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Current understanding of the human microbiome.

Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R.

Nat Med. 2018 Apr 10;24(4):392-400. doi: 10.1038/nm.4517. Review.


Dog introduction alters the home dust microbiota.

Sitarik AR, Havstad S, Levin AM, Lynch SV, Fujimura KE, Ownby DR, Johnson CC, Wegienka G.

Indoor Air. 2018 Feb 22. doi: 10.1111/ina.12456. [Epub ahead of print]


Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation.

Durack J, Kimes NE, Lin DL, Rauch M, McKean M, McCauley K, Panzer AR, Mar JS, Cabana MD, Lynch SV.

Nat Commun. 2018 Feb 16;9(1):707. doi: 10.1038/s41467-018-03157-4.


Role of the lung microbiome in HIV pathogenesis.

Shenoy MK, Lynch SV.

Curr Opin HIV AIDS. 2018 Jan;13(1):45-52. doi: 10.1097/COH.0000000000000427.


Lung Microbiota Is Related to Smoking Status and to Development of Acute Respiratory Distress Syndrome in Critically Ill Trauma Patients.

Panzer AR, Lynch SV, Langelier C, Christie JD, McCauley K, Nelson M, Cheung CK, Benowitz NL, Cohen MJ, Calfee CS.

Am J Respir Crit Care Med. 2018 Mar 1;197(5):621-631. doi: 10.1164/rccm.201702-0441OC.


Early-life home environment and risk of asthma among inner-city children.

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.

J Allergy Clin Immunol. 2018 Apr;141(4):1468-1475. doi: 10.1016/j.jaci.2017.06.040. Epub 2017 Sep 19.


Prenatal antimicrobial use and early-childhood body mass index.

Cassidy-Bushrow AE, Burmeister C, Havstad S, Levin AM, Lynch SV, Ownby DR, Rundle AG, Woodcroft KJ, Zoratti EM, Johnson CC, Wegienka G.

Int J Obes (Lond). 2018 Jan;42(1):1-7. doi: 10.1038/ijo.2017.205. Epub 2017 Aug 17.


Breast Milk Transforming Growth Factor β Is Associated With Neonatal Gut Microbial Composition.

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.

J Pediatr Gastroenterol Nutr. 2017 Sep;65(3):e60-e67. doi: 10.1097/MPG.0000000000001585.


Limited engraftment of donor microbiome via one-time fecal microbial transplantation in treated HIV-infected individuals.

Vujkovic-Cvijin I, Rutishauser RL, Pao M, Hunt PW, Lynch SV, McCune JM, Somsouk M.

Gut Microbes. 2017 Sep 3;8(5):440-450. doi: 10.1080/19490976.2017.1334034. Epub 2017 May 25.


Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences.

Cope EK, Goldberg AN, Pletcher SD, Lynch SV.

Microbiome. 2017 May 12;5(1):53. doi: 10.1186/s40168-017-0266-6.


Lactobacillus johnsonii supplementation attenuates respiratory viral infection via metabolic reprogramming and immune cell modulation.

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.

Mucosal Immunol. 2017 Nov;10(6):1569-1580. doi: 10.1038/mi.2017.13. Epub 2017 Mar 15.


The Lung Microbiome and Airway Disease.

Lynch SV.

Ann Am Thorac Soc. 2016 Dec;13(Supplement_5):S462-S465. doi: 10.1513/AnnalsATS.201605-356AW. Review.


The Human Intestinal Microbiome in Health and Disease.

Lynch SV, Pedersen O.

N Engl J Med. 2016 Dec 15;375(24):2369-2379. Review. No abstract available.


Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment.

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; National Heart, Lung and Blood Institute's “AsthmaNet”.

J Allergy Clin Immunol. 2017 Jul;140(1):63-75. doi: 10.1016/j.jaci.2016.08.055. Epub 2016 Nov 10.


Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls.

Tremlett H, Fadrosh DW, Faruqi AA, Hart J, Roalstad S, Graves J, Spencer CM, Lynch SV, Zamvil SS, Waubant E; US Network of Pediatric MS Centers.

BMC Neurol. 2016 Sep 21;16(1):182.


Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation.

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.

Nat Med. 2016 Oct;22(10):1187-1191. doi: 10.1038/nm.4176. Epub 2016 Sep 12.


A chronic rhinosinusitis-derived isolate of Pseudomonas aeruginosa induces acute and pervasive effects on the murine upper airway microbiome and host immune response.

Cope EK, Goldberg AN, Pletcher SD, Lynch SV.

Int Forum Allergy Rhinol. 2016 Dec;6(12):1229-1237. doi: 10.1002/alr.21819. Epub 2016 Sep 6.


Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity.

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.

