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 β Is Associated With Neonatal Gut Microbial Composition. J Pediatr Gastroenterol Nutr. 2017; 65(3):e60-e67.

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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. Gut Microbes. 2017. doi: 10.1080/19490976.2017.1334034.

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Cope EK, Goldberg AN, Pletcher SD and Lynch, SV. Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences. Microbiome. 2017 DOI10.1186/s40168-017-0266-6.

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Fonseca W, Lucey K, Jang S, Fujimura KE, Rasky A, Ting HA, Petersen J, Johnson CC, Boushey HA, Zoratti E, Ownby DR, Levine AM, Bobbit KR, Lynch SV, Lukacs NW. Lactobacillus johnsonii  supplementation attenuates respiratory viral infection via metabolic reprogramming and immune cell modulation. Mucosal Immunol. 2017 doi: 10.1038/mi.2017.13. 

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Sitarik AR, Bobbitt KR, Havstad SL, Fujimura KE, Levin AM, Zoratti EM, Kim H, Woodcroft KJ, Wegienka G, Ownby DR, Joseph CL, Lynch SV, Johnson CC. Breast Milk TGFβ is Associated with Neonatal Gut Microbial Composition.  J Pediatr Gastroenterol Nutr. 2017 doi: 10.1097/MPG.0000000000001585.

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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 HIV-Pneumonia Patients. Am J Respir Crit Care Med. 2017; 195(1): 104-14. 

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Lynch, S.V. and Pedersen, O. The Human Intestinal Microbiome in Health and Disease. N Eng J Med. 2016; 375 (24), 2369-2379.

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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 M, Wenzel SE, Boushey HA, Huang YJ; National Heart, Lung and Blood Institute's "AsthmaNet". Features of the bronchial bacterial microbiome associated with atopy, asthma and responsiveness to inhaled corticosteroid treatment. J Allergy Clin Immunol. 2016; doi: 10.1016/j.jaci.2016.08.055. 

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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. BMC Neurol. 2016; 16(1): 182

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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. Nat Med. 2016; 22(10): 1187-1191

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Durack J, Lynch SV. Promotion of epithelial barrier integrity via probiotic-derived products. J Pediatr Gastroenterol Nutr; DOI: 10.1097/MPG.0000000000001350

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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. Sci Rep. 2016; 6:31775. PMID: 27558272.

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Mar JS, LaMere BJ, Lin DL, Levan S, Nazareth M, Mahadevan ULynch SV. Disease Severity and Immune Activity Relate to Distinct Interkingdom Gut Microbiome States in Ethnically Distinct Ulcerative Colitis Patients. MBio. 2016; 7(4). PMID: 27531910.

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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. JCI Insight. 2016; 1(10). pii: e85395.

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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. Microbiome. 2016; 4(1):34. PMID: 27364497.

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Durack J, Boushey HA, Lynch SV. Airway Microbiota and the Implications of Dysbiosis in Asthma. Curr Allergy Asthma Rep. 2016 Jul; 16(8):52. PMID: 27393699.

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Lynch SVBoushey HA. The microbiome and development of allergic disease. Curr Opin Allergy Clin Immunol. 2016 Apr; 16(2):165-71. PMID: 26885707.

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Lynch SV. Gut Microbiota and Allergic Disease. New Insights. Ann Am Thorac Soc. 2016 Mar; 13 Suppl 1:S51-4. PMID: 27027953.

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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. Ethn Dis. 2016; 26(1):61-8. PMID: 26843797.

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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. J Pediatr. 2016 Apr; 171:133-139.e1. PMID: 26787374.

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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. Am J Respir Crit Care Med. 2015 Dec 1; 192(11):1366-72. PMID: 26305520.

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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. Am J Respir Crit Care Med. 2015 Dec 1; 192(11):1335-44. PMID: 26247840.

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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 FMPilcher CD, Klatt NR, Brenchley JM, Lynch SV, 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.

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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. J Allergy Clin Immunol. 2015 Oct; 136(4):874-84. PMID: 26220531; PMCID: PMC4600429 [Available on 10/01/16].

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Panzer AR, Lynch SV. Influence and effect of the human microbiome in allergy and asthma. Curr Opin Rheumatol. 2015 Jul; 27(4):373-80. PMID: 26002029.

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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? Matern Child Health J. 2015 Jun; 19(6):1426-33. PMID: 25427878; PMCID: PMC4446256 [Available on 06/01/16].

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Fujimura KELynch SV. 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 [Available on 05/13/16].

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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. PLoS One. 2015; 10(2):e0117617. PMID: 25658760; PMCID: PMC4319838.

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Lynch SV. 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.

