Susan Lynch, PhD
Professor
Medicine
School of Medicine

Taking a "populations to molecules" approach we leverage the microbiome to determine the origins of childhood allergy and asthma and the early life molecular and cellular drivers of immune dysfunction that lead to childhood disease development. We also leverage human population studies and clinical trials to gain insights into the role of the gut microbiome in inflammatory bowel disease. Our studies allow us to develop rationally designed microbial therapeutics, leading to the founding of Siolta Therapeutics which is currently testing a lead product developed in our lab for the prevention of childhood allergy and asthma.

• Early-life nasal microbiota dynamics relate to longitudinal respiratory phenotypes in urban children.
  The Journal of allergy and clinical immunology 2024 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, …
• 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 2024 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 2023 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, …
• Precocious infant fecal microbiome promotes enterocyte barrier dysfuction, altered neuroendocrine signaling and associates with increased childhood obesity risk.
  Gut microbes 2023 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 2023 Montassier E, Kitsios GD, Radder JE, Le Bastard Q, Kelly BJ, Panzer A, Lynch SV, Calfee CS, Dickson RP, Roquilly A
• Short-chain fatty acid producers in the gut are associated with pediatric multiple sclerosis onset.
  Annals of clinical and translational neurology 2023 Schoeps VA, Zhou X, Horton MK, Zhu F, McCauley KE, Nasr Z, Virupakshaiah A, Gorman MP, Benson LA, Weinstock-Guttman B, Waldman A, Banwell BL, Bar-Or A, Marrie RA, van Domselaar G, O'Mahony J, Mirza AI…
• Contributions of the early-life microbiome to childhood atopy and asthma development.
  Seminars in immunology 2023 Steininger H, Moltzau-Anderson J, Lynch SV
• Progression of C-reactive protein from birth through preadolescence varies by mode of delivery.
  Frontiers in pediatrics 2023 Sitarik AR, Johnson CC, Levin AM, Lynch SV, Ownby DR, Rundle AG, Straughen JK, Wegienka G, Woodcroft KJ, Cassidy-Bushrow AE
• Mild SARS-CoV-2 infection results in long-lasting microbiota instability.
  mBio 2023 Upadhyay V, Suryawanshi RK, Tasoff P, McCavitt-Malvido M, Kumar RG, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha CWY, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ
• Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research.
  medRxiv : the preprint server for health sciences 2023 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, …
• VMAP: Vaginal Microbiome Atlas During Pregnancy.
  medRxiv : the preprint server for health sciences 2023 Parraga-Leo A, 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, …
• The Associations of Maternal Health Characteristics, Newborn Metabolite Concentrations, and Child Body Mass Index among US Children in the ECHO Program.
  Metabolites 2023 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 2023 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
• Interactions between host epigenetics and microbiota: Who does what to whom, when, and why?
  The Journal of allergy and clinical immunology 2023 Vercelli D, Lynch SV
• Gluten Degradation by the Gut Microbiota of Ulcerative Colitis Patients.
  Microorganisms 2022 Harringer EOS, Durack J, Piceno Y, Andersen V, Lynch SV
• Complete Genome Sequence of Lactobacillus johnsonii MR1, Isolated from a BALB/c Mouse Cecum.
  Microbiology resource announcements 2022 Ravi K, Rauch M, Lynch SV, Lukacs NW, Huffnagle GB
• Mild SARS-CoV-2 infection results in long-lasting microbiota instability.
  bioRxiv : the preprint server for biology 2022 Upadhyay V, Suryawanshi R, Tasoff P, McCavitt-Malvido M, Kumar GR, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha C, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ
• Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy.
  Cell reports. Medicine 2022 McCauley KE, Rackaityte E, LaMere B, Fadrosh DW, Fujimura KE, Panzer AR, Lin DL, Lynch KV, Halkias J, Mendoza VF, Burt TD, Bendixsen C, Barnes K, Kim H, Jones K, Ownby DR, Johnson CC, Seroogy CM, Gern…
• Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome.
  Investigative ophthalmology & visual science 2022 Chang CJ, Somohano K, Zemsky C, Uhlemann AC, Liebmann J, Cioffi GA, Al-Aswad LA, Lynch SV, Winn BJ
• Gut Bifidobacteria enrichment following oral Lactobacillus-supplementation is associated with clinical improvements in children with cystic fibrosis.
  BMC pulmonary medicine 2022 Ray KJ, Santee C, McCauley K, Panzer AR, Lynch SV
• Maternal prenatal immunity, neonatal trained immunity, and early airway microbiota shape childhood asthma development.
