Microbiome analysis of stool samples from African Americans with colon polyps

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Brim, Hassan ^a   Yooseph, Shibu ^b   Zoetendal, Erwin G ^d   Lee, Edward ^a   Torralbo, Manolito ^c   Laiyemo, Adeyinka O ^a   Shokrani, Babak ^a   Nelson, Karen ^c   Ashktorab, Hassan ^a  

^a HOWARD UNIVERSITY COLLEGE OF MEDICINE   (United States)

^b JCVI   (United States)

^c JCVI   (United States)

^d WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

16S RRNA GENE; ADULT; AFRICAN AMERICAN; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTEROIDES; CLINICAL ARTICLE; COLON POLYP; CONTROLLED STUDY; FECES ANALYSIS; FECES MICROFLORA; FEMALE; HUMAN; MALE; MALIGNANT TRANSFORMATION; METAGENOMICS; MICROBIOME; NONHUMAN; PRECANCER; PYROSEQUENCING; BACTERIA; CLASSIFICATION; DNA MICROARRAY; DNA SEQUENCE; FECES; GENETICS; MICROBIOLOGY; MICROFLORA; PHYLOGENY;

AFRICAN AMERICANS; BACTERIA; COLONIC POLYPS; FECES; HUMANS; METAGENOMICS; MICROBIOTA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84893408527     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0081352     Document Type: Article

References (60)

