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Susan Lynch, PhD

Address513 Parnassus Ave, Med Sci
San Francisco CA 94122
Phone415-476-6784
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    Collapse Biography 
    Collapse Education and Training
    University College Dublin, IrelandPhD2000Mircobiology
    University College Dublin, IrelandBS1995Microbiology/Biostatistics
    Collapse Awards and Honors
    American Society of Microbiology2017  - 2019Distinguished Lecturer
    Foreign Policy Magazine2016  - 2016Global Thinker
    American Association for Allergy Asthma and Immunology2015  - 2015Rebecca Buckley Lectureship
    International Innovationns2014  - 2014Women in Healthcare
    2013  - 2013Irish Health and Science 100 award

    Collapse Overview 
    Collapse Overview
    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.


    Collapse Research 
    Collapse Research Activities and Funding
    Interactions between Environmental Microbiome, Maternal Immunity, Neonatal Epigenome and Respiratory Microbiome Development as Determinants of Asthma In Childhood
    NIH/NIAID R21AI133765Aug 15, 2017 - Jul 31, 2019
    Role: Co-Principal Investigator
    Inner City Asthma Consortium (ICAC): Immunologic Approaches to Reduce Asthma (University of Wisconsin System)
    NIH/NIAID AI114271Sep 1, 2016 - Aug 31, 2023
    Role: UCSF PI
    Children’s Respiratory Research and the Environment Workgroup (CREW).
    NIH/NIAID PO515267Sep 1, 2016 - Aug 31, 2023
    Role: UCSF PI
    Delivery mode, environment and the gut microbiome: influence on childhood body size
    NIH/NICHD R01 DH082147Sep 1, 2015 - Aug 31, 2020
    Role: Co-I
    Modulating the Impact of Critical Events in Early HIV Infection: Effect of ART Initiation and Alcohol Use
    NIH/NIDA R01DA040532Aug 1, 2015 - May 31, 2020
    Role: Co-I
    Fecal microbial transplantation to reduce HIV-associated inflammation.
    NIH/NIDDK R21DK104664Jul 1, 2015 - Jun 30, 2017
    Role: Co-I
    Fungal microbiome of the house environment and its relationship to human microbiome composition
    Sloan Foundation Jun 1, 2013 - May 31, 2016
    Pets and the Infant Microbiome: Effect on Immune Maturation & Atopic Asthma
    NIH P01AI089473Jul 6, 2012 - Jun 30, 2017
    Role: Co-Investigator
    Gut and Airway Microbiome in Allergy and Asthma: Relationships to Immune and Clinical Phenotype. Effects of Inhaled Corticosteroid Treatment
    NIAID Jul 1, 2012 - Jun 30, 2015
    Role: Co-Investigator
    Role of the human microbiome in inflammatory bowel disease amongst migrant South Asian populations.
    Broad Foundation IBD-0327R-2May 1, 2012 - Apr 30, 2015
    Cigarette Smoke Exposure and Acute Lung Injury After Severe Blunt Trauma
    NIH/NHLBI R01HL110969Dec 15, 2011 - Nov 30, 2016
    Role: Co-Investigator
    Sinusitis in Children and the Nasopharyngeal Microbiome
    NIH R01AI097172Dec 1, 2011 - Nov 30, 2016
    Role: Co-Investigator
    Relationships between gut microbiota and immunity in the liver.
    UCSF Liver Center Pilot and Feasibility award May 1, 2011 - Apr 30, 2012
    Role: Co-Investigator
    Lung Microbiome in Cohorts of HIV-Infected Persons (Lung MicroCHIP) Study.
    NIH/NHLBI 1U01HL098964Oct 1, 2009 - Oct 1, 2015
    Probiotic Outcomes of Enteric Microflora (POEM) Study
    NIH/NCCAM R21AT004732Oct 1, 2009 - Sep 30, 2011
    Role: Co-Investigator
    Effect of Probiotics on CF Bacterial Communities.
    CFF Sep 1, 2009 - Aug 31, 2013
    Role: Co-Investigator
    Heterogeneity among human CD4 T lymphocytes.
    NIH/NIAID AI-026322-18A2Jul 1, 2009 - Jun 30, 2011
    Role: Co-Investigator
    The human microbiome in pediatric abdominal pain and Intestinal Inflammation.
