Susan Lynch, PhD

Director, Benioff Center for Microbiome Medicine
Professor,
Medicine
+1 415 476-6784

Our human microbiome research program focuses on the gastrointestinal and airway microbiomes and their influence on the development and maintenance of chronic inflammatory disease. We study the early-life origins of chronic inflammatory disease and have demonstrated a role for the neonatal gut microbiome and its metabolic products as a predictor of allergic asthma development in childhood. We are also interested in established inflammatory conditions and have shown that distinct microbiota exist in adults with IBD, chronic sinusitus or HIV-infection, which relate to immunologically and pathologically distinct disease endotypes. Our group has pioneered the application of newly developed statistical approaches to the multi-dimensional microbiome data sets developed by next generation sequencing approaches. We have developed and made publicly available custom scripts and novel tools to facilitate such analyses. In addition, we have developed novel ex vivo assays to assess the capacity of human microbiota, specific microbial species or their products to elicit host immune responses ex vivo, providing an objective assessment of their immunomodulatory capacity. I founded and direct the Microbiome Research Core, and am the Associate Director of the Microbiome in Inflammatory Bowel Disease Research Program at UCSF. I have also co-founded and serve as a board member of Siolta Therapeutics, a start-up company at QB3 that focuses on translating our bench-based human microbiome findings into effective therapeutics for prevention or treatment of immune disorders.

Publications: 

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

The human microbiome in the 21st century.

Nature communications

Rackaityte E, Lynch SV

Distinct lung microbiota associate with HIV-associated chronic lung disease in children.

Scientific reports

Bhadriraju S, Fadrosh DW, Shenoy MK, Lin DL, Lynch KV, McCauley K, Ferrand RA, Majonga ED, McHugh G, Huang L, Lynch SV, Metcalfe JZ

Gut Microbial Regulation of Autism Spectrum Disorder Symptoms.

Trends in endocrinology and metabolism: TEM

Panzer AR, Lynch SV

Association between cesarean delivery types and obesity in preadolescence.

International journal of obesity (2005)

Sitarik AR, Havstad SL, Johnson CC, Jones K, Levin AM, Lynch SV, Ownby DR, Rundle AG, Straughen JK, Wegienka G, Woodcroft KJ, Yong GJM, Cassidy-Bushrow AE

Fetal and early postnatal lead exposure measured in teeth associates with infant gut microbiota.

Environment international

Sitarik AR, Arora M, Austin C, Bielak LF, Eggers S, Johnson CC, Lynch SV, Kyun Park S, Hank Wu KH, Yong GJM, Cassidy-Bushrow AE

Distinct associations of sputum and oral microbiota with atopic, immunologic, and clinical features in mild asthma.

The Journal of allergy and clinical immunology

Durack J, Christian LS, Nariya S, Gonzalez J, Bhakta NR, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Peters SP, Rosenberg SR, Sorkness CA, Wechsler ME, Wenzel SE, White SR, Lynch SV, Boushey HA, Huang YJ

Author Correction: Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance.

Nature microbiology

Levan SR, Stamnes KA, Lin DL, Panzer AR, Fukui E, McCauley K, Fujimura KE, McKean M, Ownby DR, Zoratti EM, Boushey HA, Cabana MD, Johnson CC, Lynch SV

Translating the gut microbiome: ready for the clinic?

Nature reviews. Gastroenterology & hepatology

Lynch SV, Ng SC, Shanahan F, Tilg H

Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance.

Nature microbiology

Levan SR, Stamnes KA, Lin DL, Panzer AR, Fukui E, McCauley K, Fujimura KE, McKean M, Ownby DR, Zoratti EM, Boushey HA, Cabana MD, Johnson CC, Lynch SV

Fecal Microbiota Transplantation in Pouchitis: Clinical, Endoscopic, Histologic, and Microbiota Results from a Pilot Study.

Digestive diseases and sciences

Selvig D, Piceno Y, Terdiman J, Zydek M, Umetsu SE, Balitzer D, Fadrosh D, Lynch K, Lamere B, Leith T, Kassam Z, Beck K, Lewin S, Ma A, Somsouk M, Lynch SV, El-Nachef N

A20 in dendritic cells restrains intestinal anti-bacterial peptide expression and preserves commensal homeostasis.

