Inferred metagenomic comparison of mucosal and fecal microbiota from individuals undergoing routine screening colonoscopy reveals similar differences observed during active inflammation

Gut Microbes

Volumn 6, Issue 1, 2015, Pages 48-56

  Tang, Mei San ^a   Poles, Jordan ^a   Leung, Jacqueline M ^a   Wolff, Martin J ^a   Davenport, Michael ^a   Lee, Soo Ching ^b   Lim, Yvonne Al ^b   Chua, Kek Heng ^b   Loke, P'ng ^a   Cho, Ilseung ^a,c  

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

^b UNIVERSITY OF MALAYA   (Malaysia)

^c VETERANS AFFAIRS MEDICAL CENTER   (United States)

Author keywords

Acinetobacter; Colitis; Inflammation; Microbiome; Mucosa; Proteobacteria

Indexed keywords

ACINETOBACTER; ARTICLE; BACTEROIDETES; CARBOHYDRATE METABOLISM; CLINICAL ARTICLE; COLONOSCOPY; FECES ANALYSIS; FECES MICROFLORA; FIRMICUTES; GASTROINTESTINAL BIOPSY; HUMAN; HUMAN TISSUE; INFLAMMATION; INTESTINE; INTESTINE EPITHELIUM; METAGENOMICS; MICROBIAL DIVERSITY; MICROBIAL METABOLISM; MICROBIOME; MICROFLORA; MUCOSAL MICROBIOTA; MUCUS; NONHUMAN; NUCLEOTIDE METABOLISM; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROTEOBACTERIA; SPECIES RICHNESS; ULCERATIVE COLITIS; BIOTA; COLITIS; COMPARATIVE STUDY; FECES; GENETICS; INTESTINE MUCOSA; MALE; METABOLISM; MICROBIOLOGY; MIDDLE AGED;

ACINETOBACTER; BACTERIA (MICROORGANISMS); PROTEOBACTERIA;

BIOTA; COLITIS; FECES; HUMANS; INTESTINAL MUCOSA; MALE; METABOLIC NETWORKS AND PATHWAYS; MIDDLE AGED;

EID: 84924279721     PISSN: 19490976     EISSN: 19490984     Source Type: Journal    
DOI: 10.1080/19490976.2014.1000080     Document Type: Article

References (37)