    NIH/NIDDK 1UH2DK083990-01Apr 1, 2009 - Mar 31, 2013
    Role: Co-Investigator
    NKT cells recognize and respond to microbes at mucosal surfaces
    NIH/NIAID AI083523-01Mar 1, 2009 - Feb 28, 2011
    Role: Co-Investigator
    S100 protein potentiation of Pseudomonas aeruginosa in cystic fibrosis
    Resource Allocation Project Award, University of California San Francisco Oct 1, 2008 - Sep 30, 2010
    Probiotic Improvement of Genitourinary and Gastrointestinal Health in Girls with Spina Bifida.
    Spina Bifida Association Sep 1, 2008 - Aug 30, 2009
    Role Description: Young Investigator Award
    Microarray Analysis of Chronic Rhinosinusitis
    American Rhinological Society Jul 1, 2008 - Jun 30, 2009
    Role of PAI-1 in lung injury induced by P. aeruginosa
    UCSF REAC Award Mar 1, 2008 - Feb 28, 2009
    Resequencing microarray for rapid detection &antimicrobial resistance profiling
    NIH/NIAID U01AI075410Aug 1, 2007 - Jul 31, 2013
    Role: Principal Investigator
    Analysis of bacterial community dynamics in adult patients with exacerbations of Chronic Obstructive Pulmonary Disease
    American Lung Association Jul 1, 2007 - Jun 30, 2009
    Anti-PcrV against P. aeruginosa in CF
    Cystic Fibrosis Foundation Sep 1, 2006 - Aug 31, 2008
    Role: Co-Investigator
    Quantitative Search for Microbes in Bronchial Biopsies from Asthmatic and Healthy Subjects
    NIH/NHLBI HL074207Aug 1, 2006 - Jul 31, 2009
    16S Ancillary Study MIA Supplement
    NIH/NHLBI U10 HL074207Aug 1, 2006 - Jul 31, 2007
    Role: Co-Investigator
    Effect of quorum sensing inhibiting furanones on clinically relevant isolates of pseudomonas aeruginosa
    UCSF Academic Committee on Research Feb 8, 2006 - Mar 1, 2007
    Use of anti-PcrV IgG against P. aeruginosa in Cystic Fibrosis
    CFRDP Jan 9, 2006 - Jan 8, 2007
    Role: Co-Investigator
    The role of infection in asthma pathogenesis
    Sandler Asthma Basic Research Center Jan 1, 2006 - Dec 31, 2007
    Role: Co-Investigator
    Expression and pathogenicity of Pseudomonas aeruginosa The goal of this study is to examine virulence systems and evolution of resistance of P. aeruginosa clinical isolates.
    NIH/NHLBI HL69809Dec 11, 2003 - Nov 30, 2008
    Role: Co-Investigator
    Gene Expression and Pathogenicity of P.aeruginosa
    NIH/NHLBI R01HL069809Dec 11, 2003 - Nov 30, 2008
    Role: Principal Investigator
    Project 2: Mechanisms of Bacterial Induced Lung Injury
    NIH/NHLBI P50 HL074005Dec 1, 2003 - Jun 30, 2008
    Role: Co-Investigator
    Dean's Fellowship
    Stanford University School of Medicine Aug 1, 2002 - Aug 1, 2003
    Postdoctoral Fellowship
    Enterprise Ireland Aug 1, 2001 - Aug 1, 2002
    Research Award
    Enterprise Ireland Basic Aug 1, 1995 - Aug 1, 1998

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    Collapse In The News
    Collapse Global Health
    Collapse Featured Publications

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Panzer AR, Lynch S, Langelier C, Christie JD, McCauley K, Nelson M, Cheung CK, Benowitz NL, Cohen MJ, Calfee CS. Lung Microbiota is Related to Smoking Status and to Development of ARDS in Critically Ill Trauma Patients. Am J Respir Crit Care Med. 2017 Oct 16. PMID: 29035085.
      View in: PubMed
    2. Sitarik AR, Bobbitt KR, Havstad SL, Fujimura KE, Levin AM, Zoratti EM, Kim H, Woodcroft KJ, Wegienka G, Ownby DR, Joseph CLM, Lynch S, Johnson CC. Breast Milk Transforming Growth Factor ß Is Associated With Neonatal Gut Microbial Composition. J Pediatr Gastroenterol Nutr. 2017 09; 65(3):e60-e67. PMID: 28827481.
