Susan Lynch, PhD

Professor

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.
Education
2020 - Diversity, Equity, and Inclusion Champion Training, University of California
PhD, 2000 - Mircobiology, University College Dublin
BS, 1995 - Microbiology/Biostatistics, University College Dublin
Honors and Awards
  • Distinguished Lecturer, American Society of Microbiology, 2017-2019
  • Global Thinker, Foreign Policy Magazine, 2016
  • Rebecca Buckley Lectureship, American Association for Allergy Asthma and Immunology, 2015
  • Women in Healthcare, International Innovationns, 2014
  • Irish Health and Science 100 award, 2013
Websites
Publications
  1. 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. Maternal and cord blood vitamin D level and the infant gut microbiota in a birth cohort study. 2020. PMID: 33101701


  2. Rackaityte E, Lynch SV. The human microbiome in the 21st century. 2020. PMID: 33067429


  3. Bhadriraju S, Fadrosh DW, Shenoy MK, Lin DL, Lynch KV, McCauley K, Ferrand RA, Majonga ED, McHugh G, Huang L, Lynch SV, Metcalfe JZ. Distinct lung microbiota associate with HIV-associated chronic lung disease in children. 2020. PMID: 32999331


  4. Panzer AR, Lynch SV. Gut Microbial Regulation of Autism Spectrum Disorder Symptoms. 2020. PMID: 32972817


  5. 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. Association between cesarean delivery types and obesity in preadolescence. 2020. PMID: 32873910


  6. 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. Fetal and early postnatal lead exposure measured in teeth associates with infant gut microbiota. 2020. PMID: 32871381


  7. 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. Distinct associations of sputum and oral microbiota with atopic, immunologic, and clinical features in mild asthma. 2020. PMID: 32298699


  8. 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. Author Correction: Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance. 2019. PMID: 31492948


  9. Lynch SV, Ng SC, Shanahan F, Tilg H. Translating the gut microbiome: ready for the clinic? 2019. PMID: 31562390


  10. 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. Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance. 2019. PMID: 31332384


  11. 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. Fecal Microbiota Transplantation in Pouchitis: Clinical, Endoscopic, Histologic, and Microbiota Results from a Pilot Study. 2019. PMID: 31302808


  12. Talpin A, Kattah MG, Advincula R, Fadrosh D, Lynch K, LaMere B, Fujimura KE, Nagalingam NA, Malynn BA, Lynch SV, Ma A. A20 in dendritic cells restrains intestinal anti-bacterial peptide expression and preserves commensal homeostasis. 2019. PMID: 31295268


  13. Combellick JL, Shin H, Shin D, Cai Y, Hagan H, Lacher C, Lin DL, McCauley K, Lynch SV, Dominguez-Bello MG. Author Correction: Differences in the fecal microbiota of neonates born at home or in the hospital. 2019. PMID: 31209226


  14. 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. Distinct Nasal Airway Bacterial Microbiota Differentially Relate to Exacerbation in Pediatric Asthma. 2019. PMID: 31201890


  15. Gilbert JA, Lynch SV. Community ecology as a framework for human microbiome research. 2019. PMID: 31133693


  16. 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. Fecal microbiota transplant for Crohn disease: A study evaluating safety, efficacy, and microbiome profile. 2019. PMID: 31316785


  17. 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. Gut microbiota in HIV-pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction. 2019. PMID: 30857553


  18. Fernandes MA, Verstraete SG, Phan TG, Deng X, Stekol E, LaMere B, Lynch SV, Heyman MB, Delwart E. Enteric Virome and Bacterial Microbiota in Children with Ulcerative Colitis and Crohn's Disease. 2018. PMID: 30169455


  19. 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. Longitudinal Phenotypes of Respiratory Health in a High-Risk Urban Birth Cohort. 2018. PMID: 30079758


  20. Sharpton SR, Yong GJM, Terrault NA, Lynch SV. Gut Microbial Metabolism and Nonalcoholic Fatty Liver Disease. 2018. PMID: 30619992