1. Sinicrope PS, Goode EL, Limburg PJ, Vernon SW, Wick JB et al. (2012) A population-based study of prevalence and adherence trends in average risk colorectal cancer screening, 1997 to 2008. Cancer Epidemiol Biomarkers Prev 21: 347-350. doi:10.1158/1055-9965.EPI-11-0818. PubMed: 22144500.
2. Friedenberg FK, Singh M, George NS, Sankineni A, Shah S (2012) Prevalence and distribution of adenomas in black Americans undergoing colorectal cancer screening. Dig Dis Sci 57: 489-495. doi:10.1007/s10620-011-1952-z. PubMed: 22052446.
3. Blumenstein I, Tacke W, Bock H, Filmann N, Lieber E et al. (2013) Prevalence of colorectal cancer and its precursor lesions in symptomatic and asymptomatic patients undergoing total colonoscopy: results of a large prospective, multicenter, controlled endoscopy study. Eur J Gastroenterol Hepatol 25: 556-61. PubMed: 23283303.
4. Nelson RL, Persky V, Turyk M (1999) Carcinoma in situ of the colorectum: SEER trends by race, gender, and total colorectal cancer. J Surg Oncol 71: 123-129. doi:10.1002/(SICI)1096-9098(199906)71:2. PubMed: 10389871.
5. Smith RA, von Eschenbach AC, Wender R, Levin B, Byers T, et al. (2001) American Cancer Society guidelines for the early detection of cancer: update of early detection guidelines for prostate, colorectal, and endometrial cancers. Also: update 2001 - testing for early lung cancer detection. CA: a cancer journal for clinicians 51: 38-80; quiz
6. Agrawal S, Bhupinderjit A, Bhutani MS, Boardman L, Nguyen C et al. (2005) Colorectal cancer in African Americans. Am J Gastroenterol 100: 514-523; discussion 10.1111/j.1572-0241.2005.41829.x. PubMed: 15743345.
7. Nouraie M, Hosseinkhah F, Brim H, Zamanifekri B, Smoot DT et al. (2010) Clinicopathological features of colon polyps from African-Americans. Dig Dis Sci 55: 1442-1449. doi:10.1007/s10620-010-1133-5. PubMed: 20225129.
8. Ashktorab H, Belgrave K, Hosseinkhah F, Brim H, Nouraie M et al. (2009) Global histone H4 acetylation and HDAC2 expression in colon adenoma and carcinoma. Dig Dis Sci 54: 2109-2117. doi:10.1007/s10620-008-0601-7. PubMed: 19057998.
9. Ashktorab H, Green W, Finzi G, Sessa F, Nouraie M et al. (2012) SEL1L, an UPR response protein, a potential marker of colonic cell transformation. Dig Dis Sci 57: 905-912. doi:10.1007/s10620-011-2026-y. PubMed: 22350780.
10. Ashktorab H, Nguza B, Fatemi M, Nouraie M, Smoot DT et al. (2011) Case-control study of vitamin D, dickkopf homolog 1 (DKK1) gene methylation, VDR gene polymorphism and the risk of colon adenoma in African Americans. PLOS ONE 6: e25314. doi:10.1371/journal.pone.0025314. PubMed: 22022386.
11. Ashktorab H, Schäffer AA, Daremipouran M, Smoot DT, Lee E et al. (2010) Distinct genetic alterations in colorectal cancer. PLOS ONE 5: e8879. doi:10.1371/journal.pone.0008879. PubMed: 20126641.
12. Brim H, Kumar K, Nazarian J, Hathout Y, Jafarian A et al. (2011) SLC5A8 gene, a transporter of butyrate: a gut flora metabolite, is frequently methylated in African American colon adenomas. PLOS ONE 6: e20216. doi:10.1371/journal.pone.0020216. PubMed: 21687703.
13. Brim H, Lee E, Abu-Asab MS, Chaouchi M, Razjouyan H et al. (2012) Genomic aberrations in an African American colorectal cancer cohort reveals a MSI-specific profile and chromosome X amplification in male patients. PLOS ONE 7: e40392. doi:10.1371/journal.pone.0040392. PubMed: 22879877.
14. Brim H, Mokarram P, Naghibalhossaini F, Saberi-Firoozi M, Al-Mandhari M et al. (2008) Impact of BRAF, MLH1 on the incidence of microsatellite instability high colorectal cancer in populations based study. Mol Cancer 7: 68. doi:10.1186/1476-4598-7-68. PubMed: 18718023.
15. Kumar K, Brim H, Mokarram P, Naghibalhossaini F, Saberi-Firoozi M, et al. (2009) Distinct BRAF (V600E) and KRAS mutations in high microsatellite instability sporadic colorectal cancer in African Americans. Clin Cancer Res. In press: 68
16. Graham A, Adeloye D, Grant L, Theodoratou E, Campbell H (2012) Estimating the incidence of colorectal cancer in Sub-Saharan Africa: A systematic analysis. J Glob Health 2: 20404. PubMed: 23289079.
17. Sears CL (2005) A dynamic partnership: celebrating our gut flora. Anaerobe 11: 247-251. doi:10.1016/j.anaerobe.2005.05.001. PubMed: 16701579.
18. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI (2005) Host-bacterial mutualism in the human intestine. Science 307: 1915-1920. doi:10.1126/science.1104816. PubMed: 15790844.
19. Hooper LV, Gordon JI (2001) Commensal host-bacterial relationships in the gut. Science 292: 1115-1118. doi:10.1126/science.1058709. PubMed: 11352068. (Pubitemid 32440925)
20. López-Boado YS, Wilson CL, Hooper LV, Gordon JI, Hultgren SJ et al. (2000) Bacterial exposure induces and activates matrilysin in mucosal epithelial cells. J Cell Biol 148: 1305-1315. doi:10.1083/jcb.148.6.1305. PubMed: 10725342.
21. Wu S, Morin PJ, Maouyo D, Sears CL (2003) Bacteroides fragilis enterotoxin induces c-Myc expression and cellular proliferation. Gastroenterology 124: 392-400. doi:10.1016/S0016-5085(03)81986-8. PubMed: 12557145. (Pubitemid 36169256)
22. Wu S, Rhee KJ, Albesiano E, Rabizadeh S, Wu X et al. (2009) A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. Nat Med 15: 1016-1022. doi:10.1038/nm.2015. PubMed: 19701202.
23. Savage DC (1977) Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 31: 107-133. doi:10.1146/annurev.mi.31.100177.000543. PubMed: 334036.
24. Human Microbiome Project Consortium (2012) A framework for human microbiome research. Nature 486: 215-221. doi:10.1038/nature11209. PubMed: 22699610.
25. Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214. doi:10.1038/nature11234. PubMed: 22699609.
26. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635-1638. doi:10.1126/science.1110591. PubMed: 15831718. (Pubitemid 40807514)
27. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359. doi:10.1126/science.1124234. PubMed: 16741115. (Pubitemid 43839542)
28. Huycke MM, Gaskins HR (2004) Commensal bacteria, redox stress, and colorectal cancer: mechanisms and models. Exp Biol Med (Maywood) 229: 586-597. PubMed: 15229352. (Pubitemid 38885671)