      View in: PubMed
    3. Cabana MD, McKean M, Caughey AB, Fong L, Lynch S, Wong A, Leong R, Boushey HA, Hilton JF. Early Probiotic Supplementation for Eczema and Asthma Prevention: A Randomized Controlled Trial. Pediatrics. 2017 Sep; 140(3). PMID: 28784701.
      View in: PubMed
    4. Vujkovic-Cvijin I, Rutishauser RL, Pao M, Hunt PW, Lynch S, McCune JM, Somsouk M. Limited engraftment of donor microbiome via one-time fecal microbial transplantation in treated HIV-infected individuals. Gut Microbes. 2017 May 25; 1-11. PMID: 28541799.
      View in: PubMed
    5. Cope EK, Goldberg AN, Pletcher SD, Lynch S. Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences. Microbiome. 2017 May 12; 5(1):53. PMID: 28494786.
      View in: PubMed
    6. Durack J, Lynch S. Promotion of Epithelial Barrier Integrity Via Probiotic-derived Products. J Pediatr Gastroenterol Nutr. 2017 Mar; 64(3):335-336. PMID: 27472476.
      View in: PubMed
    7. 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 S. Immune Response and Mortality Risk Relate to Distinct Lung Microbiomes in Patients with HIV and Pneumonia. Am J Respir Crit Care Med. 2017 Jan 01; 195(1):104-114. PMID: 27447987.
      View in: PubMed
    8. Lynch S, Pedersen O. The Human Intestinal Microbiome in Health and Disease. N Engl J Med. 2016 Dec 15; 375(24):2369-2379. PMID: 27974040.
      View in: PubMed
    9. Lynch S. The Lung Microbiome and Airway Disease. Ann Am Thorac Soc. 2016 Dec; 13(Supplement_5):S462-S465. PMID: 28005424.
      View in: PubMed
    10. Tremlett H, Fadrosh DW, Faruqi AA, Hart J, Roalstad S, Graves J, Spencer CM, Lynch S, Zamvil SS, Waubant E. Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls. BMC Neurol. 2016 Sep 21; 16(1):182. PMID: 27652609.
      View in: PubMed
    11. 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 S. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nat Med. 2016 Oct; 22(10):1187-1191. PMID: 27618652.
      View in: PubMed
    12. Cope EK, Goldberg AN, Pletcher SD, Lynch S. A chronic rhinosinusitis-derived isolate of Pseudomonas aeruginosa induces acute and pervasive effects on the murine upper airway microbiome and host immune response. Int Forum Allergy Rhinol. 2016 Dec; 6(12):1229-1237. PMID: 27598436.
      View in: PubMed
    13. Levin AM, Sitarik AR, Havstad SL, Fujimura KE, Wegienka G, Cassidy-Bushrow AE, Kim H, Zoratti EM, Lukacs NW, Boushey HA, Ownby DR, Lynch S, Johnson CC. Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity. Sci Rep. 2016 Aug 25; 6:31775. PMID: 27558272; PMCID: PMC4997337.
    14. Belinson H, Savage AK, Fadrosh D, Kuo YM, Lin D, Valladares R, Nusse Y, Wynshaw-Boris A, Lynch S, Locksley RM, Klein OD. Dual epithelial and immune cell function of Dvl1 regulates gut microbiota composition and intestinal homeostasis. JCI Insight. 2016 Jul 07; 1(10). PMID: 27525310.
      View in: PubMed
    15. Santee CA, Nagalingam NA, Faruqi AA, DeMuri GP, Gern JE, Wald ER, Lynch S. Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis. Microbiome. 2016 Jul 01; 4(1):34. PMID: 27364497; PMCID: PMC4929776.
    16. Durack J, Boushey HA, Lynch S. Airway Microbiota and the Implications of Dysbiosis in Asthma. Curr Allergy Asthma Rep. 2016 Jul; 16(8):52. PMID: 27393699.
      View in: PubMed
    17. Lynch S, Boushey HA. The microbiome and development of allergic disease. Curr Opin Allergy Clin Immunol. 2016 Apr; 16(2):165-71. PMID: 26885707.
      View in: PubMed
    18. Lynch S. Gut Microbiota and Allergic Disease. New Insights. Ann Am Thorac Soc. 2016 Mar; 13 Suppl 1:S51-4. PMID: 27027953; PMCID: PMC5015732 [Available on 03/01/17].
    19. Cassidy-Bushrow AE, Wegienka G, Havstad S, Levin AM, Lynch S, Ownby DR, Rundle AG, Woodcroft KJ, Zoratti EM, Johnson CC. Race-specific Association of Caesarean-Section Delivery with Body Size at Age 2 Years. Ethn Dis. 2016 Jan 21; 26(1):61-8. PMID: 26843797; PMCID: PMC4738856.