1. Peterson LW, Artis D. Intestinal epithelial cells: regula­tors of barrier function and immune homeostasis. Nat Rev 2014; 14:141-53; PMID:24566914; http://dx.doi.org/10.1038/nri3608.
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; PMID: 15260992; http://dx.doi.org/10.1016/jxell.2004.07.002.
3. Abraham C, Medzhitov R Interactions between the host innate immune system and microbes in inflamma­tory bowel disease. Gastroenterology 2011; 140:1729-37; PMID:21530739; http://dx.doi.org/10.1053/j.gastro.2011.02.012.
4. Honda K, Littman D. The microbiome in infectious disease and inflammation. Annu Rev Immunol 2012; 30:759-95; PMID:22224764; http://dx.doi.org/10.1146/annurev-immunol-020711-074937.
5. Manichanh C, Borruel N, Casellas F, Guarner F. The gut microbiota in IBD. Nat Rev Gastroenterol Hepatol 2012; 9:599-608; PMID:22907164; http://dx.doi.org/10.1038/nrgastro.2012.152.
6. Frank D, St Amand A, Feldman R, Boedeker E, Harpaz N, Pace N. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA 2007; 104:13780-5; PMID:17699621; http://dx.doi.org/10.1073/pnas.0706625104.
7. Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L et al. Reduced diversity offaecal microbiota in crohn's disease revealed by a metagenomic approach. Gut 2006; 55:205-11; PMID: 16188921; http://dx.doi.org/10.1136/gut.2005.073817.
8. Packey C, Sartor R. Interplay ofcommensal and patho­genic bacteria, genetic mutations, and immunoregula-tory defects in the pathogenesis of inflammatory bowel diseases. J Intern Med 2008; 263:597-606; PMID:18479259; http://dx.doi.org/10.1111/j.1365-2796.2008.01962.x.
9. Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treat­ment. Genome Biol 2012; 13:R79; PMID:23013615; http://dx.doi.org/10.1186/gb-2012-13-9-r79.
10. Eckburg P, Bik E, Bernstein C, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbialflora. Science 2005; 308:1635-8; PMID:15831718; http://dx.doi.org/10.1126/science.1110591.
11. Momozawa Y, Deffontaine V, Louis E, Medrano J. Characterization of bacteria in biopsies of colon and stools by high throughput sequencing of the V2 region of bacterial 16S rRNA gene in human. PLoS One 2011; 6:e16952; PMID:21347324; http://dx.doi.org/10.1371/journal.pone.0016952.
12. Zoetendal E, von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans A, de Vos W. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 2002; 68:3401-7; PMID:12089021; http://dx.doi.org/10.1128/AEM.68.7.3401-3407.2002.
13. Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA et al. Predictive functional profil­ing of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 2013; 31:814-21; PMID:23975157; http://dx.doi.org/10.1038/nbt.2676.
14. Davenport M, Poles J, Leung J, Wolff M, Abidi W, Ullman T et al. Metabolic alterations to the mucosal microbiota in inflammatory bowel disease. Inflamm Bowel Dis 2014; 20:721-31; PMID:24583479.
15. Leung JM, Davenport M, Wolff MJ, Wiens KE, Abidi WM, Poles MA, et al. IL-22-producing CD4+ cells are depleted in actively inflamed colitis tissue. Mucosal Immunol 2013; 7:124-33; PMID:23695510; http://dx.doi.org/10.1038/mi.2013.31.
16. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol 2011; 12:R60; PMID:21702898; http://dx.doi.org/10.1186/gb-2011-12-6-r60.
17. Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 2014; 15:382-92; PMID:24629344; http://dx.doi.org/10.1016/j.chom.2014.02.005.
18. Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A et al. Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology 2014; 147:1055-63; PMID:25046162; http://dx.doi.org/10.1053/j-gastro.2014.07.020..
19. Peleg AY, Seifert H, Paterson DL. Acinetobacter bau-mannii: emergence of a successful pathogen. Clinical Microbiol Rev 2008; 21:538-82; PMID:18625687; http://dx.doi.org/10.1128/CMR.00058-07.
20. Leung J, Davenport M, Wolff M, Wiens K, Abidi W, Poles M et al. IL-22-producing CD4+ cells are depleted in actively inflamed colitis tissue. Mucosal Immunol 2014; 7:124-33; PMID:23695510; http://dx.doi.org/10.1038/mi.2013.31.
21. Shafquat A, Joice R, Simmons SL, Huttenhower C. Functional and phylogenetic assembly of microbial communities in the human microbiome. Trends Microbiol 2014; 22:261-6; PMID:24618403; http://dx.doi.org/10.1016/j.tim.2014.01.011.
22. Rooks M, Veiga P, Wardwell-Scott L, Tickle T, Segata N, Michaud M et al. Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. ISME J 2014; 8:1403-17; PMID:24500617; http://dx.doi.org/10.1038/ismej.2014.3..
23. Morita H, Nakanishi K, Dohi T, Yasugi E, Oshima M. Phospholipid turnover in the inflamed intestinal mucosa: arachidonic acid-rich phosphatidyl/plasmenyl-ethanolamine in the mucosa in inflammatory bowel disease. J Gastroenterol 1999; 34:46-53; PMID: 10204610; http://dx.doi.org/10.1007/s005350050215.
24. Arthur JC, Perez-Chanona E, Muhlbauer M, Tomko-vich S, Uronis JM, Fan TJ et al. Intestinal inflamma­tion targets cancer-inducing activity of the microbiota. Science 2012; 338:120-3; PMID:22903521; http://dx.doi.org/10.1126/science.1224820.
25. Maynard C, Elson C, Hatton R, Weaver C. Reciprocal interactions of the intestinal microbiota and immune system. Nature 2012; 489:231-41; PMID:22972296; http://dx.doi.org/10.1038/nature11551.
26. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ et al. Global patterns of 16S rRNAdiversity at a depth ofmillions ofsequences per sample. Proc Natl Acad Sci U S A 2011; 108 1:4516-22; PMID:20534432; http://dx.doi.org/10.1073/pnas.1000080107.
27. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010; 7:335-6; PMID:20383131; http://dx.doi.org/10.1038/nmeth.f.303.
28. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26:2460-1; PMID:20709691; http://dx.doi.org/10.1093/bioinformatics/btq461.
29. Wang Q, Garrity GM, Tiedje JM, Cole JR, Na'ive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73:5261-7; PMID:17586664; http://dx.doi.org/10.1128/AEM.00062-07.
30. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinfor-matics 2010; 26:266-7; PMID:19914921; http://dx.doi.org/10.1093/bioinformatics/btp636.
31. Shannon CE. A mathematical theory of communication. Bell System Tech J 1948; 27:379-423; 623­56; http://dx.doi.org/10.1002/j.1538-7305.1948.tb01338.x.
32. Chao A. Nonparametric estimation of the number of classes in a population. Scandinavian J Statistics 1984:265-70; PMID:6422541..
33. Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J 2011; 5:169-72; PMID:20827291; http://dx.doi.org/10.1038/ismej.2010.133.
34. Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD et al. Associating microbiome composition with environmental covariates using generalized unifrac distances. Bioinformatics 2012; 28:2106-13; PMID: 22711789; http://dx.doi.org/10.1093/bioinformatics/bts342.
35. Vazquez-Baeza Y, Pirrung M, Gonzalez A, Knight R. EMPeror: a tool for visualizing high-throughput micro-bial community data. Gigascience 2013; 2:16; PMID:24280061; http://dx.doi.org/10.1186/2047-217X-2-16.
36. Vanbroekhoven K, Ryngaert A, Wattiau P, Mot R, Springael D. Acinetobacter diversity in environmental samples assessed by 16S rRNA gene PCR-DGGE fin­gerprinting. FEMS Microbiol Ecol 2004; 50:37-50; PMID:19712375; http://dx.doi.org/10.1016/j.femsec.2004.05.007.
37. Ramanan D, Tang MS, Bowcutt R, Loke P, Cadwell K. Bacterial sensor Nod2 prevents inflammation of the small intestine by restricting the expansion of the com­mensal bacteroides vulgatus. Immunity 2014; 41:311-24; PMID:25088769; http://dx.doi.org/10.1016/j.immuni.2014.06.015.