  21. Rackaityte E, Lynch SV. Rules of engagement in the gut microbiome. 2018. PMID: 30401869


  22. Combellick JL, Shin H, Shin D, Cai Y, Hagan H, Lacher C, Lin DL, McCauley K, Lynch SV, Dominguez-Bello MG. Differences in the fecal microbiota of neonates born at home or in the hospital. 2018. PMID: 30353125


  23. 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. Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization. 2018. PMID: 30185226


  24. Durack J, Huang YJ, Nariya S, Christian LS, Mark Ansel K, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV, Boushey HA. Bacterial biogeography of adult airways in atopic asthma. 2018. PMID: 29885665


  25. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. 2018. PMID: 29634682


  26. Panzer AR, Lynch SV, 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. Volume 197 of Issue 5. 2017. PMID: 29035085


  27. Durack J, Kimes NE, Lin DL, Rauch M, McKean M, McCauley K, Panzer AR, Mar JS, Cabana MD, Lynch SV. Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation. 2018. PMID: 29453431


  28. Shenoy MK, Lynch SV. Role of the lung microbiome in HIV pathogenesis. Volume 13 of Issue 1. 2018. PMID: 29035946


  29. Howard BM, Kornblith LZ, Christie SA, Conroy AS, Nelson MF, Campion EM, Callcut RA, Calfee CS, Lamere BJ, Fadrosh DW, Lynch S, Cohen MJ. Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury. Volume 2 of Issue 1. 2017. PMID: 29766103


  30. 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. Early-life home environment and risk of asthma among inner-city children. 2017. PMID: 28939248


  31. 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. Breast Milk Transforming Growth Factor ß Is Associated With Neonatal Gut Microbial Composition. Volume 65 of Issue 3. 2017. PMID: 28827481


  32. 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. 2017. PMID: 28784701


  33. Vujkovic-Cvijin I, Rutishauser RL, Pao M, Hunt PW, Lynch SV, McCune JM, Somsouk M. Limited engraftment of donor microbiome via one-time fecal microbial transplantation in treated HIV-infected individuals. Volume 8 of Issue 5. 2017. PMID: 28541799


  34. Durack J, Lynch SV. Promotion of Epithelial Barrier Integrity Via Probiotic-derived Products. Volume 64 of Issue 3. 2017. PMID: 27472476


  35. 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. Immune Response and Mortality Risk Relate to Distinct Lung Microbiomes in Patients with HIV and Pneumonia. Volume 195 of Issue 1. 2017. PMID: 27447987


  36. Lynch SV, Pedersen O. The Human Intestinal Microbiome in Health and Disease. Volume 375 of Issue 24. 2016. PMID: 27974040


  37. Lynch SV. The Lung Microbiome and Airway Disease. Volume 13 of Issue Supplement_5. 2016. PMID: 28005424


  38. 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. Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment. 2016. PMID: 27838347


  39. Tremlett H, Fadrosh DW, Faruqi AA, Hart J, Roalstad S, Graves J, Spencer CM, Lynch SV, Zamvil SS, Waubant E. Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls. Volume 16 of Issue 1. 2016. PMID: 27652609


  40. 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. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. 2016. PMID: 27618652


  41. 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. Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity. 2016. PMID: 27558272


  42. Mar JS, LaMere BJ, Lin DL, Levan S, Nazareth M, Mahadevan U, Lynch SV. Disease Severity and Immune Activity Relate to Distinct Interkingdom Gut Microbiome States in Ethnically Distinct Ulcerative Colitis Patients. Volume 7 of Issue 4. 2016. PMID: 27531910


  43. Belinson H, Savage AK, Fadrosh D, Kuo YM, Lin D, Valladares R, Nusse Y, Wynshaw-Boris A, Lynch SV, Locksley RM, Klein OD. Dual epithelial and immune cell function of Dvl1 regulates gut microbiota composition and intestinal homeostasis. Volume 1 of Issue 10. 2016. PMID: 27525310