29. Lax AJ, Thomas W (2002) How bacteria could cause cancer: one step at a time. Trends Microbiol 10: 293-299. doi:10.1016/S0966-842X(02)02360-0. PubMed: 12088666.
30. McGarr SE, Ridlon JM, Hylemon PB (2005) Diet, anaerobic bacterial metabolism, and colon cancer: a review of the literature. J Clin Gastroenterol 39: 98-109. PubMed: 15681903. (Pubitemid 40130020)
31. Zoetendal EG, Rajilic-Stojanovic M, de Vos WM (2008) High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57: 1605-1615. doi:10.1136/gut.2007.133603. PubMed: 18941009.
32. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG et al. (2012) Human gut microbiome viewed across age and geography. Nature 486: 222-227. PubMed: 22699611.
33. Costello EK, Stagaman K, Dethlefsen L, Bohannan BJ, Relman DA (2012) The application of ecological theory toward an understanding of the human microbiome. Science 336: 1255-1262. doi:10.1126/science.1224203. PubMed: 22674335.
34. Balter M (2012) Taking stock of the human microbiome and disease. Science 336: 1246-1247. doi:10.1126/science.336.6086.1246. PubMed: 22674333.
35. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65. doi:10.1038/nature08821. PubMed: 20203603.
36. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T et al. (2011) Enterotypes of the human gut microbiome. Nature 473: 174-180. doi:10.1038/nature09944. PubMed: 21508958.
37. Lyra A, Forssten S, Rolny P, Wettergren Y, Lahtinen SJ et al. (2012) Comparison of bacterial quantities in left and right colon biopsies and faeces. World J Gastroenterol 18: 4404-4411. doi:10.3748/wjg.v18.i32.4404. PubMed: 22969206.
38. Rajilić-Stojanović M, Heilig HG, Molenaar D, Kajander K, Surakka A et al. (2009) Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol 11: 1736-1751. doi:10.1111/j.1462-2920.2009.01900.x. PubMed: 19508560.
39. Jeraldo P, Chia N, Goldenfeld N (2011) On the suitability of short reads of 16S rRNA for phylogeny-based analyses in environmental surveys. Environ Microbiol 13: 3000-3009. doi:10.1111/j.1462-2920.2011.02577.x. PubMed: 21910812.
40. Cole JR, Wang Q, Cardenas E, Fish J, Chai B et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145. doi:10.1093/nar/gkp353. PubMed: 19004872.
41. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541. doi:10.1128/AEM.01541-09. PubMed: 19801464.
42. Bond PL, Hugenholtz P, Keller J, Blackall LL (1995) Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol 61: 1910-1916. PubMed: 7544094.
43. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659. doi:10.1093/bioinformatics/btl158. PubMed: 16731699. (Pubitemid 43985301)
44. Schütze T, Rubelt F, Repkow J, Greiner N, Erdmann VA et al. (2011) A streamlined protocol for emulsion polymerase chain reaction and subsequent purification. Anal Biochem 410: 155-157. doi:10.1016/j.ab.2010.11.029. PubMed: 21111698.
45. Rho M, Tang H, Ye Y (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res 38: e191. doi:10.1093/nar/gkq747. PubMed: 20805240.
46. Bodaker I, Sharon I, Suzuki MT, Feingersch R, Shmoish M et al. (2010) Comparative community genomics in the Dead Sea: an increasingly extreme environment. ISME J 4: 399-407. doi:10.1038/ismej.2009.141. PubMed: 20033072.
47. Sharon I, Bercovici S, Pinter RY, Shlomi T (2011) Pathway-based functional analysis of metagenomes. J Comput Biol 18: 495-505. doi:10.1089/cmb.2010.0260. PubMed: 21385050.
48. Pick M (2012) Gut flora on a crusade for good. A brief overview of probiotics. Adv NPs PAs 3: 35-36.
49. Berer K, Krishnamoorthy G (2012) Commensal gut flora and brain autoimmunity: a love or hate affair? Acta Neuropathol 123: 639-651. doi:10.1007/s00401-012-0949-9. PubMed: 22322994.
50. Goto Y, Kiyono H (2012) Epithelial barrier: an interface for the cross-communication between gut flora and immune system. Immunol Rev 245: 147-163. doi:10.1111/j.1600-065X.2011.01078.x. PubMed: 22168418.
51. Chandran P, Satthaporn S, Robins A, Eremin O (2003) Inflammatory bowel disease: dysfunction of GALT and gut bacterial flora (I). Surgeon 1: 63-75. doi:10.1016/S1479-666X(03)80118-X. PubMed: 15573623.
52. van den Bogert B, de Vos WM, Zoetendal EG, Kleerebezem M (2011) Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples. Appl Environ Microbiol 77: 2071-2080. doi:10.1128/AEM.02477-10. PubMed: 21257804.
53. Boleij A, Dutilh BE, Kortman GA, Roelofs R, Laarakkers CM et al. (2012) Bacterial responses to a simulated colon tumor microenvironment. Mol Cell Proteomics 11: 851-862. doi:10.1074/mcp.M112.019315. PubMed: 22713208.
54. Marteau P, Chaput U (2011) Bacteria as trigger for chronic gastrointestinal disorders. Dig Dis 29: 166-171. doi:10.1159/000323879. PubMed: 21734380.
55. Yoshino Y, Kitazawa T, Ikeda M, Tatsuno K, Yanagimoto S et al. (2012) Clinical features of Bacteroides bacteremia and their association with colorectal carcinoma. Infection 40: 63-67. doi:10.1007/s15010-011-0159-8. PubMed: 21773761.
56. Toprak NU, Yagci A, Gulluoglu BM, Akin ML, Demirkalem P et al. (2006) A possible role of Bacteroides fragilis enterotoxin in the aetiology of colorectal cancer. Clinical Microbiology and Infection: the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 12: 782-786. (Pubitemid 43983804)
57. Samavati L, Rastogi R, Du W, Hüttemann M, Fite A et al. (2009) STAT3 tyrosine phosphorylation is critical for interleukin 1 beta and interleukin-6 production in response to lipopolysaccharide and live bacteria. Mol Immunol 46: 1867-1877. doi:10.1016/j.molimm.2009.02.018. PubMed: 19299019.
58. Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M et al. (2012) Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res 22: 299-306. doi:10.1101/gr.126516.111. PubMed: 22009989.
59. Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F et al. (2012) Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res 22: 292-298. doi:10.1101/gr.126573.111. PubMed: 22009990.
60. Ray K (2011) Colorectal cancer: Fusobacterium nucleatum found in colon cancer tissue - could an infection cause colorectal cancer? Nat Rev Gastroenterol Hepatol 8: 662. doi:10.1038/nrgastro.2011.208. PubMed: 22083120.