PloS one

Talpin A, Kattah MG, Advincula R, Fadrosh D, Lynch K, LaMere B, Fujimura KE, Nagalingam NA, Malynn BA, Lynch SV, Ma A

Author Correction: Differences in the fecal microbiota of neonates born at home or in the hospital.

Scientific reports

Combellick JL, Shin H, Shin D, Cai Y, Hagan H, Lacher C, Lin DL, McCauley K, Lynch SV, Dominguez-Bello MG

Distinct Nasal Airway Bacterial Microbiota Differentially Relate to Exacerbation in Pediatric Asthma.

The Journal of allergy and clinical immunology

McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ, Lynch SV

Fecal microbiota transplant for Crohn disease: A study evaluating safety, efficacy, and microbiome profile.

United European gastroenterology journal

Gutin L, Piceno Y, Fadrosh D, Lynch K, Zydek M, Kassam Z, LaMere B, Terdiman J, Ma A, Somsouk M, Lynch S, El-Nachef N

Gut microbiota in HIV-pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction.

Microbiome

Shenoy MK, Fadrosh DW, Lin DL, Worodria W, Byanyima P, Musisi E, Kaswabuli S, Zawedde J, Sanyu I, Chang E, Fong S, McCauley K, Davis JL, Huang L, Lynch SV

Enteric Virome and Bacterial Microbiota in Children With Ulcerative Colitis and Crohn Disease.

Journal of pediatric gastroenterology and nutrition

Fernandes MA, Verstraete SG, Phan TG, Deng X, Stekol E, LaMere B, Lynch SV, Heyman MB, Delwart E

Longitudinal Phenotypes of Respiratory Health in a High-Risk Urban Birth Cohort.

American journal of respiratory and critical care medicine

Bacharier LB, Beigelman A, Calatroni A, Jackson DJ, Gergen PJ, O'Connor GT, Kattan M, Wood RA, Sandel MT, Lynch SV, Fujimura KE, Fadrosh DW, Santee CA, Boushey H, Visness CM, Gern JE

Gut Microbial Metabolism and Nonalcoholic Fatty Liver Disease.

Hepatology communications

Sharpton SR, Yong GJM, Terrault NA, Lynch SV

Rules of engagement in the gut microbiome.

Nature medicine

Rackaityte E, Lynch SV

Differences in the fecal microbiota of neonates born at home or in the hospital.

Scientific reports

Combellick JL, Shin H, Shin D, Cai Y, Hagan H, Lacher C, Lin DL, McCauley K, Lynch SV, Dominguez-Bello MG

The gut microbiome: Relationships with disease and opportunities for therapy.

The Journal of experimental medicine

Durack J, Lynch SV

Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization.

Microbiome

Chang HW, Yan D, Singh R, Liu J, Lu X, Ucmak D, Lee K, Afifi L, Fadrosh D, Leech J, Vasquez KS, Lowe MM, Rosenblum MD, Scharschmidt TC, Lynch SV, Liao W

Bacterial biogeography of adult airways in atopic asthma.

Microbiome

Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, 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

Current understanding of the human microbiome.

Nature medicine

Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R

Dynamics of Bacterial Colonization With Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis During Symptomatic and Asymptomatic Viral Upper Respiratory Tract Infection.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

DeMuri GP, Gern JE, Eickhoff JC, Lynch SV, Wald ER

Lung Microbiota Is Related to Smoking Status and to Development of Acute Respiratory Distress Syndrome in Critically Ill Trauma Patients.

American journal of respiratory and critical care medicine

Panzer AR, Lynch SV, Langelier C, Christie JD, McCauley K, Nelson M, Cheung CK, Benowitz NL, Cohen MJ, Calfee CS

Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation.

Nature communications

Durack J, Kimes NE, Lin DL, Rauch M, McKean M, McCauley K, Panzer AR, Mar JS, Cabana MD, Lynch SV

Role of the lung microbiome in HIV pathogenesis.