  44. Durack J, Boushey HA, Lynch SV. Airway Microbiota and the Implications of Dysbiosis in Asthma. 2016. PMID: 27393699


  45. Santee CA, Nagalingam NA, Faruqi AA, DeMuri GP, Gern JE, Wald ER, Lynch SV. Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis. Volume 4 of Issue 1. 2016. PMID: 27364497


  46. Lynch SV, Boushey HA. The microbiome and development of allergic disease. 2016. PMID: 26885707


  47. Lynch SV. Gut Microbiota and Allergic Disease. New Insights. Volume 13 Suppl 1. 2016. PMID: 27027953


  48. Cassidy-Bushrow AE, Wegienka G, Havstad S, Levin AM, Lynch SV, Ownby DR, Rundle AG, Woodcroft KJ, Zoratti EM, Johnson CC. Race-specific Association of Caesarean-Section Delivery with Body Size at Age 2 Years. Volume 26 of Issue 1. 2016. PMID: 26843797


  49. DeMuri GP, Gern JE, Moyer SC, Lindstrom MJ, Lynch SV, Wald ER. Clinical Features, Virus Identification, and Sinusitis as a Complication of Upper Respiratory Tract Illness in Children Ages 4-7 Years. Volume 171. 2016. PMID: 26787374


  50. 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. Future Research Directions in Asthma. An NHLBI Working Group Report. Volume 192 of Issue 11. 2015. PMID: 26305520


  51. 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. Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. Volume 192 of Issue 11. 2015. PMID: 26247840


  52. 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. Gut-Resident Lactobacillus Abundance Associates with IDO1 Inhibition and Th17 Dynamics in SIV-Infected Macaques. Volume 13 of Issue 8. 2015. PMID: 26586432


  53. Huang YJ, Nariya S, Harris JM, Lynch SV, Choy DF, Arron JR, Boushey H. The airway microbiome in patients with severe asthma: Associations with disease features and severity. 2015. PMID: 26220531


  54. Panzer AR, Lynch SV. Influence and effect of the human microbiome in allergy and asthma. Volume 27 of Issue 4. 2015. PMID: 26002029


  55. Cassidy-Bushrow AE, Wegienka G, Havstad S, Levin AM, Lynch SV, Ownby DR, Rundle AG, Woodcroft KJ, Zoratti EM, Johnson CC. Does pet-keeping modify the association of delivery mode with offspring body size? Volume 19 of Issue 6. 2015. PMID: 25427878


  56. Fujimura KE, Lynch SV. Microbiota in allergy and asthma and the emerging relationship with the gut microbiome. Volume 17 of Issue 5. 2015. PMID: 25974301


  57. Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch SV. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. Volume 10 of Issue 2. 2015. PMID: 25658760


  58. Ardeshir A, Narayan NR, Méndez-Lagares G, Lu D, Rauch M, Huang Y, Van Rompay KK, Lynch SV, Hartigan-O'Connor DJ. Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems. Volume 6 of Issue 252. 2014. PMID: 25186175


  59. Merenstein D, El-Nachef N, Lynch SV. Fecal microbial therapy: promises and pitfalls. Volume 59 of Issue 2. 2014. PMID: 24796803


  60. Mar JS, Nagalingam NA, Song Y, Onizawa M, Lee JW, Lynch SV. Amelioration of DSS-induced murine colitis by VSL#3 supplementation is primarily associated with changes in ileal microbiota composition. Volume 5 of Issue 4. 2014. PMID: 25144681


  61. 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. Effects of early-life exposure to allergens and bacteria on recurrent wheeze and atopy in urban children. 2014. PMID: 24908147


  62. Huang YJ, Sethi S, Murphy T, Nariya S, Boushey HA, Lynch SV. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. 2014. PMID: 24850358


