Esophageal microbiome in eosinophilic esophagitis

PLoS ONE

Volumn 10, Issue 5, 2015, Pages

  Harris, J Kirk ^a   Fang, Rui ^b   Wagner, Brandie D ^a,b   Choe, Ha Na ^c   Kelly, Caleb J ^c   Schroeder, Shauna ^c   Moore, Wendy ^c   Stevens, Mark J ^a   Yeckes, Alyson ^c   Amsden, Katie ^d,e   Kagalwalla, Amir F ^d,e   Zalewski, Angelika ^d   Hirano, Ikuo ^d   Gonsalves, Nirmala ^d   Henry, Lauren N ^c   Masterson, Joanne C ^c   Robertson, Charles E ^f   Leung, Donald Y ^g   Pace, Norman R ^f   Ackerman, Steven J ^h   Furuta, Glenn T ^c   Fillon, Sophie A ^c   more..

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b Global Health and Health Disparities   (United States)

^c UNIVERSITY OF COLORADO   (United States)

^d NORTHWESTERN UNIVERSITY   (United States)

^e Jr Hospital of Cook County   (United States)

^f UNIVERSITY OF COLORADO   (United States)

^g DEPARTMENT OF MEDICINE   (United States)

^h UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTON PUMP INHIBITOR; RNA 16S; BACTERIAL RNA;

ADOLESCENT; ADULT; ANIMAL TISSUE; ARTICLE; BACTERIAL LOAD; CHILD; CONTROLLED STUDY; DISEASE ASSOCIATION; EOSINOPHILIA; EOSINOPHILIC ESOPHAGITIS; ESOPHAGEAL STRING TEST; ESOPHAGUS MUCOSA; FEMALE; GASTROESOPHAGEAL REFLUX; GENE AMPLIFICATION; HAEMOPHILUS; HUMAN; LABORATORY TEST; MAJOR CLINICAL STUDY; MALE; MICROBIAL COMMUNITY; MICROBIOME; NONHUMAN; POLYMERASE CHAIN REACTION; PROSPECTIVE STUDY; PYROSEQUENCING; QUANTITATIVE ANALYSIS; STREPTOCOCCUS; CLINICAL TRIAL; GENETICS; HIGH THROUGHPUT SEQUENCING; MICROBIOLOGY; MICROFLORA; MIDDLE AGED;

BACTERIA (MICROORGANISMS); HAEMOPHILUS; STREPTOCOCCUS;

ADOLESCENT; ADULT; CHILD; EOSINOPHILIC ESOPHAGITIS; FEMALE; GASTROESOPHAGEAL REFLUX; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MICROBIOTA; MIDDLE AGED; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S;

EID: 84934992212     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0128346     Document Type: Article

References (35)