    20. DeMuri GP, Gern JE, Moyer SC, Lindstrom MJ, Lynch S, Wald ER. Clinical Features, Virus Identification, and Sinusitis as a Complication of Upper Respiratory Tract Illness in Children Ages 4-7 Years. J Pediatr. 2016 Apr; 171:133-9.e1. PMID: 26787374; PMCID: PMC4808614 [Available on 04/01/17].
    21. 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 S, Moore WC, Morgan WJ, Nadeau KC, Ownby DR, Solway J, Szefler SJ, Wenzel SE, Wright RJ, Smith RA, Erzurum SC. Future Research Directions in Asthma. An NHLBI Working Group Report. Am J Respir Crit Care Med. 2015 Dec 01; 192(11):1366-72. PMID: 26305520; PMCID: PMC4731702 [Available on 12/01/16].
    22. 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 S, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB. Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. Am J Respir Crit Care Med. 2015 Dec 01; 192(11):1335-44. PMID: 26247840; PMCID: PMC4731698 [Available on 12/01/16].
    23. 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 S, McCune JM. Gut-Resident Lactobacillus Abundance Associates with IDO1 Inhibition and Th17 Dynamics in SIV-Infected Macaques. Cell Rep. 2015 Nov 24; 13(8):1589-97. PMID: 26586432; PMCID: PMC4782968.
    24. Huang YJ, Nariya S, Harris JM, Lynch S, Choy DF, Arron JR, Boushey H. The airway microbiome in patients with severe asthma: Associations with disease features and severity. J Allergy Clin Immunol. 2015 Oct; 136(4):874-84. PMID: 26220531; PMCID: PMC4600429 [Available on 10/01/16].
    25. Panzer AR, Lynch S. Influence and effect of the human microbiome in allergy and asthma. Curr Opin Rheumatol. 2015 Jul; 27(4):373-80. PMID: 26002029.
      View in: PubMed
    26. Cassidy-Bushrow AE, Wegienka G, Havstad S, Levin AM, Lynch S, Ownby DR, Rundle AG, Woodcroft KJ, Zoratti EM, Johnson CC. Does pet-keeping modify the association of delivery mode with offspring body size? Matern Child Health J. 2015 Jun; 19(6):1426-33. PMID: 25427878; PMCID: PMC4446256.
    27. Fujimura KE, Lynch S. Microbiota in allergy and asthma and the emerging relationship with the gut microbiome. Cell Host Microbe. 2015 May 13; 17(5):592-602. PMID: 25974301; PMCID: PMC4443817.
    28. Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch S. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PLoS One. 2015; 10(2):e0117617. PMID: 25658760; PMCID: PMC4319838.
    29. Lynch S. Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in Pediatric Patients: Encouragement Wrapped in Caution. J Pediatr Gastroenterol Nutr. 2015 Jan; 60(1):1-3. PMID: 25546336.
      View in: PubMed
    30. Ardeshir A, Narayan NR, Méndez-Lagares G, Lu D, Rauch M, Huang Y, Van Rompay KK, Lynch S, Hartigan-O'Connor DJ. Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems. Sci Transl Med. 2014 Sep 03; 6(252):252ra120. PMID: 25186175; PMCID: PMC4362692.
    31. Merenstein D, El-Nachef N, Lynch S. Fecal microbial therapy: promises and pitfalls. J Pediatr Gastroenterol Nutr. 2014 Aug; 59(2):157-61. PMID: 24796803; PMCID: PMC4669049.
    32. Mar JS, Nagalingam NA, Song Y, Onizawa M, Lee JW, Lynch S. Amelioration of DSS-induced murine colitis by VSL#3 supplementation is primarily associated with changes in ileal microbiota composition. Gut Microbes. 2014 Jul 01; 5(4):494-503. PMID: 25144681.
      View in: PubMed
    33. Lynch S, 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. Effects of early-life exposure to allergens and bacteria on recurrent wheeze and atopy in urban children. J Allergy Clin Immunol. 2014 Sep; 134(3):593-601.e12. PMID: 24908147; PMCID: PMC4151305.
    34. Huang YJ, Sethi S, Murphy T, Nariya S, Boushey HA, Lynch S. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. J Clin Microbiol. 2014 Aug; 52(8):2813-23. PMID: 24850358; PMCID: PMC4136157.