  63. Iwai S, Huang D, Fong S, Jarlsberg LG, Worodria W, Yoo S, Cattamanchi A, Davis JL, Kaswabuli S, Segal M, Huang L, Lynch SV. The lung microbiome of Ugandan HIV-infected pneumonia patients is compositionally and functionally distinct from that of San Franciscan patients. Volume 9 of Issue 4. 2014. PMID: 24752365


  64. Lynch SV. Viruses and microbiome alterations. Volume 11 Suppl 1. 2014. PMID: 24437408


  65. Fujimura KE, Demoor T, Rauch M, Faruqi AA, Jang S, Johnson CC, Boushey HA, Zoratti E, Ownby D, Lukacs NW, Lynch SV. House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection. 2013. PMID: 24344318


  66. 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. Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan catabolism. Volume 5 of Issue 193. 2013. PMID: 23843452


  67. Nagalingam NA, Cope EK, Lynch SV. Probiotic strategies for treatment of respiratory diseases. Volume 21 of Issue 9. 2013. PMID: 23707554


  68. 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. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Volume 187 of Issue 10. 2013. PMID: 23491408


  69. 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. Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Volume 187 of Issue 10. 2013. PMID: 23392441


  70. Lynch SV, Bruce KD. The cystic fibrosis airway microbiome. Volume 3 of Issue 3. 2013. PMID: 23457293


  71. Lynch SV, Goldfarb KC, Wild YK, Kong W, De Lisle RC, Brodie EL. Cystic fibrosis transmembrane conductance regulator knockout mice exhibit aberrant gastrointestinal microbiota. Volume 4 of Issue 1. 2012. PMID: 23060053


  72. Abreu NA, Nagalingam NA, Song Y, Roediger FC, Pletcher SD, Goldberg AN, Lynch SV. Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis. Volume 4 of Issue 151. 2012. PMID: 22972842


  73. 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. Development of a standardized approach for environmental microbiota investigations related to asthma development in children. 2012. PMID: 22975469


  74. Iwai S, Fei M, Huang D, Fong S, Subramanian A, Grieco K, Lynch SV, Huang L. Oral and airway microbiota in HIV-infected pneumonia patients. Volume 50 of Issue 9. 2012. PMID: 22760045


  75. Scanlan PD, Buckling A, Kong W, Wild Y, Lynch SV, Harrison F. Gut dysbiosis in cystic fibrosis. Volume 11 of Issue 5. 2012. PMID: 22538067


  76. Huang YJ, Lynch SV, Wiener-Kronish JP. From microbe to microbiota: considering microbial community composition in infections and airway diseases. Volume 185 of Issue 7. 2012. PMID: 22467799


  77. Schwarzer C, Fu Z, Patanwala M, Hum L, Lopez-Guzman M, Illek B, Kong W, Lynch SV, Machen TE. Pseudomonas aeruginosa biofilm-associated homoserine lactone C12 rapidly activates apoptosis in airway epithelia. Volume 14 of Issue 5. 2012. PMID: 22233488


  78. 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. Significance of the microbiome in obstructive lung disease. 2012. PMID: 22318161


  79. 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. Volume 185 of Issue 8. 2012. PMID: 22312017


  80. Song Y, Baer M, Srinivasan R, Lima J, Yarranton G, Bebbington C, Lynch SV. PcrV antibody-antibiotic combination improves survival in Pseudomonas aeruginosa-infected mice. Volume 31 of Issue 8. 2011. PMID: 22187351


  81. Rauch M, Lynch SV. The potential for probiotic manipulation of the gastrointestinal microbiome. Volume 23 of Issue 2. 2011. PMID: 22137452


  82. Xu X, Zhang H, Song Y, Lynch SV, Lowell CA, Wiener-Kronish JP, Caughey GH. Strain-dependent induction of neutrophil histamine production and cell death by Pseudomonas aeruginosa. Volume 91 of Issue 2. 2011. PMID: 22075928


