Susan Lynch, PhD

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



Early-life Nasal Microbiota Dynamics Relate to Longitudinal Respiratory Phenotypes in Urban Children.

The Journal of allergy and clinical immunology

McCauley KE, Durack J, Lynch KV, Fadrosh DW, Fujimura KE, Vundla F, Özçam M, LeBeau P, Caltroni A, Burns P, Tran HT, Bacharier LB, Kattan M, O'Connor GT, Wood RA, Togias A, Boushey HA, Jackson DJ, Gern JE, Lynch SV, National Institute of Allergy and Infectious Diseases-sponsored Childhood Asthma in Urban Settings C

Alteration in the gut microbiome is associated with changes in bone metabolism after laparoscopic sleeve gastrectomy.

Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research

Wu KC, McCauley KE, Lynch SV, Nayak RR, King NJ, Patel S, Kim TY, Condra K, Fadrosh D, Nguyen D, Lin DL, Lynch K, Rogers SJ, Carter JT, Posselt AM, Stewart L, Schafer AL

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research.

Cell reports. Medicine

Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Oskotsky B, 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, De 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 YS, Diaz-Gimeno P, 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

Precocious infant fecal microbiome promotes enterocyte barrier dysfuction, altered neuroendocrine signaling and associates with increased childhood obesity risk.

Gut microbes

Yong GJM, Porsche CE, Sitarik AR, Fujimura KE, McCauley K, Nguyen DT, Levin AM, Woodcroft KJ, Ownby DR, Rundle AG, Johnson CC, Cassidy-Bushrow A, Lynch SV

Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia.

Nature medicine

Montassier E, Kitsios GD, Radder JE, Le Bastard Q, Kelly BJ, Panzer A, Lynch SV, Calfee CS, Dickson RP, Roquilly A