Susan Lynch, PhD

PROF IN RES-HCOMP

Our translational human microbiome research program focuses on gastrointestinal and airway microbiome interactions with host immunity that promote or prevent development/maintenance of chronic inflammatory disease. 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.

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
  • Odell Lecture, University of Wisconsin, 2022
  • 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 Innovations, 2014
  • Irish Health and Science award, 2013
  • Dean's Fellow, Stanford University, 2003-2005
Websites
Publications

  1. Altman MC, Janczyk T, Murphy RC, Jayavelu ND, Calatroni A, Kattan M, Gill MA, Stokes J, Liu AH, Khurana Hershey GK, Sherenian M, Kumar R, Robison RG, Gruchalla RS, O'Connor GT, Zoratti EM, Teach SJ, Lynch SV, Dill-McFarland KA, Becker PM, Togias A, Gern JE, Bacharier LB, Busse WW, Jackson DJ, Inner City Asthma Consortium and Childhood Asthma in Urban Settings Network. Inflammatory Pathways in Residual Asthma Exacerbations Among Mepolizumab-Treated Urban Children: A Secondary Analysis of a Randomized Clinical Trial. JAMA pediatrics 2025. PMID: 40658400


  2. Schoettler N, Gebretsadik T, Singh S, Gress L, Mendonça EA, Snyder BM, Eapen AA, LeBeau P, Gangnon R, Seroogy CM, Bacharier LB, Lemanske RF, Lynch SV, Gold DR, Miller RL, Jackson DJ, Hershey GKK, Johnson CC, Martinez FD, Ober C, Hartert TV, Gern JE, ECHO Children's Respiratory and Environmental Workgroup. Genotypes in the 17q12-q21 asthma risk locus and early-life viral wheezing illnesses. Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology 2025. PMID: 40755347


  3. Özçam M, Lin DL, Gupta CL, Li A, Gomez JC, Wheatley LM, Baloh CH, Sanda S, Jones SM, Lynch SV. Gut microbial bile and amino acid metabolism associate with peanut oral immunotherapy failure. Nature communications 2025. PMID: 40634275


  4. Dwyer LR, DeRogatis AM, Clancy S, Gouirand V, Chien C, Rogers EE, Oltman SP, Jelliffe-Pawlowski LL, Lynch SV, Rutishauser RL, Wagner A, Combes AJ, Scharschmidt TC. CD38 expression by neonatal human naïve CD4 + T cells shapes their distinct metabolic state and tolerogenic potential. bioRxiv : the preprint server for biology 2025. PMID: 40667020


  5. Gilbert JA, Azad MB, Bäckhed F, Blaser MJ, Byndloss M, Chiu CY, Chu H, Dugas LR, Elinav E, Gibbons SM, Gilbert KE, Henn MR, Ishaq SL, Ley RE, Lynch SV, Segal E, Spector TD, Strandwitz P, Suez J, Tropini C, Whiteson K, Knight R. Clinical translation of microbiome research. Nature medicine 2025. PMID: 40217076


  6. Phelan KJ, Roskin KM, Burkle JW, Chang WC, Martin LJ, Biagini JM, Satish L, Haslam DB, Spagna D, Jenkins S, Parmar E, Bacharier LB, Gebretsadik T, Gill M, Gold DR, Jackson DJ, Johnson CC, Lynch SV, McCauley KE, McKennan CG, Miller R, Ober C, Ownby DR, Ryan PH, Schoettler N, Singh S, Visness CM, Altman MC, Gern JE, Khurana Hershey GK, Environmental Influences on Child Health Outcomes–Children’s Respiratory and Environmental Workgroup. Early-life wheeze trajectories are associated with distinct asthma transcriptomes later in life. The Journal of allergy and clinical immunology 2025. PMID: 40189159


  7. Claytor JD, Lin DL, Magnaye KM, Guerrero YS, Langelier CR, Lynch SV, El-Nachef N. Effect of Fecal Microbiota Transplant on Antibiotic Resistance Genes Among Patients with Chronic Pouchitis. Digestive diseases and sciences 2025. PMID: 39804518


  8. Eapen AA, Ma T, Sitarik AR, Meng Z, Ownby DR, Cassidy-Bushrow AE, Wegeinka G, Zoratti EM, Lynch SV, Johnson CC, Levin AM. The relationship between the early life gastrointestinal microbiome and childhood nocturnal cough. The Journal of allergy and clinical immunology 2025. PMID: 39814146


