuses on fungal and bacterial biology, gastrointestinal and immune-related conditions, reproductive health, and the use of sequencing, multi-omics and analytics to improve diagnosis, risk prediction and treatment strategies.

Candida albicans

C. albicans is a type of fungus that is commonly found within the human microbiome. It is known for causing infections such as thrush, diaper rash and potentially even systemic disease.

C. albicans also can interact with other microbes within the microbiome, either positively or negatively. For example, interactions with beneficial bacteria can help inhibit the growth of C. albicans, while interactions with other pathogenic bacteria can promote its growth and increase the risk of infection. In addition, C. albicans can produce substances — such as metabolites or toxins — that can alter the microbiome's environment, which can further influence the interactions between the fungus and the microbiome that may affect immune response and development.

This project seeks to understand the role of C. albicans in diseases and conditions such as asthma, atopic dermatitis, food allergies, intestinal dysbiosis and immune response.

Gluten sensitivity

Changes in the makeup of the intestinal microflora have been linked to disorders of the gastrointestinal tract, including gluten sensitivity and the risk of symptoms like those of irritable bowel syndrome (IBS).

This study observes and describes the intestinal microflora of patients with celiac disease and a subset of patients with IBS. The goal is to identify and develop new and unique therapies and preventive interventions for individuals with a high risk of developing gluten sensitivity and IBS-like symptoms.

Clostridium difficile infection

C. difficile infection is the leading cause of hospital-acquired diarrhea in the U.S. Despite advances in treatment, C. difficile infection continues to be associated with poor outcomes. Some patients require urgent surgery for life-threatening infections. Others experience relapses and chronic disabling symptoms.

This project is describing the makeup of the microflora in feces in the colon. The goal is to develop tools that can predict response to treatment and the risk of relapse.

Rheumatoid arthritis

Changes to a normal gut microbiome that go on for an extended period of time, along with a weakened intestinal mucosal barrier, can have an extended effect on systemic immune response. This can be a precursor to chronic inflammatory and autoimmune disorders, such as rheumatoid arthritis.

Researchers are describing the makeup of the intestinal microflora of patients with rheumatoid arthritis and their healthy family members. The research team aims to identify specific microbial species or ecological properties — such as biodiversity — that may be responsible for microbial imbalances in patients.

This research will improve how healthcare professionals predict and diagnose people who are at high risk of developing rheumatoid arthritis. It also may lead to new and unique treatment strategies.

Colon cancer

Scientists know that dietary factors influence people's risk of developing colon cancer. But they have not figured out the exact ways that dietary factors damage cells and DNA. Without this underlying information, healthcare professionals can only observe and experiment to correct patients' dietary effects. So far, such preventive strategies have mostly been unsuccessful.

This project assumes that people's diets and resulting intestinal microbiome communities create metabolites that can harm bowel cells and produce DNA damage. This damage can lead to cancer. Researchers are testing two metabolic pathways with toxic potential, including sulfate-reducing bacteria and methanogens.

Bacterial vaginosis

Bacterial vaginosis is a condition that can have important implications for reproductive health at many levels. Growing evidence suggests it may be a result of changes in the microbiome of the vagina.

In this study, researchers are using genomic sequencing to evaluate the roles of microbial communities and individual microbes in this disease. The research team plans to use this information to develop new and unique ways to diagnose and treat bacterial vaginosis.

Point-of-care devices

Diagnosing diseases early and monitoring treatments across time can help healthcare professionals adjust interventional strategies for each patient at the right time. This project focuses on developing a device that healthcare professionals can use at the time and place they see patients — the point of care. The device will be used to quickly detect bacterial infectious diseases to help patients get timely treatment. Researchers also are developing a portable microfluidic platform to monitor how patients' immune systems respond to treatments.

The goal is to deploy these platforms in intensive care units, operating rooms and homes to help medical professionals make decisions about individualized care.

Cancer risk prediction

Researchers are developing and testing a group of causal inference, artificial intelligence and machine learning tools that will use multi-omic data to better predict patients' risk of getting cancer. These tools will identify the specific genotypes and phenotypes of future cancers. They will help healthcare professionals use individualized medicine to prevent and treat cancer.

These risk prediction algorithms will provide personalized cancer risk estimates for guiding clinical decision-making based on multi-omic risk factors.