Current opinion in HIV and AIDS

Shenoy MK, Lynch SV

Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury.

Trauma surgery & acute care open

Howard BM, Kornblith LZ, Christie SA, Conroy AS, Nelson MF, Campion EM, Callcut RA, Calfee CS, Lamere BJ, Fadrosh DW, Lynch S, Cohen MJ

Early-life home environment and risk of asthma among inner-city children.

The Journal of allergy and clinical immunology

O'Connor GT, Lynch SV, Bloomberg GR, Kattan M, Wood RA, Gergen PJ, Jaffee KF, Calatroni A, Bacharier LB, Beigelman A, Sandel MT, Johnson CC, Faruqi A, Santee C, Fujimura KE, Fadrosh D, Boushey H, Visness CM, Gern JE

Breast Milk Transforming Growth Factor ß Is Associated With Neonatal Gut Microbial Composition.

Journal of pediatric gastroenterology and nutrition

Sitarik AR, Bobbitt KR, Havstad SL, Fujimura KE, Levin AM, Zoratti EM, Kim H, Woodcroft KJ, Wegienka G, Ownby DR, Joseph CLM, Lynch SV, Johnson CC

Early Probiotic Supplementation for Eczema and Asthma Prevention: A Randomized Controlled Trial.

Pediatrics

Cabana MD, McKean M, Caughey AB, Fong L, Lynch S, Wong A, Leong R, Boushey HA, Hilton JF

Limited engraftment of donor microbiome via one-time fecal microbial transplantation in treated HIV-infected individuals.

Gut microbes

Vujkovic-Cvijin I, Rutishauser RL, Pao M, Hunt PW, Lynch SV, McCune JM, Somsouk M

Promotion of Epithelial Barrier Integrity Via Probiotic-derived Products.

Journal of pediatric gastroenterology and nutrition

Durack J, Lynch SV

Immune Response and Mortality Risk Relate to Distinct Lung Microbiomes in Patients with HIV and Pneumonia.

American journal of respiratory and critical care medicine

Shenoy MK, Iwai S, Lin DL, Worodria W, Ayakaka I, Byanyima P, Kaswabuli S, Fong S, Stone S, Chang E, Davis JL, Faruqi AA, Segal MR, Huang L, Lynch SV

The Human Intestinal Microbiome in Health and Disease.

The New England journal of medicine

Lynch SV, Pedersen O

The Lung Microbiome and Airway Disease.

Annals of the American Thoracic Society

Lynch SV

Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment.

The Journal of allergy and clinical immunology

Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA, Huang YJ

Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls.

BMC neurology

Tremlett H, Fadrosh DW, Faruqi AA, Hart J, Roalstad S, Graves J, Spencer CM, Lynch SV, Zamvil SS, Waubant E

Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation.

Nature medicine

Fujimura KE, Sitarik AR, Havstad S, Lin DL, Levan S, Fadrosh D, Panzer AR, LaMere B, Rackaityte E, Lukacs NW, Wegienka G, Boushey HA, Ownby DR, Zoratti EM, Levin AM, Johnson CC, Lynch SV

Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity.

Scientific reports

Levin AM, Sitarik AR, Havstad SL, Fujimura KE, Wegienka G, Cassidy-Bushrow AE, Kim H, Zoratti EM, Lukacs NW, Boushey HA, Ownby DR, Lynch SV, Johnson CC

Dual epithelial and immune cell function of Dvl1 regulates gut microbiota composition and intestinal homeostasis.

JCI insight

Belinson H, Savage AK, Fadrosh D, Kuo YM, Lin D, Valladares R, Nusse Y, Wynshaw-Boris A, Lynch SV, Locksley RM, Klein OD

Airway Microbiota and the Implications of Dysbiosis in Asthma.

Current allergy and asthma reports

Durack J, Boushey HA, Lynch SV

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis.

Microbiome

Santee CA, Nagalingam NA, Faruqi AA, DeMuri GP, Gern JE, Wald ER, Lynch SV

The microbiome and development of allergic disease.