  9. Parraga-Leo A, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang AS, Ha CWY, Wong RJ, Minot SS, Andreoletti G, Kosti I, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Lynch SV, Romero R, Tarca AL, Stevenson DK, Aghaeepour N, Golob JL, Sirota M. VMAP: Vaginal Microbiome Atlas during Pregnancy. JAMIA Open 2024. PMID: 39345789


  10. Ramratnam SK, Johnson M, Visness CM, Calatroni A, Altman MC, Janczyk T, McCauley KE, Schachtschneider C, Fujimura KE, Fadrosh DW, Lynch SV, Bacharier LB, O'Connor GT, Sandel MT, Kattan M, Wood RA, Gergen PJ, Jackson DJ, Togias A, Gern JE, Childhood Asthma in Urban Settings (CAUSE) network. Clinical and Molecular Analysis of Longitudinal Rhinitis Phenotypes in an Urban Birth Cohort. The Journal of allergy and clinical immunology 2024. PMID: 39307288


  11. Zhang B, Magnaye KM, Stryker E, Moltzau-Anderson J, Porsche CE, Hertz S, McCauley KE, Smith BJ, Zydek M, Pollard KS, Ma A, El-Nachef N, Lynch SV. Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients. Scientific Reports 2024. PMID: 39122767


  12. Özçam M, Lin DL, Gupta CL, Li A, Wheatley LM, Baloh CH, Sanda S, Jones SM, Lynch SV. Enhanced Gut Microbiome Capacity for Amino Acid Metabolism is associated with Peanut Oral Immunotherapy Failure. medRxiv : the preprint server for health sciences 2024. PMID: 39072014


  13. Lin DL, Magnaye KM, Porsche CE, Levan SR, Rackaityte E, Özçam M, Lynch SV. 12,13-diHOME Promotes Inflammatory Macrophages and Epigenetically Modifies Their Capacity to Respond to Microbes and Allergens. Journal of immunology research 2024. PMID: 38974097


  14. Özçam M, Lynch SV. The gut-airway microbiome axis in health and respiratory diseases. Nature reviews. Microbiology 2024. PMID: 38778224


  15. Hertz S, Anderson JM, Nielsen HL, Schachtschneider C, McCauley KE, Özçam M, Larsen L, Lynch SV, Nielsen H. Fecal microbiota is associated with extraintestinal manifestations in inflammatory bowel disease. Annals of medicine 2024. PMID: 38648495


  16. 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. 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. PMID: 38477719


  17. 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, Gern JE, Lynch SV, National Institute of Allergy and Infectious Diseases-sponsored Childhood Asthma in Urban Settings C. Early-life Nasal Microbiota Dynamics Relate to Longitudinal Respiratory Phenotypes in Urban Children. The Journal of allergy and clinical immunology 2024. PMID: 38423369


  18. Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Oskotsky B, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Preterm Birth DREAM Community, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research. Cell reports. Medicine 2023. PMID: 38134931


  19. 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. Precocious infant fecal microbiome promotes enterocyte barrier dysfuction, altered neuroendocrine signaling and associates with increased childhood obesity risk. Gut microbes 2023. PMID: 38117587


  20. Montassier E, Kitsios GD, Radder JE, Le Bastard Q, Kelly BJ, Panzer A, Lynch SV, Calfee CS, Dickson RP, Roquilly A. Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia. Nature medicine 2023. PMID: 37957375


  21. 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, Bernstein CN, Yeh EA, Casper TC, Lynch SV, Tremlett H, Baranzini S, Waubant E, US Network of Pediatric MS Centers. Short-chain fatty acid producers in the gut are associated with pediatric multiple sclerosis onset. Annals of clinical and translational neurology 2023. PMID: 37955284


  22. Steininger H, Moltzau-Anderson J, Lynch SV. Contributions of the early-life microbiome to childhood atopy and asthma development. Seminars in immunology 2023. PMID: 37379671


  23. Sitarik AR, Johnson CC, Levin AM, Lynch SV, Ownby DR, Rundle AG, Straughen JK, Wegienka G, Woodcroft KJ, Cassidy-Bushrow AE. Progression of C-reactive protein from birth through preadolescence varies by mode of delivery. Frontiers in pediatrics 2023. PMID: 37388285


