Channing Human Microbiome Research

Methodology Development and Cohort Studies of Human Microbial Dynamics and Ecological Networks

Rather than simple passengers in and on our bodies, commensal microorganisms play key roles in human physiology and diseases. Many scientific advances have been made through the work of large-scale, consortium-driven metagenomic projects.

Despite these technical advances that help us acquire more accurate organismal compositions and functional profiles of human-associated microbial communities, there are still many fundamental questions to be addressed at the systems level. After all, microbes form very complex and dynamic ecosystems, which can be altered by dietary changes, medical interventions, and many other factors.

The alterability of our microbiome offers a promising future for practical microbiome-based therapies, such as fecal microbiota transplantation (FMT), but also raises long-term safety concerns. Indeed, due to its high complexity, untargeted interventions could shift our microbiome to an undesired state with unintended health consequences.

To attain the bright future promised by microbiota-based therapies, we must better understand the structure, dynamics, and control of our microbial ecosystems.

Current Research

Investigators at the Channing Division of Network Medicine have built a comprehensive research strategy to conduct both methodology development and cohort studies.

Methodology Development

Cohort Studies

  • Vitamin D Antenatal Asthma Reduction Trial (VDAART), which has been renewed for another period so that we may follow the children born during the initial clinical trial until age 6, when a definitive asthma diagnosis may be made by a physician. This trial has served as the basis for several active ancillary studies that are now also examining the effects of vitamin D on the gut microbiome, preeclampsia, the development of allergies and atopic disorders, and we continue to study potential associations of the effects of vitamin D supplementation/insufficiency on other conditions.
  • Nurses' Health Study II (NHS II). NHS II was launched in 1989, when 120,000 nurses aged 25-42 years responded to a mailed questionnaire regarding their health and lifestyle. The questionnaire includes items on many relevant variables: diet, body mass index (BMI), cigarette smoking, medications, physical activity, sleeping habits, alcohol consumption, chronic disease and health conditions (e.g., heart disease, cancers, neurologic diseases, etc.), relevant psychosocial factors assessed using validated measures, socioeconomic status (e.g., education, husband's education, father's occupation; census tract data from geocoded addresses), neighborhood characteristics (e.g., rural vs. urban, based on geocoding), race/ethnicity, marital status, living status (e.g., home, retirement community, etc.). NHS II recently received a large infrastructure grant to fund the new collection of 30,000 stool samples from participants. With these resources, it will be possible to examine many critical research questions on human microbiome and to evaluate numerous sources of bias or confounding in all proposed research.