Metabolic alterations to the mucosal microbiota in inflammatory bowel disease

Inflammatory Bowel Diseases

Volumn 20, Issue 4, 2014, Pages 723-731

  Davenport, Michael ^a   Poles, Jordan ^a   Leung, Jacqueline M ^a   Wolff, Martin J ^a   Abidi, Wasif M ^b   Ullman, Thomas ^b   Mayer, Lloyd ^b   Cho, Ilseung ^a,c   Loke, P'ng ^a  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^c VETERANS AFFAIRS MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CD4 ANTIGEN; RNA 16S; TRANSCRIPTION FACTOR FOXP3; AMINO ACID; NUCLEOTIDE;

ADULT; AMINO ACID METABOLISM; ARTICLE; CARBOHYDRATE METABOLISM; CD4+ T LYMPHOCYTE; CELL INFILTRATION; CELL ISOLATION; CLINICAL ARTICLE; COLON BIOPSY; CONTROLLED STUDY; CROHN DISEASE; CYTOKINE PRODUCTION; EPITHELIUM; FEMALE; FLOW CYTOMETRY; HISTOPATHOLOGY; HUMAN; HUMAN CELL; HUMAN TISSUE; INFLAMMATION; INTESTINE FLORA; LEUKOCYTE; LIPID METABOLISM; MALE; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL METABOLISM; NEUTROPHIL; NUCLEOTIDE METABOLISM; PRIORITY JOURNAL; ULCERATIVE COLITIS; CD4 LYMPHOCYTE COUNT; COLON; INTESTINE MUCOSA; METABOLISM; MICROBIOLOGY; MICROFLORA; PHYSIOLOGY; REGULATORY T LYMPHOCYTE;

AMINO ACIDS; CARBOHYDRATE METABOLISM; CD4 LYMPHOCYTE COUNT; COLITIS, ULCERATIVE; COLON; CROHN DISEASE; HUMANS; INFLAMMATION; INTESTINAL MUCOSA; LIPID METABOLISM; METABOLIC NETWORKS AND PATHWAYS; METAGENOMICS; MICROBIOTA; NUCLEOTIDES; T-LYMPHOCYTES, REGULATORY;

EID: 84898764780     PISSN: 10780998     EISSN: 15364844     Source Type: Journal    
DOI: 10.1097/MIB.0000000000000011     Document Type: Article

References (36)

1. Khor B, Gardet A, Xavier RJ. Genetics and pathogenesis of inflammatory bowel disease. Nature. 2011;474:307-317.
2. Manichanh C, Borruel N, Casellas F, et al. The gut microbiota in IBD. Nat Rev Gastroenterol Hepatol. 2012;9:599-608.
3. Abraham C, Medzhitov R. Interactions between the host innate immune system and microbes in inflammatory bowel disease. Gastroenterology. 2011;140:1729-1737.
4. 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 U S A. 2007;104: 13780-13785.
5. 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;55:205-211.
6. Morgan XC, Tickle TL, Sokol H, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13:R79.
7. Fite A, Macfarlane S, Furrie E, et al. Longitudinal analyses of gut mucosal microbiotas in ulcerative colitis in relation to patient age and disease severity and duration. J Clin Microbiol. 2013;51:849-856.
8. Honda K, Littman DR. The microbiome in infectious disease and inflammation. Annu Rev Immunol. 2012;30:759-795.
9. 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: 858-867.
10. Ott SJ, Musfeldt M, Wenderoth DF, et al. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut. 2004;53:685-693.
11. Swidsinski A, Ladhoff A, Pernthaler A, et al. Mucosal flora in inflammatory bowel disease. Gastroenterology. 2002;122:44-54.
12. Lepage P, Hasler R, Spehlmann ME, et al. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology. 2011;141:227-236.
13. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207-214.
14. Stearns JC, Lynch MD, Senadheera DB, et al. Bacterial biogeography of the human digestive tract. Sci Rep. 2011;1:170.
15. Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science. 2012;336:1268-1273.
16. Yatsunenko T, Rey FE, Manary MJ, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486:222-227.
17. Langille MG, Zaneveld J, Caporaso JG, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31:814-821.
18. Meyer F, Trimble WL, Chang EB, et al. Functional predictions from inference and observation in sequence-based inflammatory bowel disease research. Genome Biol. 2012;13:169.
19. Greenblum S, Turnbaugh PJ, Borenstein E. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc Natl Acad Sci U S A. 2012; 109:594-599.
20. Caporaso JG, Lauber CL, Walters WA, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2011;108(suppl 1):4516-4522.
21. Caporaso JG, Lauber CL, Walters WA, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621-1624.
22. Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7: 335-336.
23. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460-2461.
24. DeSantis TZ, Hugenholtz P, Larsen N, et al. Greengenes, a chimerachecked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72:5069-5072.
25. Segata N, Izard J, Waldron L, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60.
26. Geboes K, De Hertogh G. Indeterminate colitis. Inflamm Bowel Dis. 2003; 9:324-331.
27. Smith PM, Howitt MR, Panikov N, et al. The microbial metabolites, shortchain fatty acids, regulate colonic Treg cell homeostasis. Science. 2013; 341:569-573.
28. Leung JM, Davenport M, Wolff MJ, et al. IL-22-producing CD4+ cells are depleted in actively inflamed colitis tissue. Mucosal Immunol. 2013;7: 124-133.
29. Elson CO, Cong Y. Host-microbiota interactions in inflammatory bowel disease. Gut Microbes. 2012;3:332-344.
30. Brown SJ, Mayer L. The immune response in inflammatory bowel disease. Am J Gastroenterol. 2007;102:2058-2069.
31. Hansen R, Russell RK, Reiff C, et al. Microbiota of de-novo pediatric IBD: increased Faecalibacterium prausnitzii and reduced bacterial diversity in Crohn's but not in ulcerative colitis. Am J Gastroenterol. 2012;107: 1913-1922.
32. Mariat D, Firmesse O, Levenez F, et al. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol. 2009; 9:123.
33. Kamada N, Chen GY, Inohara N, et al. Control of pathogens and pathobionts by the gut microbiota. Nat Immunol. 2013;14:685-690.
34. Sczesnak A, Segata N, Qin X, et al. The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Cell Host Microbe. 2011;10: 260-272.
35. Machiels K, Joossens M, Sabino J, et al. A decrease of the butyrateproducing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut. [published online ahead of print September 10, 2013]. doi: 10.1136/gutjnl-2013-304833.
36. Boltin D, Perets TT, Vilkin A, et al. Mucin function in inflammatory bowel disease: an update. J Clin Gastroenterol. 2013;47:106-111.