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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. Sci Transl Med. 2014 Sep 3; 6(252):252ra120. PMID: 25186175; PMCID: PMC4362692.

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Merenstein D, El-Nachef NLynch SV. Fecal microbial therapy: promises and pitfalls. J Pediatr Gastroenterol Nutr. 2014 Aug; 59(2):157-61. PMID: 24796803.

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Mar JS, Nagalingam NA, Song Y, Onizawa MLee JWLynch SV. Amelioration of DSS-induced murine colitis by VSL#3 supplementation is primarily associated with changes in ileal microbiota composition. Gut Microbes. 2014 Jul 1; 5(4):494-503. PMID: 25144681.

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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 DRWright RJFujimura 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.

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Huang YJ, Sethi S, Murphy T, Nariya S, Boushey HALynch SV. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. J Clin Microbiol. 2014 Aug; 52(8):2813-23. PMID: 24850358; PMCID: PMC4136157.

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Iwai S, Huang D, Fong S, Jarlsberg LG, Worodria W, Yoo S, Cattamanchi ADavis JL, Kaswabuli S, Segal MHuang LLynch SV. 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.

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Lynch SV. Viruses and microbiome alterations. Ann Am Thorac Soc. 2014 Jan; 11 Suppl 1:S57-60. PMID: 24437408.

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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. Proc Natl Acad Sci U S A. 2014 Jan 14; 111(2):805-10. PMID: 24344318; PMCID: PMC3896155.

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Vujkovic-Cvijin I, Dunham RM, Iwai S, Maher MC, Albright RG, Broadhurst MJ, Hernandez RD, Lederman MM, Huang Y, Somsouk MDeeks SGHunt PWLynch SV, 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.

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Nagalingam NA, Cope EKLynch SV. Probiotic strategies for treatment of respiratory diseases. Trends Microbiol. 2013 Sep; 21(9):485-92. PMID: 23707554.

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Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SCFontenot 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. Am J Respir Crit Care Med. 2013 May 15; 187(10):1067-75. PMID: 23491408; PMCID: PMC3734620.

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Lozupone CCota-Gomez APalmer BELinderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TBFlores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SVHuang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight RFontenot 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.

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Lynch SV, Bruce KD. The cystic fibrosis airway microbiome. Cold Spring Harb Perspect Med. 2013 Mar; 3(3):a009738. PMID: 23457293; PMCID: PMC3579208.

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Lynch SV, 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.

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Abreu NA, Nagalingam NA, Song Y, Roediger FCPletcher SDGoldberg ANLynch SV. Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis. Sci Transl Med. 2012 Sep 12; 4(151):151ra124. PMID: 22972842.

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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. J Microbiol Methods. 2012 Nov; 91(2):231-9. PMID: 22975469; PMCID: PMC3615718.

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Iwai S, Fei M, Huang D, Fong S, Subramanian A, Grieco K, Lynch SVHuang L. Oral and airway microbiota in HIV-infected pneumonia patients. J Clin Microbiol. 2012 Sep; 50(9):2995-3002. PMID: 22760045; PMCID: PMC3421777.

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Scanlan PD, Buckling A, Kong W, Wild YLynch SV, Harrison F. Gut dysbiosis in cystic fibrosis. J Cyst Fibros. 2012 Sep; 11(5):454-5. PMID: 22538067.

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Huang YJ, Lynch SVWiener-Kronish JP. From microbe to microbiota: considering microbial community composition in infections and airway diseases. Am J Respir Crit Care Med. 2012 Apr 1; 185(7):691-2. PMID: 22467799.

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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. Cell Microbiol. 2012 May; 14(5):698-709. PMID: 22233488; PMCID: PMC4112999.

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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. Thorax. 2012 May; 67(5):456-63. PMID: 22318161; PMCID: PMC3578398.

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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.

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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. Eur J Clin Microbiol Infect Dis. 2012 Aug; 31(8):1837-45. PMID: 22187351.

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Huang YJ, Lynch SV. 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.

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Rauch M, Lynch SV. The potential for probiotic manipulation of the gastrointestinal microbiome. Curr Opin Biotechnol. 2012 Apr; 23(2):192-201. PMID: 22137452.

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Xu X, Zhang H, Song Y, Lynch SVLowell CAWiener-Kronish JPCaughey 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.

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Nagalingam NA, Lynch SV. Role of the microbiota in inflammatory bowel diseases. Inflamm Bowel Dis. 2012 May; 18(5):968-84. PMID: 21936031.

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Havstad S, Wegienka G, Zoratti EM, Lynch SVBoushey 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.