  83. Nagalingam NA, Lynch SV. Role of the microbiota in inflammatory bowel diseases. Volume 18 of Issue 5. 2011. PMID: 21936031


  84. Havstad S, Wegienka G, Zoratti EM, Lynch SV, Boushey HA, Nicholas C, Ownby DR, Johnson CC. Effect of prenatal indoor pet exposure on the trajectory of total IgE levels in early childhood. 2011. PMID: 21820714


  85. 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. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Volume 141 of Issue 5. 2011. PMID: 21741921


  86. Fricks-Lima J, Hendrickson CM, Allgaier M, Zhuo H, Wiener-Kronish JP, Lynch SV, Yang K. Differences in biofilm formation and antimicrobial resistance of Pseudomonas aeruginosa isolated from airways of mechanically ventilated patients and cystic fibrosis patients. Volume 37 of Issue 4. 2011. PMID: 21382698


  87. 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. Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. 2010. PMID: 21194740


  88. Fujimura KE, Johnson CC, Ownby DR, Cox MJ, Brodie EL, Havstad SL, Zoratti EM, Woodcroft KJ, Bobbitt KR, Wegienka G, Boushey HA, Lynch SV. Man's best friend? The effect of pet ownership on house dust microbial communities. 2010. PMID: 20633927


  89. Roediger FC, Slusher NA, Allgaier S, Cox MJ, Pletcher SD, Goldberg AN, Lynch SV. Nucleic acid extraction efficiency and bacterial recovery from maxillary sinus mucosal samples obtained by brushing or biopsy. Volume 24 of Issue 4. 2010. PMID: 20819463


  90. 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. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. Volume 5 of Issue 6. 2010. PMID: 20585638


  91. Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. Volume 1 of Issue 3. 2010. PMID: 20802827


  92. Shane AL, Cabana MD, Vidry S, Merenstein D, Hummelen R, Ellis CL, Heimbach JT, Hempel S, Lynch SV, Sanders ME, Tancredi DJ. Guide to designing, conducting, publishing and communicating results of clinical studies involving probiotic applications in human participants. Volume 1 of Issue 4. 2010. PMID: 21327031


  93. Singh G, Wu B, Baek MS, Camargo A, Nguyen A, Slusher NA, Srinivasan R, Wiener-Kronish JP, Lynch SV. Secretion of Pseudomonas aeruginosa type III cytotoxins is dependent on pseudomonas quinolone signal concentration. Volume 49 of Issue 4. 2010. PMID: 20570614


  94. Fujimura KE, Slusher NA, Cabana MD, Lynch SV. Role of the gut microbiota in defining human health. Volume 8 of Issue 4. 2010. PMID: 20377338


  95. 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. Polymorphisms in the Pseudomonas aeruginosa type III secretion protein, PcrV - implications for anti-PcrV immunotherapy. Volume 48 of Issue 6. 2010. PMID: 20211240


  96. 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. Relationship between cystic fibrosis respiratory tract bacterial communities and age, genotype, antibiotics and Pseudomonas aeruginosa. Volume 12 of Issue 5. 2010. PMID: 20192960


  97. Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV. A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. Volume 14 of Issue 1. 2010. PMID: 20141328


  98. Cox MJ, Huang YJ, Fujimura KE, Liu JT, McKean M, Boushey HA, Segal MR, Brodie EL, Cabana MD, Lynch SV. Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome. 2010. PMID: 20090909


  99. 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. Induction of intestinal Th17 cells by segmented filamentous bacteria. Volume 139 of Issue 3. 2009. PMID: 19836068


  100. 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. Volume 77 of Issue 11. 2009. PMID: 19737893


  101. El-Solh AA, Amsterdam D, Alhajhusain A, Akinnusi ME, Saliba RG, Lynch SV, Wiener-Kronish JP. Matrix metalloproteases in bronchoalveolar lavage fluid of patients with type III Pseudomonas aeruginosa pneumonia. Volume 59 of Issue 1. 2009. PMID: 19535150