    35. Iwai S, Huang D, Fong S, Jarlsberg LG, Worodria W, Yoo S, Cattamanchi A, Davis JL, Kaswabuli S, Segal M, Huang L, Lynch S. The lung microbiome of Ugandan HIV-infected pneumonia patients is compositionally and functionally distinct from that of San Franciscan patients. PLoS One. 2014; 9(4):e95726. PMID: 24752365; PMCID: PMC3994144.
    36. Lynch S. Viruses and microbiome alterations. Ann Am Thorac Soc. 2014 Jan; 11 Suppl 1:S57-60. PMID: 24437408.
      View in: PubMed
    37. Fujimura KE, Demoor T, Rauch M, Faruqi AA, Jang S, Johnson CC, Boushey HA, Zoratti E, Ownby D, Lukacs NW, Lynch S. House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection. Proc Natl Acad Sci U S A. 2014 Jan 14; 111(2):805-10. PMID: 24344318; PMCID: PMC3896155.
    38. 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 S, McCune JM. Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism. Sci Transl Med. 2013 Jul 10; 5(193):193ra91. PMID: 23843452; PMCID: PMC4094294.
    39. Nagalingam NA, Cope EK, Lynch S. Probiotic strategies for treatment of respiratory diseases. Trends Microbiol. 2013 Sep; 21(9):485-92. PMID: 23707554.
      View in: PubMed
    40. 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 S, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med. 2013 May 15; 187(10):1067-75. PMID: 23491408; PMCID: PMC3734620.
    41. 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 S, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP. Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med. 2013 May 15; 187(10):1110-7. PMID: 23392441; PMCID: PMC3734615.
    42. Lynch S, Bruce KD. The cystic fibrosis airway microbiome. Cold Spring Harb Perspect Med. 2013 Mar 01; 3(3):a009738. PMID: 23457293; PMCID: PMC3579208.
    43. Lynch S, Goldfarb KC, Wild YK, Kong W, De Lisle RC, Brodie EL. Cystic fibrosis transmembrane conductance regulator knockout mice exhibit aberrant gastrointestinal microbiota. Gut Microbes. 2013 Jan-Feb; 4(1):41-7. PMID: 23060053; PMCID: PMC3555885.
    44. 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 S. Development of a standardized approach for environmental microbiota investigations related to asthma development in children. J Microbiol Methods. 2012 Nov; 91(2):231-9. PMID: 22975469; PMCID: PMC3615718.
    45. Iwai S, Fei M, Huang D, Fong S, Subramanian A, Grieco K, Lynch S, Huang L. Oral and airway microbiota in HIV-infected pneumonia patients. J Clin Microbiol. 2012 Sep; 50(9):2995-3002. PMID: 22760045; PMCID: PMC3421777.
    46. Scanlan PD, Buckling A, Kong W, Wild Y, Lynch S, Harrison F. Gut dysbiosis in cystic fibrosis. J Cyst Fibros. 2012 Sep; 11(5):454-5. PMID: 22538067.
      View in: PubMed
    47. Huang YJ, Lynch S, Wiener-Kronish JP. From microbe to microbiota: considering microbial community composition in infections and airway diseases. Am J Respir Crit Care Med. 2012 Apr 01; 185(7):691-2. PMID: 22467799.
      View in: PubMed
    48. Schwarzer C, Fu Z, Patanwala M, Hum L, Lopez-Guzman M, Illek B, Kong W, Lynch S, Machen TE. Pseudomonas aeruginosa biofilm-associated homoserine lactone C12 rapidly activates apoptosis in airway epithelia. Cell Microbiol. 2012 May; 14(5):698-709. PMID: 22233488; PMCID: PMC4112999.
    49. Han MK, Huang YJ, Lipuma JJ, Boushey HA, Boucher RC, Cookson WO, Curtis JL, Erb-Downward J, Lynch S, Sethi S, Toews GB, Young VB, Wolfgang MC, Huffnagle GB, Martinez FJ. Significance of the microbiome in obstructive lung disease. Thorax. 2012 May; 67(5):456-63. PMID: 22318161; PMCID: PMC3578398.
    50. 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. Future directions in early cystic fibrosis lung disease research: an NHLBI workshop report. Am J Respir Crit Care Med. 2012 Apr 15; 185(8):887-92. PMID: 22312017; PMCID: PMC3360572.