Current opinion in allergy and clinical immunology

Lynch SV, Boushey HA

Gut Microbiota and Allergic Disease. New Insights.

Annals of the American Thoracic Society

Lynch SV

Race-specific Association of Caesarean-Section Delivery with Body Size at Age 2 Years.

Ethnicity & disease

Cassidy-Bushrow AE, Wegienka G, Havstad S, Levin AM, Lynch SV, Ownby DR, Rundle AG, Woodcroft KJ, Zoratti EM, Johnson CC

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

Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.

American journal of respiratory and critical care medicine

Beck JM, Schloss PD, Venkataraman A, Twigg H, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, Frank I, Ghedin E, Huang L, Lynch SV, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB

Gut-Resident Lactobacillus Abundance Associates with IDO1 Inhibition and Th17 Dynamics in SIV-Infected Macaques.

Cell reports

Vujkovic-Cvijin I, Swainson LA, Chu SN, Ortiz AM, Santee CA, Petriello A, Dunham RM, Fadrosh DW, Lin DL, Faruqi AA, Huang Y, Apetrei C, Pandrea I, Hecht FM, Pilcher CD, Klatt NR, Brenchley JM, Lynch SV, McCune JM

The airway microbiome in patients with severe asthma: Associations with disease features and severity.

The Journal of allergy and clinical immunology

Huang YJ, Nariya S, Harris JM, Lynch SV, Choy DF, Arron JR, Boushey H

Influence and effect of the human microbiome in allergy and asthma.

Current opinion in rheumatology

Panzer AR, Lynch SV

Does pet-keeping modify the association of delivery mode with offspring body size?

Maternal and child health journal

Cassidy-Bushrow AE, Wegienka G, Havstad S, Levin AM, Lynch SV, Ownby DR, Rundle AG, Woodcroft KJ, Zoratti EM, Johnson CC

Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens.

PloS one

Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch SV

Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems.

Science translational medicine

Ardeshir A, Narayan NR, Méndez-Lagares G, Lu D, Rauch M, Huang Y, Van Rompay KK, Lynch SV, Hartigan-O'Connor DJ

Fecal microbial therapy: promises and pitfalls.

Journal of pediatric gastroenterology and nutrition

Merenstein D, El-Nachef N, Lynch SV

Effects of early-life exposure to allergens and bacteria on recurrent wheeze and atopy in urban children.

The Journal of allergy and clinical immunology

Lynch SV, Wood RA, Boushey H, Bacharier LB, Bloomberg GR, Kattan M, O'Connor GT, Sandel MT, Calatroni A, Matsui E, Johnson CC, Lynn H, Visness CM, Jaffee KF, Gergen PJ, Gold DR, Wright RJ, Fujimura K, Rauch M, Busse WW, Gern JE

Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease.

Journal of clinical microbiology

Huang YJ, Sethi S, Murphy T, Nariya S, Boushey HA, Lynch SV

The lung microbiome of Ugandan HIV-infected pneumonia patients is compositionally and functionally distinct from that of San Franciscan patients.

PloS one

Iwai S, Huang D, Fong S, Jarlsberg LG, Worodria W, Yoo S, Cattamanchi A, Davis JL, Kaswabuli S, Segal M, Huang L, Lynch SV

Viruses and microbiome alterations.

Annals of the American Thoracic Society

Lynch SV

House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection.

Proceedings of the National Academy of Sciences of the United States of America

Fujimura KE, Demoor T, Rauch M, Faruqi AA, Jang S, Johnson CC, Boushey HA, Zoratti E, Ownby D, Lukacs NW, Lynch SV

Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism.

Science translational medicine

Vujkovic-Cvijin I, Dunham RM, Iwai S, Maher MC, Albright RG, Broadhurst MJ, Hernandez RD, Lederman MM, Huang Y, Somsouk M, Deeks SG, Hunt PW, Lynch SV, McCune JM

Probiotic strategies for treatment of respiratory diseases.

Trends in microbiology

Nagalingam NA, Cope EK, Lynch SV

Comparison of the respiratory microbiome in healthy nonsmokers and smokers.

