Susan Lynch, PhD

Director, Colitis and Crohn's Disease Microbiome Research Core
Associate Professor
Department of Medicine - Gastroenterology
+1 415 476-6784
Research Overview: 

A broad diversity of co-evolved microbes reside within the human body. Shaped by extrinsic and intrinsic exposures, the microbiome develops in early life and influences immune function and training. Bioactive products of the human microbiome influence host cellular populations in a co-evolved, and frequently reciprocal relationship. Our research program focuses on the role of microbiomes in the origins and chronicity of inflammatory diseases. Leveraging principals of microbial physiology with ecological theory, our research program strives to understand human microbiome genesis, establishment and influence on human immunity. Studies integrate clinical outcomes with large multi-dimensional human microbiome datasets. Leveraging observations made in human populations to inform model systems aimed at deconstructing these complex interactions, we strive to determine microbial-derived mechanisms that promote immune function and programming that contribute to the origins of childhood asthma and to established inflammation in inflammatory bowel disease.

Major goals 

  • Early-life microbiome development and immune training
  • Molecular basis of microbial-derived immunomodulation

On-going research
Inflammatory Bowel Disease. Current efforts are aimed at determining the molecular basis of fecal microbial transplant efficacy and of dietary interventions that promote disease remission in patient populations. 

Asthma. Efforts focus on determining the early-life microbial origins of allergy and asthma. In patients with established disease, identification of airway microbiome contributions to respiratory infection and exacerbation has led to a focus on development of novel interventions for specific clades of pathogenic respiratory pathogens. Other studies examine the contribution of the gut microbiome to distinct respiratory phenotypes of asthma.

Primary Thematic Area: 
Virology & Microbial Pathogenesis
Secondary Thematic Area: 
Immunology
Research Summary: 
Human Microbiome, Chronic Inflammatory Disease
Mentorship Development: 

5/2019 - ACRA: Setting training expectations for trainees on the academic career track
3/2020 - Promoting Student Mental Health
5/2021 - Sharpening your Mentoring Skills (SyMS)

Websites

Publications: 

Microscopic Colitis Patients Possess a Perturbed and Inflammatory Gut Microbiota.

Digestive diseases and sciences

Hertz S, Durack J, Kirk KF, Nielsen HL, Lin DL, Fadrosh D, Lynch K, Piceno Y, Thorlacius-Ussing O, Nielsen H, Lynch SV

Impaired antibacterial immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.

medRxiv : the preprint server for health sciences

Tsitsiklis A, Zha BS, Byrne A, Devoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay MA, Lynch SV, DeRisi JL, COMET Consortium+ , Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR

Maternal and cord blood vitamin D level and the infant gut microbiota in a birth cohort study.

Maternal health, neonatology and perinatology

Kassem Z, Sitarik A, Levin AM, Lynch SV, Havstad S, Fujimura K, Kozyrskyj A, Ownby DR, Johnson CC, Yong GJM, Wegienka G, Cassidy-Bushrow AE