1. Sherrill JD, Kc K, Wu D, Djukic Z, Caldwell JM, Stucke EM, et al. Desmoglein-1 regulates esophageal epithelial barrier function and immune responses in eosinophilic esophagitis. Mucosal immunology. 2014;7(2014):718-29. Epub 2013/11/14. doi:10.1038/mi.2013.90 PMID:24220297; PubMed Central PMCID: PMC3999291.
2. Lehrer RI, Szklarek D, Barton A, Ganz T, Hamann KJ, Gleich GJ. Antibacterial properties of eosinophil major basic protein and eosinophil cationic protein. J Immunol. 1989;142(1989):4428-34. Epub 1989/06/15. PMID:2656865.
3. Driss V, Legrand F, Hermann E, Loiseau S, Guerardel Y, Kremer L, et al. TLR2-dependent eosinophil interactions with mycobacteria: role of {alpha}-defensins. Blood. 2008. Epub 2008/11/04. doi: blood-2008-07-166595 [pii] doi:10.1182/blood-2008-07-166595 PMID:18978205.
4. Yousefi S, Gold JA, Andina N, Lee JJ, Kelly AM, Kozlowski E, et al. Catapult-like release of mitochondrial DNA by eosinophils contributes to antibacterial defense. Nat Med. 2008;14(2008):949-53. Epub 2008/08/12. doi: nm.1855 [pii] doi:10.1038/nm.1855 PMID:18690244.
5. Fillon SA, Harris JK, Wagner BD, Kelly CJ, Stevens MJ, Moore W, et al. Novel device to sample the esophageal microbiome-the esophageal string test. PloS one. 2012;7(2012):e42938. Epub 2012/09/08. doi:10.1371/journal.pone.0042938 PMID:22957025; PubMed Central PMCID: PMC3434161.
6. Furuta GT, Kagalwalla AF, Lee JJ, Alumkal P, Maybruck BT, Fillon S, et al. The oesophageal string test: a novel, minimally invasive method measures mucosal inflammation in eosinophilic oesophagitis. Gut. 2012. Epub 2012/08/17. doi:10.1136/gutjnl-2012-303171 PMID:22895393.
7. Furuta GT, Liacouras CA, Collins MH, Gupta SK, Justinich C, Putnam PE, et al. Eosinophilic esophagitis in children and adults: a systematic review and consensus recommendations for diagnosis and treatment. Gastroenterology. 2007;133(2007):1342-63. Epub 2007/10/09. doi: S0016-5085 (07) 01474-6 [pii] doi:10.1053/j.gastro.2007.08.017 PMID:17919504.
8. Liacouras CA, Furuta GT, Hirano I, Atkins D, Attwood SE, Bonis PA, et al. Eosinophilic esophagitis: Updated consensus recommendations for children and adults. J Allergy Clin Immunol. 2011;128(2011):3-20 e6. Epub 2011/04/12. doi: S0091-6749 (11) 00373-3 [pii] doi:10.1016/j.jaci.2011.02.040 PMID:21477849.
9. Attwood SE, Furuta GT. Eosinophilic Esophagitis: Historical Perspective on an Evolving Disease. Gastroenterology clinics of North America. 2014;43(2014):185-99. Epub 2014/05/13. doi:10.1016/j.gtc. 2014.02.010 PMID:24813509; PubMed Central PMCID: PMC4035232.
10. Zemanick ET, Harris JK, Wagner BD, Robertson CE, Sagel SD, Stevens MJ, et al. Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PloS one. 2013;8(2013):e62917. Epub 2013/05/07. doi:10.1371/journal.pone.0062917 PMID:23646159; PubMed Central PMCID: PMC3639911.
11. Harris JK, Sahl JW, Castoe TA, Wagner BD, Pollock DD, Spear JR. Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing. Appl Environ Microbiol. 2010;76(2010):3863-8. Epub 2010/04/27. doi:10.1128/AEM.02585-09 PMID:20418443; PubMed Central PMCID: PMC2893486.
12. Frank DN. BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics. 2009;10:362. Epub 2009/10/31. doi:10.1186/1471-2105-10-362 PMID:19874596; PubMed Central PMCID: PMC2777893.
13. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics. 2009;25(2009):1335-7. Epub 2009/03/25. doi:10.1093/bioinformatics/btp157 PMID:19307242; PubMed Central PMCID: PMC2732312.
14. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome research. 2011;21(2011):494-504. Epub 2011/01/08. doi:10.1101/gr.112730.110 PMID:21212162; PubMed Central PMCID: PMC3044863.
15. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73(2007):5261-7. Epub 2007/06/26. doi:10.1128/AEM.00062-07 PMID:17586664; PubMed Central PMCID: PMC1950982.
16. Rutebemberwa A, Stevens MJ, Perez MJ, Smith LP, Sanders L, Cosgrove G, et al. Novosphingobium and its potential role in chronic obstructive pulmonary diseases: insights from microbiome studies. PloS one. 2014;9(2014):e111150. Epub 2014/10/24. doi:10.1371/journal.pone.0111150 PMID:25340840; PubMed Central PMCID: PMC4207766.
