No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls

Scientific Reports

Volumn 5, Issue , 2014, Pages

  Dlugosz, Aldona ^a   Winckler, Björn ^b   Lundin, Elin ^c   Zakikhany, Katherina ^d   Sandström, Gunnar ^b   Ye, Weimin ^b   Engstrand, Lars ^e   Lindberg, Greger ^a  

^a KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^b KAROLINSKA INSTITUTE   (Sweden)

^c STOCKHOLM UNIVERSITY   (Sweden)

^d SWEDISH INSTITUTE FOR INFECTIOUS DISEASE CONTROL   (Sweden)

^e SCIENCE FOR LIFE LABORATORY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ADOLESCENT; ADULT; BIODIVERSITY; CASE CONTROL STUDY; CLUSTER ANALYSIS; FEMALE; HUMAN; IRRITABLE BOWEL SYNDROME; MALE; METAGENOME; MICROBIOLOGY; MICROFLORA; MIDDLE AGED; PRINCIPAL COMPONENT ANALYSIS; SMALL INTESTINE; YOUNG ADULT;

ADOLESCENT; ADULT; BIODIVERSITY; CASE-CONTROL STUDIES; CLUSTER ANALYSIS; FEMALE; HUMANS; INTESTINE, SMALL; IRRITABLE BOWEL SYNDROME; MALE; METAGENOME; MICROBIOTA; MIDDLE AGED; PRINCIPAL COMPONENT ANALYSIS; YOUNG ADULT;

EID: 84923335326     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep08508     Document Type: Article

References (48)