  24. 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. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. mBio 2023. PMID: 37294090


  25. Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Preterm Birth DREAM Community, Theis KR, Ng S, Lee Li YS, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research. medRxiv : the preprint server for health sciences 2023. PMID: 36945505


  26. Leo AP, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang A, Ha CWY, Wong RJ, Minot SS, Andreoletti G, Kosti I, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Lynch SV, Romero R, Tarca AL, Stevenson DK, Aghaeepour N, Golob J, Sirota M. VMAP: Vaginal Microbiome Atlas During Pregnancy. medRxiv : the preprint server for health sciences 2023. PMID: 36993193


  27. 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 Associations of Maternal Health Characteristics, Newborn Metabolite Concentrations, and Child Body Mass Index among US Children in the ECHO Program. Metabolites 2023. PMID: 37110168


  28. 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. 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. PMID: 36916778


  29. Vercelli D, Lynch SV. Interactions Between Host Epigenetics and Microbiota: Who Does What to Whom, When and Why? The Journal of allergy and clinical immunology 2023. PMID: 36720286


  30. Harringer EOS, Durack J, Piceno Y, Andersen V, Lynch SV. Gluten Degradation by the Gut Microbiota of Ulcerative Colitis Patients. Microorganisms 2022. PMID: 36677307


  31. Ravi K, Rauch M, Lynch SV, Lukacs NW, Huffnagle GB. Complete Genome Sequence of Lactobacillus johnsonii MR1, Isolated from a BALB/c Mouse Cecum. Microbiology resource announcements 2022. PMID: 36511660


  32. 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. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. bioRxiv : the preprint server for biology 2022. PMID: 36523400


  33. 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 JE, Boushey HA, Lynch SV, ECHO Children?s Respiratory and Environmental Workgroup. Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy. Cell reports. Medicine 2022. PMID: 35932762


  34. Chang CJ, Somohano K, Zemsky C, Uhlemann AC, Liebmann J, Cioffi GA, Al-Aswad LA, Lynch SV, Winn BJ. Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome. Investigative ophthalmology & visual science 2022. PMID: 36036910


  35. Ray KJ, Santee C, McCauley K, Panzer AR, Lynch SV. Gut Bifidobacteria enrichment following oral Lactobacillus-supplementation is associated with clinical improvements in children with cystic fibrosis. BMC pulmonary medicine 2022. PMID: 35902830


  36. DeVries A, McCauley K, Fadrosh D, Fujimura KE, Stern DA, Lynch SV, Vercelli D. Maternal prenatal immunity, neonatal trained immunity, and early airway microbiota shape childhood asthma development. Allergy 2022. PMID: 35841380


  37. Huang YJ, Porsche C, Kozik AJ, Lynch SV. Microbiome-Immune Interactions in Allergy and Asthma. The journal of allergy and clinical immunology. In practice 2022. PMID: 35724951


  38. 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. Intestinal inflammation alters the antigen-specific immune response to a skin commensal. 2022. PMID: 35649365


  39. 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. Early-life gut microbiota and attention deficit hyperactivity disorder in preadolescents. 2022. PMID: 35440767


  40. Smith BJ, Piceno Y, Zydek M, Zhang B, Syriani LA, Terdiman JP, Kassam Z, Ma A, Lynch SV, Pollard KS, El-Nachef N. Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis. 2022. PMID: 35365713


  41. 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 JL, Lynch SV, Worodria W, Huang L, Langelier CR. Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study. 2022. PMID: 35544096


  42. 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. Prebiotic to Improve Calcium Absorption in Postmenopausal Women After Gastric Bypass: A Randomized Controlled Trial. 2021. PMID: 34888663


  43. McCauley KE, Flynn K, DiMassa V, LaMere B, Fadrosh DW, Lynch KV, Gill MA, Pongracic JA, Khurana Hershey GK, Kercsmar CM, Liu AH, Johnson CC, Kim H, Kattan M, O'Connor GT, Bacharier LB, Teach SJ, Gergen PJ, Wheatley LM, Togias A, LeBeau P, Calatroni A, Presnell S, Boushey HA, Busse WW, Gern JE, Jackson DJ, Altman MC, Lynch SV, National Institute of Allergy and Infectious Diseases-sponsored Inner-City Asthma Consortium. Seasonal Airway Microbiome and Transcriptome Interactions Promote Childhood Asthma Exacerbations. 2022. PMID: 35149044