    51. Song Y, Baer M, Srinivasan R, Lima J, Yarranton G, Bebbington C, Lynch S. PcrV antibody-antibiotic combination improves survival in Pseudomonas aeruginosa-infected mice. Eur J Clin Microbiol Infect Dis. 2012 Aug; 31(8):1837-45. PMID: 22187351.
      View in: PubMed
    52. Huang YJ, Lynch S. The emerging relationship between the airway microbiota and chronic respiratory disease: clinical implications. Expert Rev Respir Med. 2011 Dec; 5(6):809-21. PMID: 22082166; PMCID: PMC3359942.
    53. Rauch M, Lynch S. The potential for probiotic manipulation of the gastrointestinal microbiome. Curr Opin Biotechnol. 2012 Apr; 23(2):192-201. PMID: 22137452.
      View in: PubMed
    54. Xu X, Zhang H, Song Y, Lynch S, Lowell CA, Wiener-Kronish JP, Caughey GH. Strain-dependent induction of neutrophil histamine production and cell death by Pseudomonas aeruginosa. J Leukoc Biol. 2012 Feb; 91(2):275-84. PMID: 22075928; PMCID: PMC3290427.
    55. Nagalingam NA, Lynch S. Role of the microbiota in inflammatory bowel diseases. Inflamm Bowel Dis. 2012 May; 18(5):968-84. PMID: 21936031.
      View in: PubMed
    56. Havstad S, Wegienka G, Zoratti EM, Lynch S, Boushey HA, Nicholas C, Ownby DR, Johnson CC. Effect of prenatal indoor pet exposure on the trajectory of total IgE levels in early childhood. J Allergy Clin Immunol. 2011 Oct; 128(4):880-885.e4. PMID: 21820714; PMCID: PMC3185205.
    57. 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 S, Shulman RJ, Versalovic J. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology. 2011 Nov; 141(5):1782-91. PMID: 21741921; PMCID: PMC3417828.
    58. Fricks-Lima J, Hendrickson CM, Allgaier M, Zhuo H, Wiener-Kronish JP, Lynch S, Yang K. Differences in biofilm formation and antimicrobial resistance of Pseudomonas aeruginosa isolated from airways of mechanically ventilated patients and cystic fibrosis patients. Int J Antimicrob Agents. 2011 Apr; 37(4):309-15. PMID: 21382698; PMCID: PMC3176759.
    59. 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 S. Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol. 2011 Feb; 127(2):372-381.e1-3. PMID: 21194740; PMCID: PMC3037020.
    60. Fujimura KE, Johnson CC, Ownby DR, Cox MJ, Brodie EL, Havstad SL, Zoratti EM, Woodcroft KJ, Bobbitt KR, Wegienka G, Boushey HA, Lynch S. Man's best friend? The effect of pet ownership on house dust microbial communities. J Allergy Clin Immunol. 2010 Aug; 126(2):410-2, 412.e1-3. PMID: 20633927; PMCID: PMC2956425.
    61. Roediger FC, Slusher NA, Allgaier S, Cox MJ, Pletcher SD, Goldberg AN, Lynch S. Nucleic acid extraction efficiency and bacterial recovery from maxillary sinus mucosal samples obtained by brushing or biopsy. Am J Rhinol Allergy. 2010 Jul-Aug; 24(4):263-5. PMID: 20819463.
      View in: PubMed
    62. 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 S. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One. 2010 Jun 23; 5(6):e11044. PMID: 20585638; PMCID: PMC2890402.
    63. Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch S, Kolter R. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. MBio. 2010 Jun 22; 1(3). PMID: 20802827; PMCID: PMC2925076.
    64. Shane AL, Cabana MD, Vidry S, Merenstein D, Hummelen R, Ellis CL, Heimbach JT, Hempel S, Lynch S, Sanders ME, Tancredi DJ. Guide to designing, conducting, publishing and communicating results of clinical studies involving probiotic applications in human participants. Gut Microbes. 2010 Jul; 1(4):243-253. PMID: 21327031.
      View in: PubMed
    65. Singh G, Wu B, Baek MS, Camargo A, Nguyen A, Slusher NA, Srinivasan R, Wiener-Kronish JP, Lynch S. Secretion of Pseudomonas aeruginosa type III cytotoxins is dependent on pseudomonas quinolone signal concentration. Microb Pathog. 2010 Oct; 49(4):196-203. PMID: 20570614; PMCID: PMC2935322.