1. Savage, D. C. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 31, 107-133 (1977).
2. Quigley, E. M. & Abu-Shanab, A. Small intestinal bacterial overgrowth. Infect Dis Clin North Am 24, 943-959, viii-ix (2010).
3. Gorbach, S. L. & Bengt E. Gustafsson memorial lecture. Function of the normal human microflora. Scand J Infect Dis Suppl 49, 17-30 (1986).
4. Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
5. Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174-180, doi:10.1038/nature09944 (2011).
6. Willing, B. et al. Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease. Inflamm Bowel Dis 15, 653-660 (2009).
7. Vijay-Kumar, M. et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328, 228-231 (2010).
8. Bäckhed, F. et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 101, 15718-15723 (2004).
9. El-Aidy, S., van den Bogert, B. & Kleerebezem, M. The small intestine microbiota, nutritional modulation and relevance for health. Curr Opin Biotechnol 32, 14-20, doi:10.1016/j.copbio.2014.09.005 (2015).
10. Zoetendal, E. G. et al. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J 6, 1415-1426, doi:10.1038/ismej.2011.212 (2012).
11. Booijink, C. C. et al. High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol 12, 3213-3227, doi:10.1111/j.1462-2920.2010.02294.x (2010).
12. Parkes, G. C. et al. Distinct microbial populations exist in the mucosa-associated microbiota of sub-groups of irritable bowel syndrome. Neurogastroenterol Motil 24, 31-39, doi:10.1111/j.1365-2982.2011.01803.x (2012).
13. Thompson, W. G. et al. Functional bowel disorders and functional abdominal pain. Gut 45 Suppl 2, II43-47 (1999).
14. Kassinen, A. et al. The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology 133, 24-33 (2007).
15. Salonen, A., de Vos, W.M. & Palva, A. Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. Microbiology 156, 3205-3215 (2010).
16. Jeffery, I. B. et al. An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut 61, 997-1006, doi:10.1136/gutjnl-2011-301501 (2012).
17. Kerckhoffs, A. P. et al. Lower Bifidobacteria counts in both duodenal mucosaassociated and fecal microbiota in irritable bowel syndrome patients. World J Gastroenterol 15, 2887-2892 (2009).
18. Pimentel, M., Chow, E. J. & Lin, H. C. Normalization of lactulose breath testing correlates with symptom improvement in irritablebowel syndrome. a double-blind, randomized, placebo-controlled study. Am J Gastroenterol 98, 412-419 (2003).
19. Stotzer, P. O., Bjornsson, E. S. & Abrahamsson, H. Interdigestive and postprandial motility in small-intestinal bacterial overgrowth. Scand J Gastroenterol 31, 875-880 (1996).
20. Bouhnik, Y. et al. Bacterial populations contaminating the upper gut in patients with small intestinal bacterial overgrowth syndrome. Am J Gastroenterol 94, 1327-1331 (1999).
21. Andersson, A. F. et al. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One 3, e2836 (2008).
22. Lundin, D. et al. Which sequencing depth is sufficient to describe patterns in bacterial alpha- and beta-diversity? Environ Microbiol Rep 4, 367-372, doi:10.1111/j.1758-2229.2012.00345.x (2012).
23. White, J. R., Nagarajan, N. & Pop, M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5, e1000352, doi:10.1371/journal.pcbi.1000352 (2009).
24. Caliński, T. & Harabasz, J. Adendrite method for cluster analysis. Commun Stat 3, 1-27 (1974).
25. Rousseeuw, P. J. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 20, 53-65 (1987).
26. Tibshirani, R. & Walther, G. Cluster validation by prediction strength. J Comput Graph Stat 14, 511-528 (2005).
27. Zilberstein, B. et al. Digestive tract microbiota in healthy volunteers. Clinics (Sao Paulo) 62, 47-54 (2007).
28. Amann, R. I., Ludwig, W. & Schleifer, K. H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59, 143-169 (1995).
29. Vaughan, E. E. et al. A molecular view of the intestinal ecosystem. Curr Issues Intest Microbiol 1, 1-12 (2000).
30. Wang, M., Ahrne, S., Jeppsson, B. & Molin, G. Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. FEMSMicrobiol Ecol 54, 219-231, doi:10.1016/j.femsec.2005.03.012 (2005).
31. Pei, Z. et al. Bacterial biota in the human distal esophagus. Proc Natl Acad Sci USA 101, 4250-4255 (2004).
32. Franzosa, E. A. et al. Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci U S A 111, E2329-2338, doi:10.1073/pnas.1319284111 (2014).
33. Krogius-Kurikka, L. et al. Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoeapredominant irritable bowel syndrome sufferers. BMC Gastroenterol 9, 95 (2009).
34. Lyra, A. et al. Diarrhoea-predominant irritable bowel syndrome distinguishable by 16S rRNA gene phylotype quantification. World J Gastroenterol 15, 5936-5945 (2009).
35. Ford, A. C., Spiegel, B. M., Talley, N. J. & Moayyedi, P. Small intestinal bacterial overgrowth in irritable bowel syndrome: systematic review and meta-analysis. Clin Gastroenterol Hepatol 7, 1279-1286 (2009).
36. Bures, J. et al. Small intestinal bacterial overgrowth syndrome. World J Gastroenterol 16, 2978-2990 (2010).
37. Yu, D., Cheeseman, F. & Vanner, S. Combined oro-caecal scintigraphy and lactulose hydrogen breath testing demonstrate that breath testing detects orocaecal transit, not small intestinal bacterial overgrowth in patients with IBS. Gut 60, 334-340 (2011).
38. Ohman, L., Tornblom, H. & Simren, M. Crosstalk at the mucosal border: importance of the gut microenvironment in IBS. Nat Rev Gastroenterol Hepatol, doi:10.1038/nrgastro.2014.200 (2014).
39. Codling, C., O'Mahony, L., Shanahan, F., Quigley, E. M. & Marchesi, J. R. A molecular analysis of fecal and mucosal bacterial communities in irritable bowel syndrome. Dig Dis Sci 55, 392-397 (2010).
40. Rajilic-Stojanovic, M., Smidt, H. & de Vos, W. M. Diversity of the human gastrointestinal tractmicrobiota revisited. Environ Microbiol 9, 2125-2136 (2007).
41. Yong, E. Gut microbial 'enterotypes' become less clear-cut. Nature, doi:10.1038/nature.2012.10276 (2012).
42. Koren, O. et al. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol 9, e1002863, doi:10.1371/journal.pcbi.1002863 (2013).
43. Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol 8, e1002606, doi:10.1371/journal.pcbi.1002606 (2012).
44. Bushman, F. D., Lewis, J. D. & Wu, G. D. Diet, gut enterotypes and health: is there a link? Nestle Nutr Inst Workshop Ser 77, 65-73, doi:10.1159/000351385 (2013).
45. Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10, 996-998, doi:10.1038/nmeth.2604 (2013).
46. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335-336, doi:10.1038/nmeth.f.303 (2010).
47. DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72, 5069-5072, doi:10.1128/aem.03006-05 (2006).
48. Haas, B. J. et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21, 494-504, doi:10.1101/gr.112730.110 (2011).