  44. Santarossa S, Sitarik AR, Johnson CC, Li J, Lynch SV, Ownby DR, Ramirez A, Yong GL, Cassidy-Bushrow AE. Associations of physical activity with gut microbiota in pre-adolescent children. 2021. PMID: 35152621


  45. McCauley KE, DeMuri G, Lynch K, Fadrosh DW, Santee C, Nagalingam NN, Wald ER, Lynch SV. Moraxella-dominated pediatric nasopharyngeal microbiota associate with upper respiratory infection and sinusitis. 2021. PMID: 34962959


  46. Tsitsiklis A, Zha BS, Byrne A, Devoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay MA, Lynch SV, DeRisi JL, COMET Consortium+ , Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR. Impaired antibacterial immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. medRxiv : the preprint server for health sciences 2021. PMID: 33791731


  47. Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ. Human gut bacterial metabolism drives Th17 activation and colitis. 2021. PMID: 34822777


  48. 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. Maternal gut microbiome regulates immunity to RSV infection in offspring. 2021. PMID: 34613328


  49. Sedghi L, DiMassa V, Harrington A, Lynch SV, Kapila YL. The oral microbiome: Role of key organisms and complex networks in oral health and disease. Periodontology 2000 2021. PMID: 34463991


  50. Horton MK, McCauley K, Fadrosh D, Fujimura K, Graves J, Ness J, Wheeler Y, Gorman MP, Benson LA, Weinstock-Guttman B, Waldman A, Rodriguez M, Tillema JM, Krupp L, Belman A, Mar S, Rensel M, Chitnis T, Casper TC, Rose J, Hart J, Shao X, Tremlett H, Lynch SV, Barcellos LF, Waubant E, U.S. Network of Pediatric MS Centers. Gut microbiome is associated with multiple sclerosis activity in children. Annals of clinical and translational neurology 2021. PMID: 34409759


  51. Hertz S, Durack J, Kirk KF, Nielsen HL, Lin DL, Fadrosh D, Lynch K, Piceno Y, Thorlacius-Ussing O, Nielsen H, Lynch SV. Microscopic Colitis Patients Possess a Perturbed and Inflammatory Gut Microbiota. Digestive diseases and sciences 2021. PMID: 34059992


  52. Magnaye KM, Lynch SV. Fungus fuels mucosal wounds in Crohn's disease. Immunity 2021. PMID: 33979584


  53. Tsitsiklis A, Zha B, Byrne A, DeVoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Neff N, Sarma A, Serpa P, Deiss T, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay M, Lynch S, DeRisi J, Consortium C, Hendrickson C, Kangelaris K, Krummel M, Woodruff P, Erle D, Rosenberg O, Calfee C, Langelier C. Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. Research square 2021. PMID: 34013247


  54. Lynch SV, Vercelli D. 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. PMID: 33493428


  55. Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. Corroborating evidence refutes batch effect as explanation for fetal bacteria. Microbiome 2021. PMID: 33436079


  56. 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. Maternal health, neonatology and perinatology 2020. PMID: 33101701


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


  58. 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. Scientific Reports 2020. PMID: 32999331


  59. Panzer AR, Lynch SV. Gut Microbial Regulation of Autism Spectrum Disorder Symptoms. Trends in endocrinology and metabolism: TEM 2020. PMID: 32972817


  60. 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. International journal of obesity (2005) 2020. PMID: 32873910


  61. 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. Environment international 2020. PMID: 32871381


  62. Ober C, McKennan CG, Magnaye KM, Altman MC, Washington C, Stanhope C, Naughton KA, Rosasco MG, Bacharier LB, Billheimer D, Gold DR, Gress L, Hartert T, Havstad S, Khurana Hershey GK, Hallmark B, Hogarth DK, Jackson DJ, Johnson CC, Kattan M, Lemanske RF, Lynch SV, Mendonca EA, Miller RL, Naureckas ET, O'Connor GT, Seroogy CM, Wegienka G, White SR, Wood RA, Wright AL, Zoratti EM, Martinez FD, Ownby D, Nicolae DL, Levin AM, Gern JE, Environmental Influences on Child Health Outcomes-Children's Respiratory Research Workgroup. Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children: a genetic association and gene expression study. 2020. PMID: 32380068