    66. Fujimura KE, Slusher NA, Cabana MD, Lynch S. Role of the gut microbiota in defining human health. Expert Rev Anti Infect Ther. 2010 Apr; 8(4):435-54. PMID: 20377338; PMCID: PMC2881665.
    67. Lynch S, 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. Polymorphisms in the Pseudomonas aeruginosa type III secretion protein, PcrV - implications for anti-PcrV immunotherapy. Microb Pathog. 2010 Jun; 48(6):197-204. PMID: 20211240; PMCID: PMC2860055.
    68. Klepac-Ceraj V, Lemon KP, Martin TR, Allgaier M, Kembel SW, Knapp AA, Lory S, Brodie EL, Lynch S, Bohannan BJ, Green JL, Maurer BA, Kolter R. Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Environ Microbiol. 2010 May; 12(5):1293-303. PMID: 20192960.
      View in: PubMed
    69. Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch S. A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. OMICS. 2010 Feb; 14(1):9-59. PMID: 20141328; PMCID: PMC3116451.
    70. Cox MJ, Huang YJ, Fujimura KE, Liu JT, McKean M, Boushey HA, Segal MR, Brodie EL, Cabana MD, Lynch S. Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome. PLoS One. 2010 Jan 18; 5(1):e8745. PMID: 20090909; PMCID: PMC2807455.
    71. Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, Wei D, Goldfarb KC, Santee CA, Lynch S, Tanoue T, Imaoka A, Itoh K, Takeda K, Umesaki Y, Honda K, Littman DR. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009 Oct 30; 139(3):485-98. PMID: 19836068; PMCID: PMC2796826.
    72. Montor WR, Huang J, Hu Y, Hainsworth E, Lynch S, Kronish JW, Ordonez CL, Logvinenko T, Lory S, LaBaer J. Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays. Infect Immun. 2009 Nov; 77(11):4877-86. PMID: 19737893; PMCID: PMC2772540.
    73. El-Solh AA, Amsterdam D, Alhajhusain A, Akinnusi ME, Saliba RG, Lynch S, Wiener-Kronish JP. Matrix metalloproteases in bronchoalveolar lavage fluid of patients with type III Pseudomonas aeruginosa pneumonia. J Infect. 2009 Jul; 59(1):49-55. PMID: 19535150; PMCID: PMC2756421.
    74. Lynch S, Wiener-Kronish JP. Novel strategies to combat bacterial virulence. Curr Opin Crit Care. 2008 Oct; 14(5):593-9. PMID: 18787455; PMCID: PMC2859961.
    75. Zhuo H, Yang K, Lynch S, Dotson RH, Glidden DV, Singh G, Webb WR, Elicker BM, Garcia O, Brown R, Sawa Y, Misset B, Wiener-Kronish JP. Increased mortality of ventilated patients with endotracheal Pseudomonas aeruginosa without clinical signs of infection. Crit Care Med. 2008 Sep; 36(9):2495-503. PMID: 18679122.
      View in: PubMed
    76. Ganter MT, Roux J, Su G, Lynch S, Deutschman CS, Weiss YG, Christiaans SC, Myazawa B, Kipnis E, Wiener-Kronish JP, Howard M, Pittet JF. Role of small GTPases and alphavbeta5 integrin in Pseudomonas aeruginosa-induced increase in lung endothelial permeability. Am J Respir Cell Mol Biol. 2009 Jan; 40(1):108-18. PMID: 18703797; PMCID: PMC2606944.
    77. El Solh AA, Akinnusi ME, Wiener-Kronish JP, Lynch S, Pineda LA, Szarpa K. Persistent infection with Pseudomonas aeruginosa in ventilator-associated pneumonia. Am J Respir Crit Care Med. 2008 Sep 01; 178(5):513-9. PMID: 18467510; PMCID: PMC2542430.
    78. Song Y, Pittet JF, Huang X, He H, Lynch S, Violette SM, Weinreb PH, Horan GS, Carmago A, Sawa Y, Bernstein XL, Wiener-Kronish JP. Role of integrin alphav beta6 in acute lung injury induced by Pseudomonas aeruginosa. Infect Immun. 2008 Jun; 76(6):2325-32. PMID: 18378634; PMCID: PMC2423078.
    79. Wong-Beringer A, Wiener-Kronish J, Lynch S, Flanagan J. Comparison of type III secretion system virulence among fluoroquinolone-susceptible and -resistant clinical isolates of Pseudomonas aeruginosa. Clin Microbiol Infect. 2008 Apr; 14(4):330-6. PMID: 18190571.