American journal of respiratory and critical care medicine

Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM

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

The cystic fibrosis airway microbiome.

Cold Spring Harbor perspectives in medicine

Lynch SV, Bruce KD

Cystic fibrosis transmembrane conductance regulator knockout mice exhibit aberrant gastrointestinal microbiota.

Gut microbes

Lynch SV, Goldfarb KC, Wild YK, Kong W, De Lisle RC, Brodie EL

Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis.

Science translational medicine

Abreu NA, Nagalingam NA, Song Y, Roediger FC, Pletcher SD, Goldberg AN, Lynch SV

Development of a standardized approach for environmental microbiota investigations related to asthma development in children.

Journal of microbiological methods

Fujimura KE, Rauch M, Matsui E, Iwai S, Calatroni A, Lynn H, Mitchell H, Johnson CC, Gern JE, Togias A, Boushey HA, Kennedy S, Lynch SV

Oral and airway microbiota in HIV-infected pneumonia patients.

Journal of clinical microbiology

Iwai S, Fei M, Huang D, Fong S, Subramanian A, Grieco K, Lynch SV, Huang L

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

From microbe to microbiota: considering microbial community composition in infections and airway diseases.

American journal of respiratory and critical care medicine

Huang YJ, Lynch SV, Wiener-Kronish JP

Pseudomonas aeruginosa biofilm-associated homoserine lactone C12 rapidly activates apoptosis in airway epithelia.

Cellular microbiology

Schwarzer C, Fu Z, Patanwala M, Hum L, Lopez-Guzman M, Illek B, Kong W, Lynch SV, Machen TE

Significance of the microbiome in obstructive lung disease.

Thorax

Han MK, Huang YJ, Lipuma JJ, Boushey HA, Boucher RC, Cookson WO, Curtis JL, Erb-Downward J, Lynch SV, Sethi S, Toews GB, Young VB, Wolfgang MC, Huffnagle GB, Martinez FJ

Future directions in early cystic fibrosis lung disease research: an NHLBI workshop report.

American journal of respiratory and critical care medicine

Ramsey BW, Banks-Schlegel S, Accurso FJ, Boucher RC, Cutting GR, Engelhardt JF, Guggino WB, Karp CL, Knowles MR, Kolls JK, LiPuma JJ, Lynch S, McCray PB, Rubenstein RC, Singh PK, Sorscher E, Welsh M

PcrV antibody-antibiotic combination improves survival in Pseudomonas aeruginosa-infected mice.

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

Song Y, Baer M, Srinivasan R, Lima J, Yarranton G, Bebbington C, Lynch SV

The potential for probiotic manipulation of the gastrointestinal microbiome.

Current opinion in biotechnology

Rauch M, Lynch SV

Strain-dependent induction of neutrophil histamine production and cell death by Pseudomonas aeruginosa.

Journal of leukocyte biology

Xu X, Zhang H, Song Y, Lynch SV, Lowell CA, Wiener-Kronish JP, Caughey GH

Role of the microbiota in inflammatory bowel diseases.

Inflammatory bowel diseases

Nagalingam NA, Lynch SV

Effect of prenatal indoor pet exposure on the trajectory of total IgE levels in early childhood.

The Journal of allergy and clinical immunology

Havstad S, Wegienka G, Zoratti EM, Lynch SV, Boushey HA, Nicholas C, Ownby DR, Johnson CC

Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.

Gastroenterology

Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ, Versalovic J

Differences in biofilm formation and antimicrobial resistance of Pseudomonas aeruginosa isolated from airways of mechanically ventilated patients and cystic fibrosis patients.

International journal of antimicrobial agents

Fricks-Lima J, Hendrickson CM, Allgaier M, Zhuo H, Wiener-Kronish JP, Lynch SV, Yang K

Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma.

The Journal of allergy and clinical immunology

Huang YJ, Nelson CE, Brodie EL, Desantis TZ, Baek MS, Liu J, Woyke T, Allgaier M, Bristow J, Wiener-Kronish JP, Sutherland ER, King TS, Icitovic N, Martin RJ, Calhoun WJ, Castro M, Denlinger LC, Dimango E, Kraft M, Peters SP, Wasserman SI, Wechsler ME, Boushey HA, Lynch SV

Man's best friend? The effect of pet ownership on house dust microbial communities.

