Susan Lynch, PhD

Director, Benioff Center for Microbiome Medicine
Associate Director, Microbiome in Inflammatory Bowel Disease program
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: 

VMAP: Vaginal Microbiome Atlas During Pregnancy.

medRxiv : the preprint server for health sciences

Leo AP, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang A, Ha CWY, Wong RJ, Minot SS, Andreoletti G, Kosti I, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Lynch SV, Romero R, Tarca AL, Stevenson DK, Aghaeepour N, Golob J, Sirota M

The Associations of Maternal Health Characteristics, Newborn Metabolite Concentrations, and Child Body Mass Index among US Children in the ECHO Program.

Metabolites

Snyder BM, Gebretsadik T, Rohrig NB, Wu P, Dupont WD, Dabelea DM, Fry RC, Lynch SV, McEvoy CT, Paneth NS, Ryckman KK, Gern JE, Hartert TV

The impact of prenatal dog keeping on infant gut microbiota development.

Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology

Panzer AR, Sitarik AR, Fadrosh D, Havstad SL, Jones K, Davidson B, Finazzo S, Wegienka GR, Woodcroft K, Lukacs NW, Levin AM, Ownby DR, Johnson CC, Lynch SV, Zoratti EM

Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research.

medRxiv : the preprint server for health sciences

Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Preterm Birth DREAM Community, Theis KR, Ng S, Lee Li YS, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M

Interactions Between Host Epigenetics and Microbiota: Who Does What to Whom, When and Why?

The Journal of allergy and clinical immunology

Vercelli D, Lynch SV