  63. 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. The Journal of allergy and clinical immunology 2020. PMID: 32298699


  64. Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. Viable bacterial colonization is highly limited in the human intestine in utero. Nature medicine 2020. PMID: 32094926


  65. 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. Nature microbiology 2019. PMID: 31492948


  66. Lynch SV, Ng SC, Shanahan F, Tilg H. Translating the gut microbiome: ready for the clinic? Nature reviews. Gastroenterology & hepatology 2019. PMID: 31562390


  67. 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. Nature microbiology 2019. PMID: 31332384


  68. 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. Digestive diseases and sciences 2019. PMID: 31302808


  69. 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. PloS one 2019. PMID: 31295268


  70. 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. Scientific Reports 2019. PMID: 31209226


  71. 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. The Journal of allergy and clinical immunology 2019. PMID: 31201890


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


  73. 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. United European gastroenterology journal 2019. PMID: 31316785


  74. 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. Microbiome 2019. PMID: 30857553


  75. 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. Journal of pediatric gastroenterology and nutrition 2018. PMID: 30169455


  76. 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. American journal of respiratory and critical care medicine 2018. PMID: 30079758


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


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


  79. 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. Scientific Reports 2018. PMID: 30353125


  80. Durack J, Lynch SV. The gut microbiome: Relationships with disease and opportunities for therapy. The Journal of experimental medicine 2018. PMID: 30322864


  81. Ovesen S, Durack J, Kirk KF, Nielsen HL, Nielsen H, Lynch SV. Motility and biofilm formation of the emerging gastrointestinal pathogen Campylobacter concisus differs under microaerophilic and anaerobic environments. Gut microbes 2018. PMID: 30252590


  82. 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. Microbiome 2018. PMID: 30185226


  83. 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. Microbiome 2018. PMID: 29885665


  84. Lee K, Pletcher SD, Lynch SV, Goldberg AN, Cope EK. 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. PMID: 29876323


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


  86. DeMuri GP, Gern JE, Eickhoff JC, Lynch SV, Wald ER. 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. PMID: 29121208


  87. 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. American journal of respiratory and critical care medicine 2017. PMID: 29035085


  88. 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. Nature communications 2018. PMID: 29453431


  89. Shenoy MK, Lynch SV. Role of the lung microbiome in HIV pathogenesis. Volume 13 of Issue 1. Current opinion in HIV and AIDS 2018. PMID: 29035946


  90. 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. Trauma surgery & acute care open 2017. PMID: 29766103


  91. 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. Volume 141 of Issue 4. The Journal of allergy and clinical immunology 2017. PMID: 28939248


  92. 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. Journal of pediatric gastroenterology and nutrition 2017. PMID: 28827481


  93. 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. Volume 140 of Issue 3. Pediatrics 2017. PMID: 28784701


  94. 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. Gut microbes 2017. PMID: 28541799


  95. Cope EK, Goldberg AN, Pletcher SD, Lynch SV. Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences. Volume 5 of Issue 1. Microbiome 2017. PMID: 28494786


  96. Durack J, Lynch SV. Promotion of Epithelial Barrier Integrity Via Probiotic-derived Products. Volume 64 of Issue 3. Journal of pediatric gastroenterology and nutrition 2017. PMID: 27472476


  97. 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. American journal of respiratory and critical care medicine 2017. PMID: 27447987


  98. Lynch SV, Pedersen O. The Human Intestinal Microbiome in Health and Disease. Volume 375 of Issue 24. The New England journal of medicine 2016. PMID: 27974040


  99. Lynch SV. The Lung Microbiome and Airway Disease. Volume 13 of Issue Supplement_5. Annals of the American Thoracic Society 2016. PMID: 28005424


  100. 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. The Journal of allergy and clinical immunology 2016. PMID: 27838347


  101. 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. BMC neurology 2016. PMID: 27652609


  102. 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. Volume 22 of Issue 10. Nature medicine 2016. PMID: 27618652


  103. Cope EK, Goldberg AN, Pletcher SD, Lynch SV. A chronic rhinosinusitis-derived isolate of Pseudomonas aeruginosa induces acute and pervasive effects on the murine upper airway microbiome and host immune response. Volume 6 of Issue 12. International forum of allergy & rhinology 2016. PMID: 27598436