The Journal of allergy and clinical immunology

Fujimura KE, Johnson CC, Ownby DR, Cox MJ, Brodie EL, Havstad SL, Zoratti EM, Woodcroft KJ, Bobbitt KR, Wegienka G, Boushey HA, Lynch SV

Nucleic acid extraction efficiency and bacterial recovery from maxillary sinus mucosal samples obtained by brushing or biopsy.

American journal of rhinology & allergy

Roediger FC, Slusher NA, Allgaier S, Cox MJ, Pletcher SD, Goldberg AN, Lynch SV

Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients.

PloS one

Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, Karaoz U, Andersen GL, Brown R, Fujimura KE, Wu B, Tran D, Koff J, Kleinhenz ME, Nielson D, Brodie EL, Lynch SV

Comparative analyses of the bacterial microbiota of the human nostril and oropharynx.

mBio

Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R

Guide to designing, conducting, publishing and communicating results of clinical studies involving probiotic applications in human participants.

Gut microbes

Shane AL, Cabana MD, Vidry S, Merenstein D, Hummelen R, Ellis CL, Heimbach JT, Hempel S, Lynch SV, Sanders ME, Tancredi DJ

Secretion of Pseudomonas aeruginosa type III cytotoxins is dependent on pseudomonas quinolone signal concentration.

Microbial pathogenesis

Singh G, Wu B, Baek MS, Camargo A, Nguyen A, Slusher NA, Srinivasan R, Wiener-Kronish JP, Lynch SV

Role of the gut microbiota in defining human health.

Expert review of anti-infective therapy

Fujimura KE, Slusher NA, Cabana MD, Lynch SV

Polymorphisms in the Pseudomonas aeruginosa type III secretion protein, PcrV - implications for anti-PcrV immunotherapy.

Microbial pathogenesis

Lynch SV, Flanagan JL, Sawa T, Fang A, Baek MS, Rubio-Mills A, Ajayi T, Yanagihara K, Hirakata Y, Kohno S, Misset B, Nguyen JC, Wiener-Kronish JP

Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa.

Environmental microbiology

Klepac-Ceraj V, Lemon KP, Martin TR, Allgaier M, Kembel SW, Knapp AA, Lory S, Brodie EL, Lynch SV, Bohannan BJ, Green JL, Maurer BA, Kolter R

A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations.

Omics : a journal of integrative biology

Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV

Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome.

PloS one

Cox MJ, Huang YJ, Fujimura KE, Liu JT, McKean M, Boushey HA, Segal MR, Brodie EL, Cabana MD, Lynch SV

Induction of intestinal Th17 cells by segmented filamentous bacteria.

Cell

Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, Wei D, Goldfarb KC, Santee CA, Lynch SV, Tanoue T, Imaoka A, Itoh K, Takeda K, Umesaki Y, Honda K, Littman DR

Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays.

Infection and immunity

Montor WR, Huang J, Hu Y, Hainsworth E, Lynch S, Kronish JW, Ordonez CL, Logvinenko T, Lory S, LaBaer J

Matrix metalloproteases in bronchoalveolar lavage fluid of patients with type III Pseudomonas aeruginosa pneumonia.

The Journal of infection

El-Solh AA, Amsterdam D, Alhajhusain A, Akinnusi ME, Saliba RG, Lynch SV, Wiener-Kronish JP

Novel strategies to combat bacterial virulence.

Current opinion in critical care

Lynch SV, Wiener-Kronish JP

Increased mortality of ventilated patients with endotracheal Pseudomonas aeruginosa without clinical signs of infection.

Critical care medicine

Zhuo H, Yang K, Lynch SV, Dotson RH, Glidden DV, Singh G, Webb WR, Elicker BM, Garcia O, Brown R, Sawa Y, Misset B, Wiener-Kronish JP

Role of small GTPases and alphavbeta5 integrin in Pseudomonas aeruginosa-induced increase in lung endothelial permeability.

