Susan Lynch, PhD

Director, Benioff Center for Microbiome Medicine
Associate Director, Microbiome in Inflammatory Bowel Disease program
Professor
Department of Medicine - Gastroenterology
Primary Thematic Area
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)

+1 415 476-6784

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.

Publications

Clinical translation of microbiome research.

Nature medicine

Gilbert JA, Azad MB, Bäckhed F, Blaser MJ, Byndloss M, Chiu CY, Chu H, Dugas LR, Elinav E, Gibbons SM, Gilbert KE, Henn MR, Ishaq SL, Ley RE, Lynch SV, Segal E, Spector TD, Strandwitz P, Suez J, Tropini C, Whiteson K, Knight R

Early-life wheeze trajectories are associated with distinct asthma transcriptomes later in life.

The Journal of allergy and clinical immunology

Phelan KJ, Roskin KM, Burkle JW, Chang WC, Martin LJ, Biagini JM, Satish L, Haslam DB, Spagna D, Jenkins S, Parmar E, Bacharier LB, Gebretsadik T, Gill M, Gold DR, Jackson DJ, Johnson CC, Lynch SV, McCauley KE, McKennan CG, Miller R, Ober C, Ownby DR, Ryan PH, Schoettler N, Singh S, Visness CM, Altman MC, Gern JE, Khurana Hershey GK, Environmental Influences on Child Health Outcomes–Children’s Respiratory and Environmental Workgroup

VMAP: Vaginal Microbiome Atlas during Pregnancy.

JAMIA open

Parraga-Leo A, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang AS, 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 JL, Sirota M

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

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

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

Seasonal Airway Microbiome and Transcriptome Interactions Promote Childhood Asthma Exacerbations.

The Journal of allergy and clinical immunology

McCauley KE, Flynn K, DiMassa V, LaMere B, Fadrosh DW, Lynch KV, Gill MA, Pongracic JA, Khurana Hershey GK, Kercsmar CM, Liu AH, Johnson CC, Kim H, Kattan M, O'Connor GT, Bacharier LB, Teach SJ, Gergen PJ, Wheatley LM, Togias A, LeBeau P, Calatroni A, Presnell S, Boushey HA, Busse WW, Gern JE, Jackson DJ, Altman MC, Lynch SV, National Institute of Allergy and Infectious Diseases-sponsored Inner-City Asthma Consortium

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

Gut microbiome is associated with multiple sclerosis activity in children.

Annals of clinical and translational neurology

Horton MK, McCauley K, Fadrosh D, Fujimura K, Graves J, Ness J, Wheeler Y, Gorman MP, Benson LA, Weinstock-Guttman B, Waldman A, Rodriguez M, Tillema JM, Krupp L, Belman A, Mar S, Rensel M, Chitnis T, Casper TC, Rose J, Hart J, Shao X, Tremlett H, Lynch SV, Barcellos LF, Waubant E, U.S. Network of Pediatric MS Centers

Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children: a genetic association and gene expression study.

The Lancet. Respiratory medicine

Ober C, McKennan CG, Magnaye KM, Altman MC, Washington C, Stanhope C, Naughton KA, Rosasco MG, Bacharier LB, Billheimer D, Gold DR, Gress L, Hartert T, Havstad S, Khurana Hershey GK, Hallmark B, Hogarth DK, Jackson DJ, Johnson CC, Kattan M, Lemanske RF, Lynch SV, Mendonca EA, Miller RL, Naureckas ET, O'Connor GT, Seroogy CM, Wegienka G, White SR, Wood RA, Wright AL, Zoratti EM, Martinez FD, Ownby D, Nicolae DL, Levin AM, Gern JE, Environmental Influences on Child Health Outcomes-Children's Respiratory Research Workgroup

Bacterial biogeography of adult airways in atopic asthma.

Microbiome

Durack J, Huang YJ, Nariya S, Christian LS, Mark Ansel K, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV, Boushey HA

Future Research Directions in Asthma. An NHLBI Working Group Report.

American journal of respiratory and critical care medicine

Levy BD, Noel PJ, Freemer MM, Cloutier MM, Georas SN, Jarjour NN, Ober C, Woodruff PG, Barnes KC, Bender BG, Camargo CA, Chupp GL, Denlinger LC, Fahy JV, Fitzpatrick AM, Fuhlbrigge A, Gaston BM, Hartert TV, Kolls JK, Lynch SV, Moore WC, Morgan WJ, Nadeau KC, Ownby DR, Solway J, Szefler SJ, Wenzel SE, Wright RJ, Smith RA, Erzurum SC

Widespread colonization of the lung by Tropheryma whipplei in HIV infection.

American journal of respiratory and critical care medicine

Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TB, Flores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SV, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP

Gut dysbiosis in cystic fibrosis.

Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society

Scanlan PD, Buckling A, Kong W, Wild Y, Lynch SV, Harrison F