  Allergy 2022 DeVries A, McCauley K, Fadrosh D, Fujimura KE, Stern DA, Lynch SV, Vercelli D
• Microbiome-Immune Interactions in Allergy and Asthma.
  The journal of allergy and clinical immunology. In practice 2022 Huang YJ, Porsche C, Kozik AJ, Lynch SV
• Intestinal inflammation alters the antigen-specific immune response to a skin commensal.
  Cell reports 2022 Merana GR, Dwyer LR, Dhariwala MO, Weckel A, Gonzalez JR, Okoro JN, Cohen JN, Tamaki CM, Han J, Tasoff P, Palacios-Calderon Y, Ha CWY, Lynch SV, Segre JA, Kong HH, Kattah MG, Ma A, Scharschmidt TC
• Early-life gut microbiota and attention deficit hyperactivity disorder in preadolescents.
  Pediatric research 2022 Cassidy-Bushrow AE, Sitarik AR, Johnson CC, Johnson-Hooper TM, Kassem Z, Levin AM, Lynch SV, Ownby DR, Phillips JM, Yong GJM, Wegienka G, Straughen JK
• Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis.
  Scientific reports 2022 Smith BJ, Piceno Y, Zydek M, Zhang B, Syriani LA, Terdiman JP, Kassam Z, Ma A, Lynch SV, Pollard KS, El-Nachef N
• Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study.
  The Lancet. Microbe 2022 Spottiswoode N, Bloomstein JD, Caldera S, Sessolo A, McCauley K, Byanyima P, Zawedde J, Kalantar K, Kaswabuli S, Rutishauser RL, Lieng MK, Davis JL, Moore J, Jan A, Iwai S, Shenoy M, Sanyu I, DeRisi …
• Prebiotic to Improve Calcium Absorption in Postmenopausal Women After Gastric Bypass: A Randomized Controlled Trial.
  The Journal of clinical endocrinology and metabolism 2022 Wu KC, Cao S, Weaver CM, King NJ, Patel S, Kingman H, Sellmeyer DE, McCauley K, Li D, Lynch SV, Kim TY, Black DM, Shafer MM, Özçam M, Lin DL, Rogers SJ, Stewart L, Carter JT, Posselt AM, Schafer AL
• Seasonal airway microbiome and transcriptome interactions promote childhood asthma exacerbations.
  The Journal of allergy and clinical immunology 2022 McCauley KE, Flynn K, Calatroni A, 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, …
• Associations of physical activity with gut microbiota in pre-adolescent children.
  Physical activity and nutrition 2021 Santarossa S, Sitarik AR, Johnson CC, Li J, Lynch SV, Ownby DR, Ramirez A, Yong GL, Cassidy-Bushrow AE
• Moraxella-dominated pediatric nasopharyngeal microbiota associate with upper respiratory infection and sinusitis.
  PloS one 2021 McCauley KE, DeMuri G, Lynch K, Fadrosh DW, Santee C, Nagalingam NN, Wald ER, Lynch SV
• Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.
  medRxiv : the preprint server for health sciences 2021 Tsitsiklis A, Zha BS, Byrne A, DeVoe C, Rackaityte E, Levan S, Sunshine S, Mick E, Ghale R, Love C, Tarashansky AJ, Pisco A, Albright J, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, …
• Human gut bacterial metabolism drives Th17 activation and colitis.
  Cell host & microbe 2021 Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ
• Maternal gut microbiome regulates immunity to RSV infection in offspring.
  The Journal of experimental medicine 2021 Fonseca W, Malinczak CA, Fujimura K, Li D, McCauley K, Li J, Best SKK, Zhu D, Rasky AJ, Johnson CC, Bermick J, Zoratti EM, Ownby D, Lynch SV, Lukacs NW, Ptaschinski C
• The oral microbiome: Role of key organisms and complex networks in oral health and disease.
  Periodontology 2000 2021 Sedghi L, DiMassa V, Harrington A, Lynch SV, Kapila YL
• Gut microbiome is associated with multiple sclerosis activity in children.
  Annals of clinical and translational neurology 2021 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,…
• Microscopic Colitis Patients Possess a Perturbed and Inflammatory Gut Microbiota.
  Digestive diseases and sciences 2021 Hertz S, Durack J, Kirk KF, Nielsen HL, Lin DL, Fadrosh D, Lynch K, Piceno Y, Thorlacius-Ussing O, Nielsen H, Lynch SV
• Fungus fuels mucosal wounds in Crohn's disease.
  Immunity 2021 Magnaye KM, Lynch SV
• Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.
