Diversity of duodenal and rectal microbiota in biopsy tissues and luminal contents in healthy volunteers

Journal of Microbiology and Biotechnology

Volumn 25, Issue 7, 2015, Pages 1136-1145

  Li, Gangping ^a   Yang, Min ^a   Zhou, Kan ^a   Zhang, Lei ^a   Tian, Lugao ^a   Lv, Shangze ^a   Jin, Yu ^a   Qian, Wei ^a   Xiong, Hanhua ^a   Lin, Rong ^a   Fu, Yu ^a   Hou, Xiaohua ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Biopsy; Duodenum; Feces; Microbiota; Mucus; Rectum

Indexed keywords

BACTERIAL DNA; RNA 16S; RIBOSOME DNA;

ACINETOBACTER; ADULT; ARTICLE; BACTERIUM ISOLATION; BACTEROIDES; BIODIVERSITY; BIOINFORMATICS; DNA ISOLATION; DUODENUM BIOPSY; FECES; FEMALE; GENETIC VARIABILITY; HUMAN; HUMAN TISSUE; INTESTINE FLORA; MALE; MICROBIAL COMMUNITY; NONHUMAN; PHYLOGENY; PREVOTELLA; PROTEOBACTERIA; PYROSEQUENCING; RECTUM BIOPSY; SEQUENCE ANALYSIS; BACTERIUM; BIOPSY; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; DUODENUM; GENETICS; INTESTINE MUCOSA; MICROBIOLOGY; MICROFLORA; MIDDLE AGED; MOLECULAR GENETICS; NORMAL HUMAN; RECTUM; YOUNG ADULT;

ACINETOBACTER; BACTERIA (MICROORGANISMS); BACTEROIDES; OTUS; PREVOTELLA; PROTEOBACTERIA;

ADULT; BACTERIA; BIOPSY; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; DUODENUM; FEMALE; GASTROINTESTINAL MICROBIOME; HEALTHY VOLUNTEERS; HUMANS; INTESTINAL MUCOSA; MALE; MICROBIOTA; MIDDLE AGED; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECTUM; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; YOUNG ADULT;

EID: 84937410038     PISSN: 10177825     EISSN: 17388872     Source Type: Journal    
DOI: 10.4014/jmb.1412.12047     Document Type: Article

References (42)

1. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. 2011. Enterotypes of the human gut microbiome. Nature 473: 174-180.
2. Baba N, Samson S, Bourdet-Sicard R, Rubio M, Sarfati M. 2008. Commensal bacteria trigger a full dendritic cell maturation program that promotes the expansion of non- Tr1 suppressor T cells. J. Leukoc. Biol. 84: 468-476.
3. Bohm M, Siwiec RM, Wo JM. 2013. Diagnosis and management of small intestinal bacterial overgrowth. Nutr. Clin. Pract. 28: 289-299.
4. Brock TD, Madigan MT. 1988. Biology of Microorganisms, pp. 42-59. 5th Ed. Prentice Hall, Englewood Cliffs, New Jersey.
5. Brown CT, Davis-Richardson AG, Giongo A, Gano KA, Crabb DB, Mukherjee N, et al. 2011. Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes. PLoS One 6: e25792.
6. Bruce-Keller AJ, Salbaum JM, Luo M, Blanchard E 4th, Taylor CM, Welsh DA, Berthoud HR. 2015. Obese-type gut microbiota induce neurobehavioral changes in the absence of obesity. Biol. Psychiatry 77: 607-615.
7. Carroll IM, Ringel-Kulka T, Siddle JP, Ringel Y. 2012. Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome. Neurogastroenterol. Motil. 24: 521-530.
8. Chen L, Wang W, Zhou R, Ng SC, Li J, Huang M, et al. 2014. Characteristics of fecal and mucosa-associated microbiota in Chinese patients with inflammatory bowel disease. Medicine (Baltimore) 93: e51.
9. Cheng J, Kalliomäki M, Heilig HG, Palva A, Lähteenoja H, de Vos WM, et al. 2013. Duodenal microbiota composition and mucosal homeostasis in pediatric celiac disease. BMC Gastroenterol. 13: 113.
10. Clarke SF, Murphy EF, O’Sullivan O, Lucey AJ, Humphreys M, Hogan A, et al. 2014. Exercise and associated dietary extremes impact on gut microbial diversity. Gut 63: 1913-1920.
11. Dethlefsen L, McFall-Ngai M, Relman DA. 2007. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449: 811-818.
12. Di Cagno R, De Angelis M, De Pasquale I, Ndagijimana M, Vernocchi P, Ricciuti P, et al. 2011. Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization. BMC Microbiol. 11: 219.
13. El Aidy S, van den Bogert B, Kleerebezem M. 2014. The small intestine microbiota nutritional modulation and relevance for health. Curr. Opin. Biotechnol. 32C: 14-20.
14. Gersemann M, Wehkamp J, Stange EF. 2012. Innate immune dysfunction in inflammatory bowel disease. J. Intern. Med. 271: 421-428.
15. Gupta A, Dhiman RK, Kumari S, Rana S, Agarwal R, Duseja A, Chawla Y. 2010. Role of small intestinal bacterial overgrowth and delayed gastrointestinal transit time in cirrhotic patients with minimal hepatic encephalopathy. J. Hepatol. 53: 849-855.
16. Jiménez E, Sánchez B, Farina A, Margolles A, Rodríguez JM. 2014. Characterization of the bile and gall bladder microbiota of healthy pigs. Microbiologyopen 3: 937-949.
17. Kalliomäki M, Satokari R, Lähteenoja H, Vähämiko S, Grönlund J, Routi T, Salminen S. 2012. Expression of microbiota, Toll-like receptors, and their regulators in the small intestinal mucosa in celiac disease. J. Pediatr. Gastroenterol. Nutr. 54: 727-732.
18. Karwautz C, Lueders T. 2014. Impact of hydraulic well restoration on native bacterial communities in drinking water wells. Microbes Environ. 29: 363-369.
19. Knights D, Ward T L, McKinlay C E, Miller H, Gonzalez A, McDonald D, Knight R. 2014. Rethinking “enterotypes”. Cell Host Microbe 16: 433-437.
20. Kunisawa T. 2011. Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison. Antonie Van Leeuwenhoek 99: 417-422.
21. Lim MY, Rho M, Song YM, Lee K, Sung J, Ko G. 2014. Stability of gut enterotypes in korean monozygotic twins and their association with biomarkers and diet. Sci. Rep. 4: 7348.
22. Madrid AM, Poniachik J, Quera R, Defilippi C. 2011. Small intestinal clustered contractions and bacterial overgrowth: a frequent finding in obese patients. Dig. Dis. Sci. 56: 155-160.
23. Nam YD, Jung MJ, Roh SW, Kim MS, Bae JW. 2011. Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing. PLoS One 6: e22109.
24. Nieuwdorp M, Gilijamse PW, Pai N, Kaplan LM. 2014. Role of the microbiome in energy regulation and metabolism. Gastroenterology 146: 1525-1533.
25. Peleg AY, de Breij A, Adams MD, Cerqueira GM, Mocali S, Galardini M, et al. 2012. The success of Acinetobacter spec ies; genetic, metabolic and virulence attributes. PLoS One 7: e46984.
26. Qin N, Yang F, Li A, Prifti E, Chen Y, Shao L, et al. 2014. Alterations of the human gut microbiome in liver cirrhosis. Nature 513: 59-64.
27. Quigley EM. 2014. Small intestinal bacterial overgrowth: what it is and what it is not. Curr. Opin. Gastroenterol. 30: 141-146.
28. Rønnestad I, Akiba Y, Kaji I, Kaunitz JD. 2014. Duodenal luminal nutrient sensing. Curr. Opin. Pharmacol. 19C: 67-75.
29. Rubio-Tapia A, Barton SH, Rosenblatt JE, Murray JA. 2009. Prevalence of small intestine bacterial overgrowth diagnosed by quantitative culture of intestinal aspirate in celiac disease. J. Clin. Gastroenterol. 43: 157-161.
30. Sánchez E, Donat E, Ribes-Koninckx C, Fernández-Murga ML, Sanz Y. 2013. Duodenal-mucosal bacteria associated with celiac disease in children. Appl. Environ. Microbiol. 79: 5472-5479.
31. Schippa S, Iebba V, Barbato M, Di Nardo G, Totino V, Checchi MP, et al. 2010. A distinctive ‘microbial signature’ in celiac pediatric patients. BMC Microbiol. 10: 175.
32. Sobhani I, Tap J, Roudot-Thoraval F, Roperch JP, Letulle S, Langella P, et al. 2011. Microbial dysbiosis in colorectal cancer (CRC) patients. PLoS One 6: e16393.
33. Stearns JC, Lynch MD, Senadheera DB, Tenenbaum HC, Goldberg MB, Cvitkovitch DG, et al. 2011. Bacterial biogeography of the human digestive tract. Sci. Rep. 1: 170.
34. Stellato G, La Storia A, Cirillo T, Ercolini D. 2015. Bacterial biogeographical patterns in a cooking center for hospital foodservice. Int. J. Food Microbiol. 193: 99-108.
35. Taverniti V, Guglielmetti S. 2014. Methodological issues in the study of intestinal microbiota in irritable bowel syndrome. World J. Gastroenterol. 20: 8821-8836.
36. Vital M, Howe AC, Tiedje JM. 2014. Revealing the bacterial butyrate synthesis pathways by analyzing (meta) genomic data. mBio 5: e00889.
37. Wacklin P, Kaukinen K, Tuovinen E, Collin P, Lindfors K, Partanen J, et al. 2013. The duodenal microbiota composition of adult celiac disease patients is associated with the clinical manifestations of the disease. Inflamm. Bowel Dis. 19: 934-941.
38. Walker MM, Talley NJ. 2014. Review article: bacteria and pathogenesis of disease in the upper gastrointestinal tract - beyond the era of Helicobacter pylori. Aliment. Pharmacol. Ther. 39: 767-779.
39. Wang ZK, Yang YS. 2013. Upper gastrointestinal microbiota and digestive diseases. World J. Gastroenterol. 19: 1541-1550.
40. Wrighton KC, Castelle CJ, Wilkins MJ, Hug LA, Sharon I, Thomas BC, et al. 2014. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. ISME J. 8: 1452-1463.
41. Zhang Z, Geng J, Tang X, Fan H, Xu J, Wen X, et al. 2014. Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota. ISME J. 8: 881-893.
42. Zhou M, Rong R, Munro D, Zhu C, Gao X, Zhang Q, Dong Q. 2013. Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing. PLoS One 8: e61516.