  102. Lynch SV, Wiener-Kronish JP. Novel strategies to combat bacterial virulence. Volume 14 of Issue 5. 2008. PMID: 18787455


  103. 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. Increased mortality of ventilated patients with endotracheal Pseudomonas aeruginosa without clinical signs of infection. Volume 36 of Issue 9. 2008. PMID: 18679122


  104. 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. Role of small GTPases and alphavbeta5 integrin in Pseudomonas aeruginosa-induced increase in lung endothelial permeability. Volume 40 of Issue 1. 2008. PMID: 18703797


  105. El Solh AA, Akinnusi ME, Wiener-Kronish JP, Lynch SV, Pineda LA, Szarpa K. Persistent infection with Pseudomonas aeruginosa in ventilator-associated pneumonia. Volume 178 of Issue 5. 2008. PMID: 18467510


  106. 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. Role of integrin alphav beta6 in acute lung injury induced by Pseudomonas aeruginosa. Volume 76 of Issue 6. 2008. PMID: 18378634


  107. 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. Volume 14 of Issue 4. 2008. PMID: 18190571


  108. Lynch SV, 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. Volume 51 of Issue 10. 2007. PMID: 17664315


  109. Yoo J, Tcheurekdjian H, Lynch SV, Cabana M, Boushey HA. Microbial manipulation of immune function for asthma prevention: inferences from clinical trials. 2007. PMID: 17607013


  110. Flanagan JL, Brodie EL, Weng L, Lynch SV, 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. Volume 45 of Issue 6. 2007. PMID: 17409203


  111. Song Y, Wiener-Kronish JP, Flanagan J, Lynch SV. Alveolar hemostasis in patients with species-specific bacterial-mediated ventilator-associated pneumonia. Volume 35 of Issue 2. 2007. PMID: 17251717


  112. 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. Increased plasminogen activator inhibitor-1 concentrations in bronchoalveolar lavage fluids are associated with increased mortality in a cohort of patients with Pseudomonas aeruginosa. Volume 106 of Issue 2. 2007. PMID: 17264718


  113. Augustin DK, Song Y, Baek MS, Sawa Y, Singh G, Taylor B, Rubio-Mills A, Flanagan JL, Wiener-Kronish JP, Lynch SV. Presence or absence of lipopolysaccharide O antigens affects type III secretion by Pseudomonas aeruginosa. Volume 189 of Issue 6. 2007. PMID: 17209027


  114. Lynch SV, Mukundakrishnan K, Benoit MR, Ayyaswamy PS, Matin A. Escherichia coli biofilms formed under low-shear modeled microgravity in a ground-based system. Volume 72 of Issue 12. 2006. PMID: 17028231


  115. Ackerley DF, Barak Y, Lynch SV, Curtin J, Matin A. Effect of chromate stress on Escherichia coli K-12. Volume 188 of Issue 9. 2006. PMID: 16621832


  116. Barak Y, Thorne SH, Ackerley DF, Lynch SV, Contag CH, Matin A. New enzyme for reductive cancer chemotherapy, YieF, and its improvement by directed evolution. Volume 5 of Issue 1. 2006. PMID: 16432167


  117. Gonzalez CF, Ackerley DF, Lynch SV, Matin A. ChrR, a soluble quinone reductase of Pseudomonas putida that defends against H2O2. Volume 280 of Issue 24. 2005. PMID: 15840577


  118. 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. Volume 343 of Issue 1. 2004. PMID: 15563836


  119. Irwin JA, Lynch SV, 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. Volume 7 of Issue 2. 2003. PMID: 12664266


  120. Caffrey P, Lynch S, Flood E, Finnan S, Oliynyk M. Amphotericin biosynthesis in Streptomyces nodosus: deductions from analysis of polyketide synthase and late genes. Volume 8 of Issue 7. 2001. PMID: 11451671