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Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis.

Glatz M, Jo JH, Kennedy EA, Polley EC, Segre JA, Simpson EL, Kong HH.

PLoS One. 2018 Feb 28;13(2):e0192443. doi: 10.1371/journal.pone.0192443. eCollection 2018.


Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance.

Weingarten RA, Johnson RC, Conlan S, Ramsburg AM, Dekker JP, Lau AF, Khil P, Odom RT, Deming C, Park M, Thomas PJ; NISC Comparative Sequencing Program, Henderson DK, Palmore TN, Segre JA, Frank KM.

MBio. 2018 Feb 6;9(1). pii: e02011-17. doi: 10.1128/mBio.02011-17.


The human skin microbiome.

Byrd AL, Belkaid Y, Segre JA.

Nat Rev Microbiol. 2018 Mar;16(3):143-155. doi: 10.1038/nrmicro.2017.157. Epub 2018 Jan 15. Review.


Carbapenemase-Producing Organisms: A Global Scourge.

Bonomo RA, Burd EM, Conly J, Limbago BM, Poirel L, Segre JA, Westblade LF.

Clin Infect Dis. 2018 Apr 3;66(8):1290-1297. doi: 10.1093/cid/cix893.


Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation.

Atarashi K, Suda W, Luo C, Kawaguchi T, Motoo I, Narushima S, Kiguchi Y, Yasuma K, Watanabe E, Tanoue T, Thaiss CA, Sato M, Toyooka K, Said HS, Yamagami H, Rice SA, Gevers D, Johnson RC, Segre JA, Chen K, Kolls JK, Elinav E, Morita H, Xavier RJ, Hattori M, Honda K.

Science. 2017 Oct 20;358(6361):359-365. doi: 10.1126/science.aan4526.


Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis.

Byrd AL, Deming C, Cassidy SKB, Harrison OJ, Ng WI, Conlan S; NISC Comparative Sequencing Program, Belkaid Y, Segre JA, Kong HH.

Sci Transl Med. 2017 Jul 5;9(397). pii: eaal4651. doi: 10.1126/scitranslmed.aal4651.


Whole-Genome Sequencing Overrules a Suspected Case of Carbapenem-Resistant Enterobacter cloacae Transmission.

Chen M, Conlan S, Lau AF, Dekker JP, Deming C; NISC Comparative Sequencing Program, Henderson DK, Frank KM, Palmore TN, Segre JA.

J Clin Microbiol. 2017 Sep;55(9):2868-2870. doi: 10.1128/JCM.00915-17. Epub 2017 Jun 28. No abstract available.


Healthcare personnel intestinal colonization with multidrug-resistant organisms.

Decker BK, Lau AF, Dekker JP, Spalding CD, Sinaii N, Conlan S, Henderson DK, Segre JA, Frank KM, Palmore TN.

Clin Microbiol Infect. 2018 Jan;24(1):82.e1-82.e4. doi: 10.1016/j.cmi.2017.05.010. Epub 2017 May 12.


Building a Translational Microbiome Toolbox.

Joglekar P, Segre JA.

Cell. 2017 Apr 20;169(3):378-380. doi: 10.1016/j.cell.2017.04.009.


The Molecular Revolution in Cutaneous Biology: Investigating the Skin Microbiome.

Kong HH, Segre JA.

J Invest Dermatol. 2017 May;137(5):e119-e122. doi: 10.1016/j.jid.2016.07.045. Review.


Performing Skin Microbiome Research: A Method to the Madness.

Kong HH, Andersson B, Clavel T, Common JE, Jackson SA, Olson ND, Segre JA, Traidl-Hoffmann C.

J Invest Dermatol. 2017 Mar;137(3):561-568. doi: 10.1016/j.jid.2016.10.033. Epub 2017 Jan 4. Review.


Skin microbiome before development of atopic dermatitis: Early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year.

Kennedy EA, Connolly J, Hourihane JO, Fallon PG, McLean WHI, Murray D, Jo JH, Segre JA, Kong HH, Irvine AD.

J Allergy Clin Immunol. 2017 Jan;139(1):166-172. doi: 10.1016/j.jaci.2016.07.029. Epub 2016 Sep 5.