  104. 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. Volume 6. Scientific Reports 2016. PMID: 27558272


  105. 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. mBio 2016. PMID: 27531910


  106. 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. JCI insight 2016. PMID: 27525310


  107. Durack J, Boushey HA, Lynch SV. Airway Microbiota and the Implications of Dysbiosis in Asthma. Volume 16 of Issue 8. Current allergy and asthma reports 2016. PMID: 27393699


  108. 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. Microbiome 2016. PMID: 27364497


  109. Lynch SV, Boushey HA. The microbiome and development of allergic disease. Volume 16 of Issue 2. Current opinion in allergy and clinical immunology 2016. PMID: 26885707


  110. Lynch SV. Gut Microbiota and Allergic Disease. New Insights. Volume 13 Suppl 1. Annals of the American Thoracic Society 2016. PMID: 27027953


  111. 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. Ethnicity & disease 2016. PMID: 26843797


  112. 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. The Journal of pediatrics 2016. PMID: 26787374


  113. 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. American journal of respiratory and critical care medicine 2015. PMID: 26305520


  114. 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. American journal of respiratory and critical care medicine 2015. PMID: 26247840


  115. 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. Cell reports 2015. PMID: 26586432


  116. 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. Volume 136 of Issue 4. The Journal of allergy and clinical immunology 2015. PMID: 26220531


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


  118. 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. Maternal and child health journal 2015. PMID: 25427878


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


  120. 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. PloS one 2015. PMID: 25658760


  121. Bocca S, Real EB, Lynch S, Stadtmauer L, Beydoun H, Mayer J, Oehninger S. Impact of serum estradiol levels on the implantation rate of cleavage stage cryopreserved-thawed embryos transferred in programmed cycles with exogenous hormonal replacement. Journal of assisted reproduction and genetics 2015. PMID: 25563580


  122. Lynch SV. Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in Pediatric Patients: Encouragement Wrapped in Caution. Volume 60 of Issue 1. Journal of pediatric gastroenterology and nutrition 2015. PMID: 25546336


  123. 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. Science translational medicine 2014. PMID: 25186175


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


  125. 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. Gut microbes 2014. PMID: 25144681


  126. 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. Volume 134 of Issue 3. The Journal of allergy and clinical immunology 2014. PMID: 24908147


  127. Huang YJ, Sethi S, Murphy T, Nariya S, Boushey HA, Lynch SV. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. Volume 52 of Issue 8. Journal of clinical microbiology 2014. PMID: 24850358


  128. Singh G, Srinivasan R, Cheng J, Peng Z, Fujimura K, Baek MS, Panzer AR, Tringe SG, Chen F, Sorek R, Weng L, Bristow J, Wiener-Kronish JP, Lynch SV. Rearrangement of a large novel Pseudomonas aeruginosa gene island in strains isolated from a patient developing ventilator-associated pneumonia. Journal of clinical microbiology 2014. PMID: 24789195


  129. 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. PloS one 2014. PMID: 24752365


  130. Lynch SV. Viruses and microbiome alterations. Volume 11 Suppl 1. Annals of the American Thoracic Society 2014. PMID: 24437408


  131. 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. Volume 111 of Issue 2. Proceedings of the National Academy of Sciences of the United States of America 2013. PMID: 24344318


  132. 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. Science translational medicine 2013. PMID: 23843452


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


  134. 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. American journal of respiratory and critical care medicine 2013. PMID: 23491408


  135. 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. American journal of respiratory and critical care medicine 2013. PMID: 23392441


  136. Lynch SV, Bruce KD. The cystic fibrosis airway microbiome. Volume 3 of Issue 3. Cold Spring Harbor perspectives in medicine 2013. PMID: 23457293


  137. 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. Gut microbes 2012. PMID: 23060053


  138. 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. Science translational medicine 2012. PMID: 22972842


  139. 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. Volume 91 of Issue 2. Journal of microbiological methods 2012. PMID: 22975469


  140. 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. Journal of clinical microbiology 2012. PMID: 22760045


  141. Scanlan PD, Buckling A, Kong W, Wild Y, Lynch SV, Harrison F. Gut dysbiosis in cystic fibrosis. Volume 11 of Issue 5. Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society 2012. PMID: 22538067