American journal of respiratory cell and molecular biology

Ganter MT, Roux J, Su G, Lynch SV, Deutschman CS, Weiss YG, Christiaans SC, Myazawa B, Kipnis E, Wiener-Kronish JP, Howard M, Pittet JF

Persistent infection with Pseudomonas aeruginosa in ventilator-associated pneumonia.

American journal of respiratory and critical care medicine

El Solh AA, Akinnusi ME, Wiener-Kronish JP, Lynch SV, Pineda LA, Szarpa K

Role of integrin alphav beta6 in acute lung injury induced by Pseudomonas aeruginosa.

Infection and immunity

Song Y, Pittet JF, Huang X, He H, Lynch SV, Violette SM, Weinreb PH, Horan GS, Carmago A, Sawa Y, Bernstein XL, Wiener-Kronish JP

Comparison of type III secretion system virulence among fluoroquinolone-susceptible and -resistant clinical isolates of Pseudomonas aeruginosa.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases

Wong-Beringer A, Wiener-Kronish J, Lynch S, Flanagan J

Role of the rapA gene in controlling antibiotic resistance of Escherichia coli biofilms.

Antimicrobial agents and chemotherapy

Lynch SV, Dixon L, Benoit MR, Brodie EL, Keyhan M, Hu P, Ackerley DF, Andersen GL, Matin A

Microbial manipulation of immune function for asthma prevention: inferences from clinical trials.

Proceedings of the American Thoracic Society

Yoo J, Tcheurekdjian H, Lynch SV, Cabana M, Boushey HA

Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa.

Journal of clinical microbiology

Flanagan JL, Brodie EL, Weng L, Lynch SV, Garcia O, Brown R, Hugenholtz P, DeSantis TZ, Andersen GL, Wiener-Kronish JP, Bristow J

Alveolar hemostasis in patients with species-specific bacterial-mediated ventilator-associated pneumonia.

Critical care medicine

Song Y, Wiener-Kronish JP, Flanagan J, Lynch SV

Increased plasminogen activator inhibitor-1 concentrations in bronchoalveolar lavage fluids are associated with increased mortality in a cohort of patients with Pseudomonas aeruginosa.

Anesthesiology

Song Y, Lynch SV, Flanagan J, Zhuo H, Tom W, Dotson RH, Baek MS, Rubio-Mills A, Singh G, Kipnis E, Glidden D, Brown R, Garcia O, Wiener-Kronish JP

Presence or absence of lipopolysaccharide O antigens affects type III secretion by Pseudomonas aeruginosa.

Journal of bacteriology

Augustin DK, Song Y, Baek MS, Sawa Y, Singh G, Taylor B, Rubio-Mills A, Flanagan JL, Wiener-Kronish JP, Lynch SV

Escherichia coli biofilms formed under low-shear modeled microgravity in a ground-based system.

Applied and environmental microbiology

Lynch SV, Mukundakrishnan K, Benoit MR, Ayyaswamy PS, Matin A

Effect of chromate stress on Escherichia coli K-12.

Journal of bacteriology

Ackerley DF, Barak Y, Lynch SV, Curtin J, Matin A

New enzyme for reductive cancer chemotherapy, YieF, and its improvement by directed evolution.

Molecular cancer therapeutics

Barak Y, Thorne SH, Ackerley DF, Lynch SV, Contag CH, Matin A

ChrR, a soluble quinone reductase of Pseudomonas putida that defends against H2O2.

The Journal of biological chemistry

Gonzalez CF, Ackerley DF, Lynch SV, Matin A

Analysis and manipulation of amphotericin biosynthetic genes by means of modified phage KC515 transduction techniques.

Gene

Carmody M, Byrne B, Murphy B, Breen C, Lynch S, Flood E, Finnan S, Caffrey P

Alanine dehydrogenase from the psychrophilic bacterium strain PA-43: overexpression, molecular characterization, and sequence analysis.

Extremophiles : life under extreme conditions

Irwin JA, Lynch SV, Coughlan S, Baker PJ, Gudmundsson HM, Alfredsson GA, Rice DW, Engel PC

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