Diverse Human Skin Fungal Communities in Children Converge in Adulthood.

Jo JH, Deming C, Kennedy EA, Conlan S, Polley EC, Ng WI; NISC Comparative Sequencing Program, Segre JA, Kong HH.

J Invest Dermatol. 2016 Dec;136(12):2356-2363. doi: 10.1016/j.jid.2016.05.130. Epub 2016 Jul 29.


EVOLUTION. Hominid superorganisms.

Segre JA, Salafsky N.

Science. 2016 Jul 22;353(6297):350-1. doi: 10.1126/science.aag2788. No abstract available.


Complete Genome Sequence of a Klebsiella pneumoniae Strain Carrying blaNDM-1 on a Multidrug Resistance Plasmid.

Conlan S, Lau AF; NISC Comparative Sequencing Program, Palmore TN, Frank KM, Segre JA.

Genome Announc. 2016 Jul 14;4(4). pii: e00664-16. doi: 10.1128/genomeA.00664-16.


Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during Long-Term Patient Colonization.

Conlan S, Park M, Deming C, Thomas PJ, Young AC, Coleman H, Sison C; NISC Comparative Sequencing Program, Weingarten RA, Lau AF, Dekker JP, Palmore TN, Frank KM, Segre JA.

MBio. 2016 Jun 28;7(3). pii: e00742-16. doi: 10.1128/mBio.00742-16.


Horizontal Transfer of Carbapenemase-Encoding Plasmids and Comparison with Hospital Epidemiology Data.

Hardiman CA, Weingarten RA, Conlan S, Khil P, Dekker JP, Mathers AJ, Sheppard AE, Segre JA, Frank KM.

Antimicrob Agents Chemother. 2016 Jul 22;60(8):4910-9. doi: 10.1128/AAC.00014-16. Print 2016 Aug.


Temporal Stability of the Human Skin Microbiome.

Oh J, Byrd AL, Park M; NISC Comparative Sequencing Program, Kong HH, Segre JA.

Cell. 2016 May 5;165(4):854-66. doi: 10.1016/j.cell.2016.04.008.


Colitis susceptibility in p47(phox-/-) mice is mediated by the microbiome.

Falcone EL, Abusleme L, Swamydas M, Lionakis MS, Ding L, Hsu AP, Zelazny AM, Moutsopoulos NM, Kuhns DB, Deming C, Quiñones M, Segre JA, Bryant CE, Holland SM.

Microbiome. 2016 Apr 5;4:13. doi: 10.1186/s40168-016-0159-0.


Signaling in Host-Associated Microbial Communities.

Fischbach MA, Segre JA.

Cell. 2016 Mar 10;164(6):1288-1300. doi: 10.1016/j.cell.2016.02.037. Review.


Detection and Whole-Genome Sequencing of Carbapenemase-Producing Aeromonas hydrophila Isolates from Routine Perirectal Surveillance Culture.

Hughes HY, Conlan SP, Lau AF, Dekker JP, Michelin AV, Youn JH, Henderson DK, Frank KM, Segre JA, Palmore TN.

J Clin Microbiol. 2016 Apr;54(4):1167-70. doi: 10.1128/JCM.03229-15. Epub 2016 Feb 17.


Draft Genome Sequence of a Klebsiella pneumoniae Carbapenemase-Positive Sequence Type 111 Pseudomonas aeruginosa Strain.

Dotson GA; NISC Comparative Sequencing Program, Dekker JP, Palmore TN, Segre JA, Conlan S.

Genome Announc. 2016 Feb 11;4(1). pii: e01663-15. doi: 10.1128/genomeA.01663-15.


Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing.

Tsai YC, Conlan S, Deming C; NISC Comparative Sequencing Program, Segre JA, Kong HH, Korlach J, Oh J.

MBio. 2016 Feb 9;7(1):e01948-15. doi: 10.1128/mBio.01948-15.


Infectious disease. Adapting Koch's postulates.

Byrd AL, Segre JA.

Science. 2016 Jan 15;351(6270):224-6. doi: 10.1126/science.aad6753. No abstract available.


"Bringing Up Baby" to Tolerate Germs.

Nagao K, Segre JA.

Immunity. 2015 Nov 17;43(5):842-4. doi: 10.1016/j.immuni.2015.10.020.


