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Khalili Laboratory

Petri Dishes

Medications and microbiome in microscopic colitis

We are examining the relationship between medications, the gut microbiome, and risk of microscopic colitis in older adults. We have identified pharmacologic determinants of MC and medications associated with risk of the disease. We are characterizing compositional and temporal changes in the gut microbiota related to disease activity and identifying microbial signatures of MC among older adults with chronic diarrhea in our prospective colonoscopy-based cohort using metagenomic sequencing. We will then identify the microbial and metabolite mediators of the association between medications and risk of MC.

Healthy Food

Specific carbohydrate diet versus Mediterranean diet in treatment of ulcerative colitis

We are conducting a randomized controlled trial to examine the influence of Mediterranean diet and Specific Carbohydrate Diet (SCD) on gut microbiota, luminal inflammation, and disease-specific clinical indices in patients with mild to moderate ulcerative colitis (UC). This comprehensive examination of the complex interaction between diet, gut commensal bacteria, and luminal inflammation will provide an unprecedented opportunity to assess the utility of dietary recommendations in the UC treatment paradigm. 


Clinical Center for NIH’s Nutrition for Precision Health: The All of Us New England Research Collaborative

Through the NIH Common Fund’s Nutrition for Precision Health Clinical Center program, we are collaborating with New England-based research teams to conduct multiple dietary intervention studies for the purpose of developing precision health for nutrition. Specifically, we will enroll a cohort of individuals heterogenous in demographics, clinical characteristics, health parameters, and disease risk factors and apply Artificial Intelligence (AI) methods to understand and predict an individual’s response to foods, nutrients, food components, and dietary patterns.

Pipetting Samples and Test Tube

Environmental Predictors and Metabolomic Signatures of Elderly Onset Inflammatory Bowel Disease

With support from the Crohn’s and Colitis Foundation, we are 1) examining the association between diet, lifestyle and medications and incident elderly-onset IBD; 2) identifying plasma metabolomic profiles that are associated with risk of elderly-onset IBD; and 3) determining whether the relationship between dietary and lifestyle factors and risk of elderly-onset IBD is mediated by plasma metabolites. 

Diet Plan

The Effect of Diet and Lifestyle Factors on Disease Outcomes in Patients with Ulcerative Colitis

We are establishing a prospective observational cohort of UC patients in remission at MGH and collecting long-term diet records, clinical information, and biospecimens to develop a registry that will enable comprehensive cross-disciplinary analyses to gain new insights into dietary risk factors for UC relapse and dietary maintenance therapy strategies. The overall aims are to evaluate the association between diet and hospitalizations, surgeries, and disease flares. 

Pipetting Samples

Statin use, lipid profile and ulcerative colitis

Through funding from Pfizer, we are examining  1) the impact of anti-TNF therapy on body weight, body mass index, and lipid profile; and 2) the relationship between statin use and risk of IBD progression as defined by rates of steroids prescription, use of biologic therapy, and colectomy. We are leveraging cohorts of IBD patients  with detailed data on demographics, lifestyle factors, medications, disease activity indices and inflammatory marker

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