  142. 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. American journal of respiratory and critical care medicine 2012. PMID: 22467799


  143. 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. Cellular microbiology 2012. PMID: 22233488


  144. 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. Volume 67 of Issue 5. Thorax 2012. PMID: 22318161


  145. 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. American journal of respiratory and critical care medicine 2012. PMID: 22312017


  146. 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. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2011. PMID: 22187351


  147. Huang YJ, Lynch SV. The emerging relationship between the airway microbiota and chronic respiratory disease: clinical implications. Volume 5 of Issue 6. Expert review of respiratory medicine 2011. PMID: 22082166


  148. Rauch M, Lynch SV. The potential for probiotic manipulation of the gastrointestinal microbiome. Volume 23 of Issue 2. Current opinion in biotechnology 2011. PMID: 22137452


  149. 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. Journal of leukocyte biology 2011. PMID: 22075928


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


  151. 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. Volume 128 of Issue 4. The Journal of allergy and clinical immunology 2011. PMID: 21820714


  152. 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. Gastroenterology 2011. PMID: 21741921


  153. 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. International journal of antimicrobial agents 2011. PMID: 21382698


  154. 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. Volume 127 of Issue 2. The Journal of allergy and clinical immunology 2010. PMID: 21194740


  155. 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. Volume 126 of Issue 2. The Journal of allergy and clinical immunology 2010. PMID: 20633927


  156. 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. American journal of rhinology & allergy 2010. PMID: 20819463


  157. 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. PloS one 2010. PMID: 20585638


  158. 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. mBio 2010. PMID: 20802827


  159. 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. Gut microbes 2010. PMID: 21327031


  160. 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. Microbial pathogenesis 2010. PMID: 20570614


  161. Fujimura KE, Slusher NA, Cabana MD, Lynch SV. Role of the gut microbiota in defining human health. Volume 8 of Issue 4. Expert review of anti-infective therapy 2010. PMID: 20377338


  162. 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. Microbial pathogenesis 2010. PMID: 20211240


  163. 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. Environmental microbiology 2010. PMID: 20192960


  164. 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. Omics : a journal of integrative biology 2010. PMID: 20141328


  165. 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. Volume 5 of Issue 1. PloS one 2010. PMID: 20090909


  166. 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. Cell 2009. PMID: 19836068


  167. 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. Infection and immunity 2009. PMID: 19737893


  168. 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. The Journal of infection 2009. PMID: 19535150


  169. Lynch SV, Wiener-Kronish JP. Novel strategies to combat bacterial virulence. Volume 14 of Issue 5. Current opinion in critical care 2008. PMID: 18787455


  170. 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. Critical care medicine 2008. PMID: 18679122


  171. 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. American journal of respiratory cell and molecular biology 2008. PMID: 18703797


  172. 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. American journal of respiratory and critical care medicine 2008. PMID: 18467510


  173. 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. Infection and immunity 2008. PMID: 18378634


  174. 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. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2008. PMID: 18190571


  175. 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. Antimicrobial agents and chemotherapy 2007. PMID: 17664315


  176. Yoo J, Tcheurekdjian H, Lynch SV, Cabana M, Boushey HA. Microbial manipulation of immune function for asthma prevention: inferences from clinical trials. Volume 4 of Issue 3. Proceedings of the American Thoracic Society 2007. PMID: 17607013


  177. 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. Journal of clinical microbiology 2007. PMID: 17409203


  178. 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. Critical care medicine 2007. PMID: 17251717


  179. 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. Anesthesiology 2007. PMID: 17264718


  180. 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. Journal of bacteriology 2007. PMID: 17209027


  181. 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. Applied and environmental microbiology 2006. PMID: 17028231


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


  183. 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. Molecular cancer therapeutics 2006. PMID: 16432167


  184. 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. The Journal of biological chemistry 2005. PMID: 15840577


  185. 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. Gene 2004. PMID: 15563836


  186. Lynch SV, Brodie EL, Matin A. Role and regulation of sigma S in general resistance conferred by low-shear simulated microgravity in Escherichia coli. Volume 186 of Issue 24. Journal of bacteriology 2004. PMID: 15576768


  187. 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. Extremophiles : life under extreme conditions 2003. PMID: 12664266


  188. 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. Chemistry & biology 2001. PMID: 11451671