  Research square 2021 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…
• Microbiota, Epigenetics, and Trained Immunity. Convergent Drivers and Mediators of the Asthma Trajectory from Pregnancy to Childhood.
  American journal of respiratory and critical care medicine 2021 Lynch SV, Vercelli D
• Maternal and cord blood vitamin D level and the infant gut microbiota in a birth cohort study.
  Maternal health, neonatology and perinatology 2020 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 2020 Rackaityte E, Lynch SV
• Distinct lung microbiota associate with HIV-associated chronic lung disease in children.
  Scientific reports 2020 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 2020 Panzer AR, Lynch SV
• Association between cesarean delivery types and obesity in preadolescence.
  International journal of obesity (2005) 2020 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 2020 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
• 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 2020 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, …
• Distinct associations of sputum and oral microbiota with atopic, immunologic, and clinical features in mild asthma.
  The Journal of allergy and clinical immunology 2020 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…
• 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 2019 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 2019 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 2019 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 2019 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 2019 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 2019 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 microbiotas differentially relate to exacerbation in pediatric patients with asthma.
  The Journal of allergy and clinical immunology 2019 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 …
• Community ecology as a framework for human microbiome research.
  Nature medicine 2019 Gilbert JA, Lynch SV
• Fecal microbiota transplant for Crohn disease: A study evaluating safety, efficacy, and microbiome profile.
  United European gastroenterology journal 2019 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 2019 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 2019 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 2019 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, NIAID sponsored …
• Gut Microbial Metabolism and Nonalcoholic Fatty Liver Disease.
  Hepatology communications 2018 Sharpton SR, Yong GJM, Terrault NA, Lynch SV
• Rules of engagement in the gut microbiome.
  Nature medicine 2018 Rackaityte E, Lynch SV
• Differences in the fecal microbiota of neonates born at home or in the hospital.
  Scientific reports 2018 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 2018 Durack J, Lynch SV
• Motility and biofilm formation of the emerging gastrointestinal pathogen Campylobacter concisus differs under microaerophilic and anaerobic environments.
  Gut microbes 2018 Ovesen S, Durack J, Kirk KF, Nielsen HL, Nielsen H, Lynch SV
• Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization.
  Microbiome 2018 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 2018 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, …
• Heterogeneity of Microbiota Dysbiosis in Chronic Rhinosinusitis: Potential Clinical Implications and Microbial Community Mechanisms Contributing to Sinonasal Inflammation.
  Frontiers in cellular and infection microbiology 2018 Lee K, Pletcher SD, Lynch SV, Goldberg AN, Cope EK
• Current understanding of the human microbiome.
  Nature medicine 2018 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 2018 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 2018 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 2018 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 2018 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 2017 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 2017 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, …
• Breast Milk Transforming Growth Factor β Is Associated With Neonatal Gut Microbial Composition.
  Journal of pediatric gastroenterology and nutrition 2017 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 2017 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 2017 Vujkovic-Cvijin I, Rutishauser RL, Pao M, Hunt PW, Lynch SV, McCune JM, Somsouk M
• Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences.
  Microbiome 2017 Cope EK, Goldberg AN, Pletcher SD, Lynch SV
• Promotion of Epithelial Barrier Integrity Via Probiotic-derived Products.
  Journal of pediatric gastroenterology and nutrition 2017 Durack J, Lynch SV
• The Lung Microbiome and Airway Disease.
  Annals of the American Thoracic Society 2016 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 2016 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, …
• Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls.
  BMC neurology 2016 Tremlett H, Fadrosh DW, Faruqi AA, Hart J, Roalstad S, Graves J, Spencer CM, Lynch SV, Zamvil SS, Waubant E, US Network of Pediatric MS Centers
• A chronic rhinosinusitis-derived isolate of Pseudomonas aeruginosa induces acute and pervasive effects on the murine upper airway microbiome and host immune response.
  International forum of allergy & rhinology 2016 Cope EK, Goldberg AN, Pletcher SD, Lynch SV
• Dual epithelial and immune cell function of Dvl1 regulates gut microbiota composition and intestinal homeostasis.
  JCI insight 2016 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 2016 Durack J, Boushey HA, Lynch SV
• Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis.
  Microbiome 2016 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 2016 Lynch SV, Boushey HA
• Gut Microbiota and Allergic Disease. New Insights.
  Annals of the American Thoracic Society 2016 Lynch SV
• Race-specific Association of Caesarean-Section Delivery with Body Size at Age 2 Years.
  Ethnicity & disease 2016 Cassidy-Bushrow AE, Wegienka G, Havstad S, Levin AM, Lynch SV, Ownby DR, Rundle AG, Woodcroft KJ, Zoratti EM, Johnson CC
• Clinical Features, Virus Identification, and Sinusitis as a Complication of Upper Respiratory Tract Illness in Children Ages 4-7 Years.