MICROBIOME. Microbial growth dynamics and human disease.

Segre JA.

Science. 2015 Sep 4;349(6252):1058-9. doi: 10.1126/science.aad0781. No abstract available.


Elucidating microbial codes to distinguish individuals.

Byrd AL, Segre JA.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):6778-9. doi: 10.1073/pnas.1507731112. Epub 2015 May 26. No abstract available.


Integrating host gene expression and the microbiome to explore disease pathogenesis.

Byrd AL, Segre JA.

Genome Biol. 2015 Apr 8;16:70. doi: 10.1186/s13059-015-0625-1.


Pseudomonas aeruginosa adaptation to human hosts.

Snitkin ES, Segre JA.

Nat Genet. 2015 Jan;47(1):2-3. doi: 10.1038/ng.3172.


Complete Genome Sequence of a Klebsiella pneumoniae Isolate with Chromosomally Encoded Carbapenem Resistance and Colibactin Synthesis Loci.

Conlan S, Deming C, Tsai YC, Lau AF, Dekker JP, Korlach J, Segre JA.

Genome Announc. 2014 Dec 24;2(6). pii: e01332-14. doi: 10.1128/genomeA.01332-14.


Commensal-dendritic-cell interaction specifies a unique protective skin immune signature.

Naik S, Bouladoux N, Linehan JL, Han SJ, Harrison OJ, Wilhelm C, Conlan S, Himmelfarb S, Byrd AL, Deming C, Quinones M, Brenchley JM, Kong HH, Tussiwand R, Murphy KM, Merad M, Segre JA, Belkaid Y.

Nature. 2015 Apr 2;520(7545):104-8. doi: 10.1038/nature14052. Epub 2015 Jan 5.


Dialogue between skin microbiota and immunity.

Belkaid Y, Segre JA.

Science. 2014 Nov 21;346(6212):954-9. doi: 10.1126/science.1260144. Review.


Biogeography and individuality shape function in the human skin metagenome.

Oh J, Byrd AL, Deming C, Conlan S; NISC Comparative Sequencing Program, Kong HH, Segre JA.

Nature. 2014 Oct 2;514(7520):59-64. doi: 10.1038/nature13786.


Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae.

Conlan S, Thomas PJ, Deming C, Park M, Lau AF, Dekker JP, Snitkin ES, Clark TA, Luong K, Song Y, Tsai YC, Boitano M, Dayal J, Brooks SY, Schmidt B, Young AC, Thomas JW, Bouffard GG, Blakesley RW; NISC Comparative Sequencing Program, Mullikin JC, Korlach J, Henderson DK, Frank KM, Palmore TN, Segre JA.

Sci Transl Med. 2014 Sep 17;6(254):254ra126. doi: 10.1126/scitranslmed.3009845.


Surveillance of carbapenem-resistant Klebsiella pneumoniae: tracking molecular epidemiology and outcomes through a regional network.

van Duin D, Perez F, Rudin SD, Cober E, Hanrahan J, Ziegler J, Webber R, Fox J, Mason P, Richter SS, Cline M, Hall GS, Kaye KS, Jacobs MR, Kalayjian RC, Salata RA, Segre JA, Conlan S, Evans S, Fowler VG Jr, Bonomo RA.

Antimicrob Agents Chemother. 2014 Jul;58(7):4035-41. doi: 10.1128/AAC.02636-14. Epub 2014 May 5.


The altered landscape of the human skin microbiome in patients with primary immunodeficiencies.

Oh J, Freeman AF; NISC Comparative Sequencing Program, Park M, Sokolic R, Candotti F, Holland SM, Segre JA, Kong HH.

Genome Res. 2013 Dec;23(12):2103-14. doi: 10.1101/gr.159467.113. Epub 2013 Oct 29.


Parental dietary fat intake alters offspring microbiome and immunity.

Myles IA, Fontecilla NM, Janelsins BM, Vithayathil PJ, Segre JA, Datta SK.

J Immunol. 2013 Sep 15;191(6):3200-9. doi: 10.4049/jimmunol.1301057. Epub 2013 Aug 9.


What does it take to satisfy Koch's postulates two centuries later? Microbial genomics and Propionibacteria acnes.

