Geographical patterns of the standing and active human gut microbiome in health and IBD

Gut

Volumn 65, Issue 2, 2016, Pages 238-248

  Rehman, Ateequr ^a   Rausch, Philipp ^a,b   Wang, Jun ^a,b   Skieceviciene, Jurgita ^a,c   Kiudelis, Gediminas ^c   Bhagalia, Ketan ^d   Amarapurkar, Deepak ^d   Kupcinskas, Limas ^c   Schreiber, Stefan ^a   Rosenstiel, Philip ^a   Baines, John F ^a,b   Ott, Stephan ^a  

^a UNIVERSITY OF KIEL   (Germany)

^b MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

^c LITHUANIAN UNIVERSITY OF HEALTH SCIENCES   (Lithuania)

^d BOMBAY HOSPITAL   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S; RNA 16S; RIBOSOME RNA;

ADOLESCENT; ADULT; AGED; ARTICLE; CLOSTRIDIUM; CLOSTRIDIUM LEPTUM; COLON BIOPSY; COMMUNITY STRUCTURE; CONTROLLED STUDY; CROHN DISEASE; FEMALE; GEOGRAPHIC ORIGIN; GERMANY; HUMAN; HUMAN TISSUE; INDIA; INTESTINE FLORA; LITHUANIA; MALE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; PRIORITY JOURNAL; RNA GENE; RNA TRANSCRIPTION; ULCERATIVE COLITIS; INFLAMMATORY BOWEL DISEASE; INTESTINE MUCOSA; ISOLATION AND PURIFICATION; MICROBIOLOGY; MICROFLORA; MIDDLE AGED; VERY ELDERLY; YOUNG ADULT;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; CLOSTRIDIUM; FEMALE; GERMANY; HUMANS; INDIA; INFLAMMATORY BOWEL DISEASES; INTESTINAL MUCOSA; LITHUANIA; MALE; MICROBIOTA; MIDDLE AGED; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; YOUNG ADULT;

EID: 84958901557     PISSN: 00175749     EISSN: 14683288     Source Type: Journal    
DOI: 10.1136/gutjnl-2014-308341     Document Type: Article

References (54)