Sci Rep. 2016 Aug 25;6:31775. doi: 10.1038/srep31775.


Disease Severity and Immune Activity Relate to Distinct Interkingdom Gut Microbiome States in Ethnically Distinct Ulcerative Colitis Patients.

Mar JS, LaMere BJ, Lin DL, Levan S, Nazareth M, Mahadevan U, Lynch SV.

MBio. 2016 Aug 16;7(4). pii: e01072-16. doi: 10.1128/mBio.01072-16.


Dual epithelial and immune cell function of Dvl1 regulates gut microbiota composition and intestinal homeostasis.

Belinson H, Savage AK, Fadrosh D, Kuo YM, Lin D, Valladares R, Nusse Y, Wynshaw-Boris A, Lynch SV, Locksley RM, Klein OD.

JCI Insight. 2016 Jul 7;1(10). pii: e85395.


Promotion of Epithelial Barrier Integrity Via Probiotic-derived Products.

Durack J, Lynch SV.

J Pediatr Gastroenterol Nutr. 2017 Mar;64(3):335-336. doi: 10.1097/MPG.0000000000001350. No abstract available.


Immune Response and Mortality Risk Relate to Distinct Lung Microbiomes in Patients with HIV and Pneumonia.

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.

Am J Respir Crit Care Med. 2017 Jan 1;195(1):104-114. doi: 10.1164/rccm.201603-0523OC.


Airway Microbiota and the Implications of Dysbiosis in Asthma.

Durack J, Boushey HA, Lynch SV.

Curr Allergy Asthma Rep. 2016 Jul;16(8):52. doi: 10.1007/s11882-016-0631-8. Review.


Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis.

Santee CA, Nagalingam NA, Faruqi AA, DeMuri GP, Gern JE, Wald ER, Lynch SV.

Microbiome. 2016 Jul 1;4(1):34. doi: 10.1186/s40168-016-0179-9.


Bacteroides are associated with GALT iNKT cell function and reduction of microbial translocation in HIV-1 infection.

Paquin-Proulx D, Ching C, Vujkovic-Cvijin I, Fadrosh D, Loh L, Huang Y, Somsouk M, Lynch SV, Hunt PW, Nixon DF, SenGupta D.

Mucosal Immunol. 2017 Jan;10(1):69-78. doi: 10.1038/mi.2016.34. Epub 2016 Apr 6.


Gut Microbiota and Allergic Disease. New Insights.

Lynch SV.

Ann Am Thorac Soc. 2016 Mar;13 Suppl 1:S51-4. doi: 10.1513/AnnalsATS.201507-451MG. Review.


The microbiome and development of allergic disease.

Lynch SV, Boushey HA.

Curr Opin Allergy Clin Immunol. 2016 Apr;16(2):165-71. doi: 10.1097/ACI.0000000000000255. Review.


Race-specific Association of Caesarean-Section Delivery with Body Size at Age 2 Years.

Cassidy-Bushrow AE, Wegienka G, Havstad S, Levin AM, Lynch SV, Ownby DR, Rundle AG, Woodcroft KJ, Zoratti EM, Johnson CC.

Ethn Dis. 2016 Jan 21;26(1):61-8. doi: 10.18865/ed.26.1.61.


Clinical Features, Virus Identification, and Sinusitis as a Complication of Upper Respiratory Tract Illness in Children Ages 4-7 Years.

DeMuri GP, Gern JE, Moyer SC, Lindstrom MJ, Lynch SV, Wald ER.

J Pediatr. 2016 Apr;171:133-9.e1. doi: 10.1016/j.jpeds.2015.12.034. Epub 2016 Jan 16.


Gut-Resident Lactobacillus Abundance Associates with IDO1 Inhibition and Th17 Dynamics in SIV-Infected Macaques.

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.

Cell Rep. 2015 Nov 24;13(8):1589-97. doi: 10.1016/j.celrep.2015.10.026. Epub 2015 Nov 12.


Future Research Directions in Asthma. An NHLBI Working Group Report.

Levy BD, Noel PJ, Freemer MM, Cloutier MM, Georas SN, Jarjour NN, Ober C, Woodruff PG, Barnes KC, Bender BG, Camargo CA Jr, 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.

Am J Respir Crit Care Med. 2015 Dec 1;192(11):1366-72. doi: 10.1164/rccm.201505-0963WS. Review.


Maternal group B Streptococcus and the infant gut microbiota.

Cassidy-Bushrow AE, Sitarik A, Levin AM, Lynch SV, Havstad S, Ownby DR, Johnson CC, Wegienka G.

J Dev Orig Health Dis. 2016 Feb;7(1):45-53. doi: 10.1017/S2040174415001361. Epub 2015 Aug 12.


Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.

