An Appropriate Cutoff Value for Determining the Colonization of Helicobacter pylori by the Pyrosequencing Method: Comparison with Conventional Methods

Helicobacter

Volumn 20, Issue 5, 2015, Pages 370-380

  Kim, Jaeyeon ^a,b   Kim, Nayoung ^a,b   Jo, Hyun Jin ^a   Park, Ji Hyun ^b   Nam, Ryoung Hee ^a   Seok, Yeong Jae ^c   Kim, Yeon Ran ^c   Kim, Joo Sung ^b   Kim, Jung Mogg ^d   Kim, Jung Min ^e   Lee, Dong Ho ^a,b   Jung, Hyun Chae ^b  

^a Seoul National University Bundang Hospital   (South Korea)

^b Seoul National University College of Medicine   (South Korea)

^c Seoul National University   (South Korea)

^d Hanyang University   (South Korea)

^e Daejeon University   (South Korea)

Author keywords

Helicobacter pylori; 16S ribosomal RNA; Gastric microbiota; Stomach

Indexed keywords

AMOXICILLIN; CLARITHROMYCIN; DNA 16S; PROTON PUMP INHIBITOR; BACTERIAL DNA; RIBOSOME DNA; RNA 16S;

ADULT; AGED; ARTICLE; ATROPHIC GASTRITIS; BACTERIAL COLONIZATION; CLINICAL ARTICLE; CONTROLLED STUDY; ERADICATION THERAPY; FEMALE; FOLLOW UP; GASTRIC MUCOSA; HELICOBACTER INFECTION; HELICOBACTER PYLORI; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; INTESTINE METAPLASIA; MALE; MIDDLE AGED; NEUTROPHIL CHEMOTAXIS; NONHUMAN; PRIORITY JOURNAL; PYROSEQUENCING; RAPID UREASE TEST; RECEIVER OPERATING CHARACTERISTIC; STOMACH BIOPSY; STOMACH CANCER; VERY ELDERLY; BACTERIAL LOAD; BIOPSY; CHEMISTRY; DNA SEQUENCE; GENETICS; HELICOBACTER INFECTIONS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PROCEDURES;

ADULT; AGED; AGED, 80 AND OVER; BACTERIAL LOAD; BIOPSY; DNA, BACTERIAL; DNA, RIBOSOMAL; FEMALE; GASTRIC MUCOSA; HELICOBACTER INFECTIONS; HELICOBACTER PYLORI; HUMANS; MALE; MIDDLE AGED; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84941749494     PISSN: 10834389     EISSN: 15235378     Source Type: Journal    
DOI: 10.1111/hel.12214     Document Type: Article

References (34)

1. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006;444:1027-31.
2. Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 2004;118:229-41.
3. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 2005;122:107-18.
4. Hattori M, Taylor TD. The human intestinal microbiome: a new frontier of human biology. DNA Res 2009;16:1-12.
5. Correa P, Houghton J. Carcinogenesis of Helicobacter pylori. Gastroenterology 2007;133:659-72.
6. Verdu EF, Armstrong D, Fraser R, Viani F, Idstrom JP, Cederberg C, Blum AL. Effect of Helicobacter pylori status on intragastric pH during treatment with omeprazole. Gut 1995;36:539-43.
7. Mowat C, Williams C, Gillen D, Hossack M, Gilmour D, Carswell A, Wirz A, Preston T, McColl KE. Omeprazole, Helicobacter pylori status, and alterations in the intragastric milieu facilitating bacterial N-nitrosation. Gastroenterology 2000;119:339-47.
8. Kuipers EJ, Lundell L, Klinkenberg-Knol EC, et al. Atrophic gastritis and Helicobacter pylori infection in patients with reflux esophagitis treated with omeprazole or fundoplication. N Engl J Med 1996;334:1018-22.
9. Dekio I, Hayashi H, Sakamoto M, Kitahara M, Nishikawa T, Suematsu M, Benno Y. Detection of potentially novel bacterial components of the human skin microbiota using culture-independent molecular profiling. J Med Microbiol 2005;54:1231-8.
10. Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature 2009;457:480-4.
11. Verma R, Verma AK, Ahuja V, Paul J. Real-time analysis of mucosal flora in patients with inflammatory bowel disease in India. J Clin Microbiol 2010;48:4279-82.
12. Noor SO, Ridgway K, Scovell L, Kemsley EK, Lund EK, Jamieson C, Johnson IT, Narbad A. Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of the gut microbiota. BMC Gastroenterol 2010;10:134.
13. Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ, Relman DA. Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci USA 2006;103:732-7.
14. Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P, Engstrand L. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One 2008;3:e2836.
15. Dicksved J, Lindberg M, Rosenquist M, Enroth H, Jansson JK, Engstrand L. Molecular characterization of the stomach microbiota in patients with gastric cancer and in controls. J Med Microbiol 2009;58:509-16.
16. Monstein HJ, Tiveljung A, Kraft CH, Borch K, Jonasson J. Profiling of bacterial flora in gastric biopsies from patients with Helicobacter pylori-associated gastritis and histologically normal control individuals by temperature gradient gel electrophoresis and 16S rDNA sequence analysis. J Med Microbiol 2000;49:817-22.
17. Hu B, El Hajj N, Sittler S, Lammert N, Barnes R, Meloni-Ehrig A. Gastric cancer: classification, histology and application of molecular pathology. J Gastrointest Oncol 2012;3:251-61.
18. Dixon MF, Genta RM, Yardley JH, Correa P. Classification and grading of gastritis. The updated Sydney System. International Workshop on the Histopathology of Gastritis, Houston 1994. Am J Surg Pathol 1996;20:1161-81.
19. Shin CM, Kim N, Lee HS, et al. Validation of diagnostic tests for Helicobacter pylori with regard to grade of atrophic gastritis and/or intestinal metaplasia. Helicobacter 2009;14:512-9.
20. Yoon H, Kim N, Lee HS, Shin CM, Park YS, Lee DH, Jung HC, Song IS. Helicobacter pylori-negative gastric cancer in South Korea: incidence and clinicopathologic characteristics. Helicobacter 2011;16:382-8.
21. Hur M, Kim Y, Song HR, Kim JM, Choi YI, Yi H. Effect of genetically modified poplars on soil microbial communities during the phytoremediation of waste mine tailings. Appl Environ Microbiol 2011;77:7611-9.
22. Chun J, Kim KY, Lee JH, Choi Y. The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer. BMC Microbiol 2010;10:101.
23. Huber T, Faulkner G, Hugenholtz P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 2004;20:2317-9.
24. Kim OS, Cho YJ, Lee K, et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716-21.
25. Yang I, Nell S, Suerbaum S. Survival in hostile territory: the microbiota of the stomach. FEMS Microbiol Rev 2013;37:736-61.
26. Wu WM, Yang YS, Peng LH. Microbiota in the stomach: new insights. J Dig Dis 2014;15:54-61.
27. von Rosenvinge EC, Song Y, White JR, Maddox C, Blanchard T, Fricke WF. Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota. ISME J 2013;7:1354-66.
28. Li XX, Wong GLH, To KF, Wong VWS, Lai LH, Chow DKL, Lau JY, Sung JJ, Ding C. Bacterial microbiota profiling in gastritis without Helicobacter pylori infection or non-steroidal anti-inflammatory drug use. PLoS One 2009;4:e7985.
29. Delgado S, Cabrera-Rubio R, Mira A, Suarez A, Mayo B. Microbiological survey of the human gastric ecosystem using culturing and pyrosequencing methods. Microb Ecol 2013;65:763-72.
30. Kim MS, Kim N, Kim SE, et al. Long-term follow up Helicobacter pylori reinfection rate and its associated factors in Korea. Helicobacter 2013;18:135-42.
31. Kim MS, Kim N, Kim SE, Jo HJ, Shin CM, Park YS, Lee DH Long-term followup Helicobacter pylori reinfection rate after second-line treatment: bismuth-containing quadruple therapy versus moxifloxacin-based triple therapy. BMC Gastroenterol 2013;13:138.
32. Gebara EC, Faria CM, Pannuti C, Chehter L, Mayer MP, Lima LA. Persistenceof Helicobacter pylori in the oral cavity after systemic eradication therapy. J Clin Periodontol 2006;33:329-33.
33. Aviles-Jimenez F, Vazquez-Jimenez F, Medrano-Guzman R, Mantilla A, Torres J. Stomach microbiota composition varies between patients with non-atrophic gastritis and patients with intestinal type of gastric cancer. Sci Rep 2014;26:4.
34. Han HS, Lee KY, Lim SD, Kim WS, Hwang TS. Molecular identification of Helicobacter DNA in human gastric adenocarcinoma tissues using Helicobacter species-specific 16S rRNA PCR amplification and pyrosequencing analysis. Oncol Lett 2010;1:555-8.