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Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin XCoarfa CMilosavljevic APetrosino JFHighlander S, Gibbs R, Lynch SVShulman RJVersalovic J. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology. 2011 Nov; 141(5):1782-91. PMID: 21741921; PMCID: PMC3417828.

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Fricks-Lima J, Hendrickson CM, Allgaier M, Zhuo H, Wiener-Kronish JPLynch SVYang 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.

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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 MPeters SPWasserman SI, Wechsler ME, Boushey HALynch SV. 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.

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

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Roediger FC, Slusher NA, Allgaier S, Cox MJ, Pletcher SDGoldberg ANLynch SV. 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.

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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 MENielson D, Brodie EL, Lynch SV. Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One. 2010; 5(6):e11044. PMID: 20585638; PMCID: PMC2890402.

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Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SVKolter R. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. MBio. 2010; 1(3). PMID: 20802827; PMCID: PMC2925076.

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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. Gut Microbes. 2010 7; 1(4):243-253. PMID: 21327031.

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

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Fujimura KE, Slusher NA, Cabana MDLynch SV. Role of the gut microbiota in defining human health. Expert Rev Anti Infect Ther. 2010 Apr; 8(4):435-54. PMID: 20377338; PMCID: PMC2881665.

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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. Microb Pathog. 2010 Jun; 48(6):197-204. PMID: 20211240; PMCID: PMC2860055.

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Klepac-Ceraj V, Lemon KPMartin 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. Environ Microbiol. 2010 May; 12(5):1293-303. PMID: 20192960.

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Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JPLynch SV. A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. OMICS. 2010 Feb; 14(1):9-59. PMID: 20141328; PMCID: PMC3116451.

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Cox MJ, Huang YJ, Fujimura KE, Liu JT, McKean M, Boushey HASegal MR, Brodie EL, Cabana MDLynch SV. Lactobacillus casei abundance is associated with profound shifts in the infant gut microbiome. PLoS One. 2010; 5(1):e8745. PMID: 20090909; PMCID: PMC2807455.

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Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, Wei D, Goldfarb KC, Santee CALynch SV, 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.

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Montor WR, Huang J, Hu Y, Hainsworth E, Lynch S, Kronish JW, Ordonez CL, Logvinenko TLory 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.

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El-Solh AA, Amsterdam D, Alhajhusain A, Akinnusi ME, Saliba RG, Lynch SVWiener-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.

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Lynch SVWiener-Kronish JP. Novel strategies to combat bacterial virulence. Curr Opin Crit Care. 2008 Oct; 14(5):593-9. PMID: 18787455; PMCID: PMC2859961.

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Zhuo H, Yang KLynch 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. Crit Care Med. 2008 Sep; 36(9):2495-503. PMID: 18679122.

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Ganter MT, Roux J, Su GLynch 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. Am J Respir Cell Mol Biol. 2009 Jan; 40(1):108-18. PMID: 18703797; PMCID: PMC2606944.

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El Solh AA, Akinnusi ME, Wiener-Kronish JPLynch SV, Pineda LA, Szarpa K. Persistent infection with Pseudomonas aeruginosa in ventilator-associated pneumonia. Am J Respir Crit Care Med. 2008 Sep 1; 178(5):513-9. PMID: 18467510; PMCID: PMC2542430.

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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. Infect Immun. 2008 Jun; 76(6):2325-32. PMID: 18378634; PMCID: PMC2423078.

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Wong-Beringer A, Wiener-Kronish JLynch 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.

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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. Antimicrob Agents Chemother. 2007 Oct; 51(10):3650-8. PMID: 17664315; PMCID: PMC2043260.

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Yoo J, Tcheurekdjian H, Lynch SVCabana MBoushey 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.

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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. J Clin Microbiol. 2007 Jun; 45(6):1954-62. PMID: 17409203; PMCID: PMC1933106.

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Song Y, Wiener-Kronish JP, Flanagan J, Lynch SV. Alveolar hemostasis in patients with species-specific bacterial-mediated ventilator-associated pneumonia. Crit Care Med. 2007 Feb; 35(2):652-3. PMID: 17251717.

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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. Anesthesiology. 2007 Feb; 106(2):252-61. PMID: 17264718.

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

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Lynch SV, 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.

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Ackerley DF, Barak Y, Lynch SV, 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.

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Barak Y, Thorne SH, Ackerley DF, Lynch SVContag CHMatin 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.

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Gonzalez CF, Ackerley DF, Lynch SVMatin 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.

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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 8; 343(1):107-15. PMID: 15563836.

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Lynch SV, 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.

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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. Extremophiles. 2003 Apr; 7(2):135-43. PMID: 12664266.

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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.

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