17. Nadkarni MA, Martin FE, Jacques NA, Hunter N. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology. 2002;148(Pt 1):257-66. Epub 2002/01/10. PMID:11782518.
18. Zemanick ET, Wagner BD, Sagel SD, Stevens MJ, Accurso FJ, Harris JK. Reliability of quantitative real-time PCR for bacterial detection in cystic fibrosis airway specimens. PloS one. 2010;5(2010):e15101. Epub 2010/12/15. doi:10.1371/journal.pone.0015101 PMID:21152087; PubMed Central PMCID: PMC2994853.
19. Jost L. Entropy and Diversity. OIKOS. 2006;113:363-75.
20. Wagner BD, Robertson CE, Harris JK. Application of two-part statistics for comparison of sequence variant counts. PloS one. 2011;6(2011):e20296. Epub 2011/06/02. doi:10.1371/journal.pone.0020296 PMID:21629788; PubMed Central PMCID: PMC3100341.
21. Aitchison J. The Statistical Analysis of Compositional Data, Monographs on statistics and applied probability. Chapman and Hall, London. 1986.
22. Filzmoser P, Hron K, Reimann C. Univariate statistical analysis of environmental (compositional) data: problems and possibilities. The Science of the total environment. 2009;407(2009):6100-8. Epub 2009/09/11. doi:10.1016/j.scitotenv. 2009.08.008 PMID:19740525.
23. Robertson CE, Harris JK, Wagner BD, Granger D, Browne K, Tatem B, et al. Explicet: Graphical user interface software for metadata-driven management, analysis, and visualization of microbiome data. Bioinformatics. 2013. Epub 2013/09/12. doi:10.1093/bioinformatics/btt526 PMID:24021386.
24. Yang L, Lu X, Nossa CW, Francois F, Peek RM, Pei Z. Inflammation and intestinal metaplasia of the distal esophagus are associated with alterations in the microbiome. Gastroenterology. 2009;137(2009):588-97. Epub 2009/04/28. doi: S0016-5085 (09) 00559-9 [pii] doi:10.1053/j.gastro.2009.04.046 PMID:19394334.
25. Amir I, Konikoff FM, Oppenheim M, Gophna U, Half EE. Gastric microbiota is altered in oesophagitis and Barrett's oesophagus and further modified by proton pump inhibitors. Environmental microbiology. 2013. Epub 2013/10/12. doi:10.1111/1462-2920.12285 PMID:24112768.
26. Vesper BJ, Jawdi A, Altman KW, Haines GK 3rd, Tao L, Radosevich JA. The effect of proton pump inhibitors on the human microbiota. Current drug metabolism. 2009;10(2009):84-9. Epub 2009/01/20. PMID:19149516.
27. Yang L, Francois F, Pei Z. Molecular pathways: pathogenesis and clinical implications of microbiome alteration in esophagitis and Barrett esophagus. Clin Cancer Res. 2012;18(2012):2138-44. Epub 2012/02/22. doi:10.1158/1078-0432. CCR-11-0934 PMID:22344232; PubMed Central PMCID: PMC3725293.
28. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(2014):559-63. Epub 2013/12/18. doi:10.1038/nature12820 PMID:24336217.
29. Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, Fontana L, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science. 2011;332(2011):970-4. Epub 2011/05/21. doi:10.1126/science.1198719 PMID:21596990; PubMed Central PMCID: PMC3303602.
30. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457(2009):480-4. Epub 2008/12/02. doi: nature07540 [pii] doi:10.1038/nature07540 PMID:19043404.
31. Albenberg LG, Wu GD. Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease. Gastroenterology. 2014. Epub 2014/02/08. doi:10.1053/j.gastro.2014.01.058 PMID:24503132.
32. Zoetendal EG, de Vos WM. Effect of diet on the intestinal microbiota and its activity. Curr Opin Gastroenterol. 2014;30(2014):189-95. Epub 2014/01/25. doi:10.1097/MOG.0000000000000048 PMID:24457346.
33. Sherrill JD, Kc K, Wu D, Djukic Z, Caldwell JM, Stucke EM, et al. Desmoglein-1 regulates esophageal epithelial barrier function and immune responses in eosinophilic esophagitis. Mucosal immunology. 2013. Epub 2013/11/14. doi:10.1038/mi.2013.90 PMID:24220297.
34. Clementi CF, Murphy TF. Non-typeable Haemophilus influenzae invasion and persistence in the human respiratory tract. Frontiers in cellular and infection microbiology. 2011;1:1. Epub 2011/01/01. doi:10.3389/fcimb.2011.00001 PMID:22919570; PubMed Central PMCID: PMC3417339.
35. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(2012):222-7. Epub 2012/06/16. doi:10.1038/nature11053 PMID:22699611; PubMed Central PMCID: PMC3376388.