1. Thia KT, Loftus JEV, Sandborn WJ, et al. An update on the epidemiology of inflammatory bowel disease in Asia. Am J Gastroenterol 2008; 103: 3167-82.
2. Burisch J, Pedersen N, Cukovic-Cavka S, et al. East-West gradient in the incidence of inflammatory bowel disease in Europe: The ECCO-EpiCom inception cohort. Gut 2014; 63: 588-97.
3. Hampe J, Heymann K, Krawczak M, et al. Association of inflammatory bowel disease with indicators for childhood antigen and infection exposure. Int J Colorectal Dis 2003; 18: 413-7.
4. Gent AE, Coggon D, Swarbrick ET, et al. Inflammatory bowel-disease and domestic hygiene in childhood. Gastroenterology 1994; 106: A686.
5. Guarner F, Bourdet-Sicard R, Brandtzaeg P, et al. Mechanisms of disease: The hygiene hypothesis revisited. Nat Clin Pract Gastroenterol Hepatol 2006; 3: 275-84.
6. Hugot JP, Alberti C, Berrebi D, et al. Crohn's disease: The cold chain hypothesis. Lancet 2003; 362: 2012-5.
7. Consortium THMP. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486: 207-14.
8. Yatsunenko T, Rey FE, Manary MJ, et al. Human gut microbiome viewed across age and geography. Nature 2012; 486: 222-7.
9. Baas-Becking LGM. Geobiologie of Inleiding Tot de Milieukunde. 1934.
10. Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci 2006; 103: 626-31.
11. Nemergut DR, Costello EK, Hamady M, et al. Global patterns in the biogeography of bacterial taxa. Environ Microbiol 2011; 13: 135-44.
12. Lindström ES, Langenheder S. Local and regional factors influencing bacterial community assembly. Environ Microbiol Rep 2012; 4: 1-9.
13. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464: 59-65.
14. Karlsson FH, Tremaroli V, Nookaew I, et al. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 2013; 498: 99-103.
15. Linnenbrink M, Wang J, Hardouin EA, et al. The role of biogeography in shaping diversity of the intestinal microbiota in house mice. Mol Ecol 2013; 22: 1904-16.
16. Rehman A, Lepage P, Nolte A, et al. Transcriptional activity of the dominant gut mucosal microbiota in chronic inflammatory bowel disease patients. J Med Microbiol 2010; 59: 1114-22.
17. Rausch P, Rehman A, Künzel S, et al. Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype. Proc Natl Acad Sci 2011; 108: 19030-5.
18. Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: Open source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009; 75: 7537-41.
19. Jost L. Partitioning diversity into independent alpha and beta components. Ecology 2007; 88: 2427-39.
20. Faith DP. Conservation evaluation and phylogenetic diversity. Biol Conserv 1992; 61: 1-10.
21. Kembel SW, Cowan PD, Helmus MR, et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 2010; 26: 1463-4.
22. Hamady M, Lozupone C, Knight R. Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 2010; 4: 17-27.
23. Oksanen J, Blanchet FG, Kindt R, et al. vegan: Community Ecology Package. 2011. http: //CRAN.R-project.org
24. Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecology 2001; 26: 32-46.
25. Legendre P, Legendre L. Numerical ecology. 2nd English edn. Developments in Environmental Modelling, 1998; 20: I-xv, 1-853.
26. De Cáceres M, Legendre P, et al. Improving indicator species analysis by combining groups of sites. Oikos 2010; 119: 1674-84.
27. Chao A. Estimating the population size for capture-recapture data with unequal catchability. Biometrics 1987; 43: 783-91.
28. Frank DN, St. Amand AL, Feldman RA, et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci 2007; 104: 13780-5.
29. Costello EK, Lauber CL, Hamady M, et al. Bacterial community variation in human body habitats across space and time. Science 2009; 326: 1694-7.
30. Whitaker RJ, Grogan DW, Taylor JW. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 2003; 301: 976-8.
31. Falush D, Wirth T, Linz B, et al. Traces of human migrations in helicobacter pylori populations. Science 2003; 299: 1582-5.
32. Lepage P, Häsler R, Spehlmann ME, et al. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 2011; 141: 227-36.
33. Gophna U, Sommerfeld K, Gophna S, et al. Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative dolitis. J Clin Microbiol 2006; 44: 4136-41.
34. Manichanh C, Rigottier-Gois L, Bonnaud E, et al. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 2006; 55: 205-11.
35. Verma R, Verma AK, Ahuja V, et al. Real-time analysis of mucosal flora in patients with inflammatory bowel disease in India. J Clin Microbiol 2010; 48: 4279-82.
36. Trosvik P, Stenseth NC, Rudi K. Convergent temporal dynamics of the human infant gut microbiota. ISME J 2009; 4: 151-8.
37. Backhed F, Ley RE, Sonnenburg JL, et al. Host-bacterial mutualism in the human intestine. Science 2005; 307: 1915-20.
38. Xu J, Mahowald MA, Ley RE, et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 2007; 5: E156.
39. Xu J, Bjursell MK, Himrod J, et al. A genomic view of the human-bacteroides thetaiotaomicron symbiosis. Science 2003; 299: 2074-6.
40. Bazzaz FA. Physiological ecology of plant succession. Annu Rev Ecol Syst 1979; 10: 351-71.
41. Lozupone C, Stombaugh J, Gonzalez A, et al. Meta-analyses of studies of the human microbiota. Genome Res 2013; 23: 1704-14.
42. May RM. Will a large complex system be stable? Nature 1972; 238: 413-4.
43. Stecher B, Hardt W-D. Mechanisms controlling pathogen colonization of the gut. Curr Opin Microbiol 2011; 14: 82-91.
44. Faith JJ, Guruge JL, Charbonneau M, et al. The long-term stability of the human gut microbiota. Science 2013; 341: 1237439.
45. Bron PA, van Baarlen P, Kleerebezem M. Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa. Nat Rev Micro 2012; 10: 66-78.
46. Jones SE, Lennon JT. Dormancy contributes to the maintenance of microbial diversity. Proc Natl Acad Sci 2010; 107: 5881-6.
47. Sokol H, Lay C, Seksik P, et al. Analysis of bacterial bowel communities of IBD patients: What has it revealed? Inflamm Bowel Dis 2008; 14: 858-67.
48. Sokol H, Pigneur B, Watterlot L, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci 2008; 105: 16731-6.
49. Fujimoto T, Imaeda H, Takahashi K, et al. Decreased abundance of Faecalibacterium prausnitzii in the gut microbiota of Crohn's disease. J Gastroenterol Hepatol 2013; 28: 613-19.
50. Shen J, Zhang B, Wei G, et al. Molecular profiling of the clostridium leptum subgroup in human fecal microflora by PCR-denaturing gradient gel electrophoresis and clone library analysis. Appl Environm Microbiol 2006; 72: 5232-8.
51. Segain J-P, de la Blétière DR, Bourreille A, et al. Butyrate inhibits inflammatory responses through NF?B inhibition: Implications for Crohn's disease. Gut 2000; 47: 397-403.
52. Kabeerdoss J, Sankaran V, Pugazhendhi S, et al. Clostridium leptum group bacteria abundance and diversity in the fecal microbiota of patients with inflammatory bowel disease: A case-control study in India. Bmc Gastroenterol 2013; 13: 20.
53. Wexler HM. Bacteroides: The good, the bad, and the Nitty-Gritty. Clin Microbiol Rev 2007; 20: 593-621.
54. Gevers D, Kugathasan S, Denson Lee A, et al. The treatment-naive microbiome in new-onset Crohn's Disease. Cell Host Microbe 2014; 15: 382-92.