Beck JM, Schloss PD, Venkataraman A, Twigg H 3rd, 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; Lung HIV Microbiome Project.

Am J Respir Crit Care Med. 2015 Dec 1;192(11):1335-44. doi: 10.1164/rccm.201501-0128OC.


The airway microbiome in patients with severe asthma: Associations with disease features and severity.

Huang YJ, Nariya S, Harris JM, Lynch SV, Choy DF, Arron JR, Boushey H.

J Allergy Clin Immunol. 2015 Oct;136(4):874-84. doi: 10.1016/j.jaci.2015.05.044. Epub 2015 Jul 26.


Influence and effect of the human microbiome in allergy and asthma.

Panzer AR, Lynch SV.

Curr Opin Rheumatol. 2015 Jul;27(4):373-80. doi: 10.1097/BOR.0000000000000191. Review.


Microbiota in allergy and asthma and the emerging relationship with the gut microbiome.

Fujimura KE, Lynch SV.

Cell Host Microbe. 2015 May 13;17(5):592-602. doi: 10.1016/j.chom.2015.04.007. Review.


Novel microbiome-based therapeutics for chronic rhinosinusitis.

Cope EK, Lynch SV.

Curr Allergy Asthma Rep. 2015 Mar;15(3):504. doi: 10.1007/s11882-014-0504-y.


Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens.

Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch SV.

PLoS One. 2015 Feb 6;10(2):e0117617. doi: 10.1371/journal.pone.0117617. eCollection 2015.


Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in Pediatric Patients: Encouragement Wrapped in Caution.

Lynch SV.

J Pediatr Gastroenterol Nutr. 2015 Jan;60(1):1-3. doi: 10.1097/MPG.0000000000000612. No abstract available.


Does pet-keeping modify the association of delivery mode with offspring body size?

Cassidy-Bushrow AE, Wegienka G, Havstad S, Levin AM, Lynch SV, Ownby DR, Rundle AG, Woodcroft KJ, Zoratti EM, Johnson CC.

Matern Child Health J. 2015 Jun;19(6):1426-33. doi: 10.1007/s10995-014-1649-y.


Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems.

Ardeshir A, Narayan NR, Méndez-Lagares G, Lu D, Rauch M, Huang Y, Van Rompay KK, Lynch SV, Hartigan-O'Connor DJ.

Sci Transl Med. 2014 Sep 3;6(252):252ra120. doi: 10.1126/scitranslmed.3008791.


Amelioration of DSS-induced murine colitis by VSL#3 supplementation is primarily associated with changes in ileal microbiota composition.

Mar JS, Nagalingam NA, Song Y, Onizawa M, Lee JW, Lynch SV.

Gut Microbes. 2014 Jul 1;5(4):494-503. doi: 10.4161/gmic.32147. Epub 2014 Aug 4.


Effects of early-life exposure to allergens and bacteria on recurrent wheeze and atopy in urban children.

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.

J Allergy Clin Immunol. 2014 Sep;134(3):593-601.e12. doi: 10.1016/j.jaci.2014.04.018. Epub 2014 Jun 4.


Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease.

Huang YJ, Sethi S, Murphy T, Nariya S, Boushey HA, Lynch SV.

J Clin Microbiol. 2014 Aug;52(8):2813-23. doi: 10.1128/JCM.00035-14. Epub 2014 May 21.


Fecal microbial therapy: promises and pitfalls.

Merenstein D, El-Nachef N, Lynch SV.

J Pediatr Gastroenterol Nutr. 2014 Aug;59(2):157-61. doi: 10.1097/MPG.0000000000000415. Review.


Rearrangement of a large novel Pseudomonas aeruginosa gene island in strains isolated from a patient developing ventilator-associated pneumonia.

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.

J Clin Microbiol. 2014 Jul;52(7):2430-8. doi: 10.1128/JCM.01626-13. Epub 2014 Apr 30.


The lung microbiome of Ugandan HIV-infected pneumonia patients is compositionally and functionally distinct from that of San Franciscan patients.

Iwai S, Huang D, Fong S, Jarlsberg LG, Worodria W, Yoo S, Cattamanchi A, Davis JL, Kaswabuli S, Segal M, Huang L, Lynch SV.

PLoS One. 2014 Apr 21;9(4):e95726. doi: 10.1371/journal.pone.0095726. eCollection 2014.


Donor-transmitted, donor-derived, and de novo cancer after liver transplant.

Chapman JR, Lynch SV.

Exp Clin Transplant. 2014 Mar;12 Suppl 1:50-4. Review.


Viruses and microbiome alterations.

Lynch SV.

Ann Am Thorac Soc. 2014 Jan;11 Suppl 1:S57-60. doi: 10.1513/AnnalsATS.201306-158MG. Review.


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