      View in: PubMed
    80. Lynch S, Dixon L, Benoit MR, Brodie EL, Keyhan M, Hu P, Ackerley DF, Andersen GL, Matin A. Role of the rapA gene in controlling antibiotic resistance of Escherichia coli biofilms. Antimicrob Agents Chemother. 2007 Oct; 51(10):3650-8. PMID: 17664315; PMCID: PMC2043260.
    81. Yoo J, Tcheurekdjian H, Lynch S, Cabana M, Boushey HA. Microbial manipulation of immune function for asthma prevention: inferences from clinical trials. Proc Am Thorac Soc. 2007 Jul; 4(3):277-82. PMID: 17607013; PMCID: PMC2647630.
    82. Flanagan JL, Brodie EL, Weng L, Lynch S, Garcia O, Brown R, Hugenholtz P, DeSantis TZ, Andersen GL, Wiener-Kronish JP, Bristow J. Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J Clin Microbiol. 2007 Jun; 45(6):1954-62. PMID: 17409203; PMCID: PMC1933106.
    83. Song Y, Wiener-Kronish JP, Flanagan J, Lynch S. Alveolar hemostasis in patients with species-specific bacterial-mediated ventilator-associated pneumonia. Crit Care Med. 2007 Feb; 35(2):652-3. PMID: 17251717.
      View in: PubMed
    84. Song Y, Lynch S, 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. 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 Feb; 106(2):252-61. PMID: 17264718.
      View in: PubMed
    85. Augustin DK, Song Y, Baek MS, Sawa Y, Singh G, Taylor B, Rubio-Mills A, Flanagan JL, Wiener-Kronish JP, Lynch S. Presence or absence of lipopolysaccharide O antigens affects type III secretion by Pseudomonas aeruginosa. J Bacteriol. 2007 Mar; 189(6):2203-9. PMID: 17209027; PMCID: PMC1899375.
    86. Lynch S, Mukundakrishnan K, Benoit MR, Ayyaswamy PS, Matin A. Escherichia coli biofilms formed under low-shear modeled microgravity in a ground-based system. Appl Environ Microbiol. 2006 Dec; 72(12):7701-10. PMID: 17028231; PMCID: PMC1694224.
    87. Ackerley DF, Barak Y, Lynch S, Curtin J, Matin A. Effect of chromate stress on Escherichia coli K-12. J Bacteriol. 2006 May; 188(9):3371-81. PMID: 16621832; PMCID: PMC1447458.
    88. Barak Y, Thorne SH, Ackerley DF, Lynch S, Contag CH, Matin A. New enzyme for reductive cancer chemotherapy, YieF, and its improvement by directed evolution. Mol Cancer Ther. 2006 Jan; 5(1):97-103. PMID: 16432167.
      View in: PubMed
    89. Gonzalez CF, Ackerley DF, Lynch S, Matin A. ChrR, a soluble quinone reductase of Pseudomonas putida that defends against H2O2. J Biol Chem. 2005 Jun 17; 280(24):22590-5. PMID: 15840577.
      View in: PubMed
    90. Carmody M, Byrne B, Murphy B, Breen C, Lynch S, Flood E, Finnan S, Caffrey P. Analysis and manipulation of amphotericin biosynthetic genes by means of modified phage KC515 transduction techniques. Gene. 2004 Dec 08; 343(1):107-15. PMID: 15563836.
      View in: PubMed
    91. Lynch S, Brodie EL, Matin A. Role and regulation of sigma S in general resistance conferred by low-shear simulated microgravity in Escherichia coli. J Bacteriol. 2004 Dec; 186(24):8207-12. PMID: 15576768; PMCID: PMC532419.
    92. Irwin JA, Lynch S, Coughlan S, Baker PJ, Gudmundsson HM, Alfredsson GA, Rice DW, Engel PC. Alanine dehydrogenase from the psychrophilic bacterium strain PA-43: overexpression, molecular characterization, and sequence analysis. Extremophiles. 2003 Apr; 7(2):135-43. PMID: 12664266.
      View in: PubMed
    93. Caffrey P, Lynch S, Flood E, Finnan S, Oliynyk M. Amphotericin biosynthesis in Streptomyces nodosus: deductions from analysis of polyketide synthase and late genes. Chem Biol. 2001 Jul; 8(7):713-23. PMID: 11451671.
      View in: PubMed
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