  The Journal of pediatrics 2016 DeMuri GP, Gern JE, Moyer SC, Lindstrom MJ, Lynch SV, Wald ER
• The airway microbiome in patients with severe asthma: Associations with disease features and severity.
  The Journal of allergy and clinical immunology 2015 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 2015 Panzer AR, Lynch SV
• Does pet-keeping modify the association of delivery mode with offspring body size?
  Maternal and child health journal 2015 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 2015 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 2014 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 2014 Merenstein D, El-Nachef N, Lynch SV
• Amelioration of DSS-induced murine colitis by VSL#3 supplementation is primarily associated with changes in ileal microbiota composition.
  Gut microbes 2014 Mar JS, Nagalingam NA, Song Y, Onizawa M, Lee JW, Lynch SV
• Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease.
  Journal of clinical microbiology 2014 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 2014 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 2014 Lynch SV
• Probiotic strategies for treatment of respiratory diseases.
  Trends in microbiology 2013 Nagalingam NA, Cope EK, Lynch SV
• Comparison of the respiratory microbiome in healthy nonsmokers and smokers.
  American journal of respiratory and critical care medicine 2013 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 …
• The cystic fibrosis airway microbiome.
  Cold Spring Harbor perspectives in medicine 2013 Lynch SV, Bruce KD
• Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis.
  Science translational medicine 2012 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 2012 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 2012 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 2012 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 2012 Huang YJ, Lynch SV, Wiener-Kronish JP
• Significance of the microbiome in obstructive lung disease.
  Thorax 2012 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
• 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 2011 Song Y, Baer M, Srinivasan R, Lima J, Yarranton G, Bebbington C, Lynch SV
• The emerging relationship between the airway microbiota and chronic respiratory disease: clinical implications.
  Expert review of respiratory medicine 2011 Huang YJ, Lynch SV
• The potential for probiotic manipulation of the gastrointestinal microbiome.
  Current opinion in biotechnology 2011 Rauch M, Lynch SV
• Strain-dependent induction of neutrophil histamine production and cell death by Pseudomonas aeruginosa.
  Journal of leukocyte biology 2011 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 2011 Nagalingam NA, Lynch SV
• 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 2011 Fricks-Lima J, Hendrickson CM, Allgaier M, Zhuo H, Wiener-Kronish JP, Lynch SV, Yang K
• Nucleic acid extraction efficiency and bacterial recovery from maxillary sinus mucosal samples obtained by brushing or biopsy.
  American journal of rhinology & allergy 2010 Roediger FC, Slusher NA, Allgaier S, Cox MJ, Pletcher SD, Goldberg AN, Lynch SV
• Comparative analyses of the bacterial microbiota of the human nostril and oropharynx.
  mBio 2010 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 2010 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 2010 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 2010 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 2010 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 2010 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 2010 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 2010 Cox MJ, Huang YJ, Fujimura KE, Liu JT, McKean M, Boushey HA, Segal MR, Brodie EL, Cabana MD, Lynch SV
• Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays.
  Infection and immunity 2009 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 2009 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 2008 Lynch SV, Wiener-Kronish JP
• Increased mortality of ventilated patients with endotracheal Pseudomonas aeruginosa without clinical signs of infection.
  Critical care medicine 2008 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 2008 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 2008 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 2008 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 2008 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 2007 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 2007 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 2007 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 2007 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 2007 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 2007 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 2006 Lynch SV, Mukundakrishnan K, Benoit MR, Ayyaswamy PS, Matin A
• Effect of chromate stress on Escherichia coli K-12.
  Journal of bacteriology 2006 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 2006 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 2005 Gonzalez CF, Ackerley DF, Lynch SV, Matin A
• Analysis and manipulation of amphotericin biosynthetic genes by means of modified phage KC515 transduction techniques.
  Gene 2004 Carmody M, Byrne B, Murphy B, Breen C, Lynch S, Flood E, Finnan S, Caffrey P
• Role and regulation of sigma S in general resistance conferred by low-shear simulated microgravity in Escherichia coli.
  Journal of bacteriology 2004 Lynch SV, Brodie EL, Matin A
• Alanine dehydrogenase from the psychrophilic bacterium strain PA-43: overexpression, molecular characterization, and sequence analysis.
  Extremophiles : life under extreme conditions 2003 Irwin JA, Lynch SV, Coughlan S, Baker PJ, Gudmundsson HM, Alfredsson GA, Rice DW, Engel PC