Segre JA.

J Invest Dermatol. 2013 Sep;133(9):2141-2. doi: 10.1038/jid.2013.260. Epub 2013 Jul 11.


Topographic diversity of fungal and bacterial communities in human skin.

Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, Schoenfeld D, Nomicos E, Park M; NIH Intramural Sequencing Center Comparative Sequencing Program, Kong HH, Segre JA.

Nature. 2013 Jun 20;498(7454):367-70. doi: 10.1038/nature12171. Epub 2013 May 22.


Genomic insights into the fate of colistin resistance and Acinetobacter baumannii during patient treatment.

Snitkin ES, Zelazny AM, Gupta J; NISC Comparative Sequencing Program, Palmore TN, Murray PR, Segre JA.

Genome Res. 2013 Jul;23(7):1155-62. doi: 10.1101/gr.154328.112. Epub 2013 Apr 5.


Probiotic/prebiotic supplementation of antiretrovirals improves gastrointestinal immunity in SIV-infected macaques.

Klatt NR, Canary LA, Sun X, Vinton CL, Funderburg NT, Morcock DR, Quiñones M, Deming CB, Perkins M, Hazuda DJ, Miller MD, Lederman MM, Segre JA, Lifson JD, Haddad EK, Estes JD, Brenchley JM.

J Clin Invest. 2013 Feb;123(2):903-7. doi: 10.1172/JCI66227. Epub 2013 Jan 16.


Pan-PCR, a computational method for designing bacterium-typing assays based on whole-genome sequence data.

Yang JY, Brooks S, Meyer JA, Blakesley RR, Zelazny AM, Segre JA, Snitkin ES.

J Clin Microbiol. 2013 Mar;51(3):752-8. doi: 10.1128/JCM.02671-12. Epub 2012 Dec 19.


The neuropathic diabetic foot ulcer microbiome is associated with clinical factors.

Gardner SE, Hillis SL, Heilmann K, Segre JA, Grice EA.

Diabetes. 2013 Mar;62(3):923-30. doi: 10.2337/db12-0771. Epub 2012 Nov 8.


Species-level analysis of DNA sequence data from the NIH Human Microbiome Project.

Conlan S, Kong HH, Segre JA.

PLoS One. 2012;7(10):e47075. doi: 10.1371/journal.pone.0047075. Epub 2012 Oct 10.


Shifts in human skin and nares microbiota of healthy children and adults.

Oh J, Conlan S, Polley EC, Segre JA, Kong HH.

Genome Med. 2012 Oct 10;4(10):77. doi: 10.1186/gm378. eCollection 2012.


Genomics: Resident risks.

Oh J, Segre JA.

Nature. 2012 Oct 4;490(7418):44-6. doi: 10.1038/490044a. No abstract available.


Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing.

Snitkin ES, Zelazny AM, Thomas PJ, Stock F; NISC Comparative Sequencing Program Group, Henderson DK, Palmore TN, Segre JA.

Sci Transl Med. 2012 Aug 22;4(148):148ra116. doi: 10.1126/scitranslmed.3004129.


Compartmentalized control of skin immunity by resident commensals.

Naik S, Bouladoux N, Wilhelm C, Molloy MJ, Salcedo R, Kastenmuller W, Deming C, Quinones M, Koo L, Conlan S, Spencer S, Hall JA, Dzutsev A, Kong H, Campbell DJ, Trinchieri G, Segre JA, Belkaid Y.

Science. 2012 Aug 31;337(6098):1115-9. doi: 10.1126/science.1225152. Epub 2012 Jul 26.


Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates.

Conlan S, Mijares LA; NISC Comparative Sequencing Program, Becker J, Blakesley RW, Bouffard GG, Brooks S, Coleman H, Gupta J, Gurson N, Park M, Schmidt B, Thomas PJ, Otto M, Kong HH, Murray PR, Segre JA.

Genome Biol. 2012 Jul 25;13(7):R64. doi: 10.1186/gb-2012-13-7-r64.


The human microbiome: our second genome.

Grice EA, Segre JA.

Annu Rev Genomics Hum Genet. 2012;13:151-70. doi: 10.1146/annurev-genom-090711-163814. Epub 2012 Jun 6. Review.

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