Colonic microbiome is altered in alcoholism

American Journal of Physiology - Gastrointestinal and Liver Physiology

Volumn 302, Issue 9, 2012, Pages

  Mutlu, Ece A ^a   Gillevet, Patrick M ^c   Rangwala, Huzefa ^c,d   Sikaroodi, Masoumeh ^c   Naqvi, Ammar ^c   Engen, Phillip A ^a   Kwasny, Mary ^b   Lau, Cynthia K ^a   Keshavarzian, Ali ^a  

^a RUSH UNIVERSITY MEDICAL CENTER   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

^c GEORGE MASON UNIVERSITY   (United States)

^d George Mason University   (United States)

Author keywords

Alcohol; Alcoholic liver disease; Colon; Colonic microbiota; Length heterogeneity polymerase chain reaction; Pyrosequencing

Indexed keywords

ENDOTOXIN;

ADULT; AGED; ALCOHOL LIVER DISEASE; ALCOHOLISM; ARTICLE; BACTEROIDETES; COLON BIOPSY; COLON FLORA; COLON MUCOSA; DYSBIOSIS; ENDOTOXEMIA; FEMALE; HUMAN; MAJOR CLINICAL STUDY; MALE; NONHUMAN; ORGANISMAL INTERACTION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEOBACTERIA; PYROSEQUENCING;

ADULT; AGED; ALCOHOLISM; COLON; FEMALE; HUMANS; LIVER DISEASES, ALCOHOLIC; METAGENOME; MIDDLE AGED;

EID: 84860515098     PISSN: 01931857     EISSN: 15221547     Source Type: Journal    
DOI: 10.1152/ajpgi.00380.2011     Document Type: Article

References (38)

1. Adachi Y, Moore LE, Bradford BU, Gao W, Thurman RG. Antibiotics prevent liver injury in rats following long-term exposure to ethanol. Gastroenterology 108: 218-224, 1995.
2. Ball SA, Tennen H, Poling JC, Kranzler HR, Rounsaville BJ. Personality, temperament, and character dimensions and the DSM-IV personality disorders in substance abusers. J Abnorm Psychol 106: 545-553, 1997.
3. Bigatello LM, Broitman SA, Fattori L, Di Paoli M, Pontello M, Bevilacqua G, Nespoli A. Endotoxemia, encephalopathy, and mortality in cirrhotic patients. Am J Gastroenterol 82: 11-15, 1987.
4. Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PloS One 2: e197, 2007.
5. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics (Oxford, England) 26: 266-267, 2010.
6. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7: 335-336, 2010.
7. Chen Y, Yang F, Lu H, Wang B, Chen Y, Lei D, Wang Y, Zhu B, Li L. Characterization of fecal microbial communities in patients with liver cirrhosis. Hepatology 54: 562-572, 2011.
8. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science 308: 1635-1638, 2005.
9. Forsyth CB, Farhadi A, Jakate SM, Tang Y, Shaikh M, Keshavarzian A. Lactobacillus GG treatment ameliorates alcohol-induced intestinal oxidative stress, gut leakiness, and liver injury in a rat model of alcoholic steatohepatitis. Alcohol 43: 163-172, 2009.
10. Foster JA, Krone SM, Forney LJ. Application of ecological network theory to the human microbiome. Interdiscip Perspect Infect Dis 2008: 839501, 2008.
11. Gillevet P, Sikaroodi M, Keshavarzian A, Mutlu EA. Quantitative assessment of the human gut microbiome using multitag pyrosequencing. Chem Biodivers 7: 1065-1075, 2010.
12. Gillevet PM. Compositions and Methods for Diagnosing Colon Disorders, PCT/US05/39887. PCT/USPTO: George Mason University, 2005.
13. Gillevet PM. Multitag Sequencing and Ecogenomic Analysis, EPO 07871488.8, PCT/US2007/084840. WPO: BioSpherex, 2006.
14. Grant BF, Dufour MC, Harford TC. Epidemiology of alcoholic liver disease. Semin Liver Dis 8: 12-25, 1988.
15. Hamady M, Knight R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome research 19: 1141-1152, 2009.
16. Hamady M, Lozupone C, Knight R. Fast UniFrac: facilitating highthroughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: 17-27, 2010.
17. Hooper LV, Wong MH, Thelin A, Hansson L, Falk PG, Gordon JI. Molecular analysis of commensal host-microbial relationships in the intestine. Science 291: 881-884, 2001.
18. Hunt NC, Goldin RD. Nitric oxide production by monocytes in alcoholic liver disease. J Hepatol 14: 146-150, 1992.
19. Keshavarzian A, Choudhary S, Holmes EW, Yong S, Banan A, Jakate S, Fields JZ. Preventing gut leakiness by oats supplementation ameliorates alcohol-induced liver damage in rats. J Pharmacol Exp Ther 299: 442-448, 2001.
20. Komanduri S, Gillevet PM, Sikaroodi M, Mutlu E, Keshavarzian A. Dysbiosis in pouchitis: evidence of unique microfloral patterns in pouch inflammation. Clin Gastroenterol Hepatol 5: 352-360, 2007.
21. Lane D. 16s/23s rRNA sequencing. In: Nucleic Acid Techniques in Bacterial Systematics, edited by Goodfellow M. West Sussex, England: John Wiley & Sons, 1991, p. 115-175.
22. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (Oxford, England) 22: 1658-1659, 2006.
23. Li W, Jaroszewski L, Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics (Oxford, England) 17: 282-283, 2001.
24. Liu Q, Duan ZP, Ha DK, Bengmark S, Kurtovic J, Riordan SM. Synbiotic modulation of gut flora: effect on minimal hepatic encephalopathy in patients with cirrhosis. Hepatology 39: 1441-1449, 2004.
25. Mutlu E, Keshavarzian A, Engen P, Forsyth CB, Sikaroodi M, Gillevet P. Intestinal dysbiosis: a possible mechanism of alcohol-induced endotoxemia and alcoholic steatohepatitis in rats. Alcohol Clin Exp Res 33: 1836-1846, 2009.
26. Nanji AA, Khettry U, Sadrzadeh SM. Lactobacillus feeding reduces endotoxemia and severity of experimental alcoholic liver (disease). Proc Soc Exp Biol Med 205: 243-247, 1994.
27. Nanji AA, Khettry U, Sadrzadeh SM, Yamanaka T. Severity of liver injury in experimental alcoholic liver disease. Correlation with plasma endotoxin, prostaglandin E2, leukotriene B4, and thromboxane B2. Am J Pathol 142: 367-373, 1993.
28. Naqvi A, Rangwala H, Keshavarzian A, Gillevet P. Network-based modeling of the human gut microbiome. Chem Biodivers 7: 1040-1050, 2010.
29. O'Connor PG, Schottenfeld RS. Patients with alcohol problems. N Engl J Med 338: 592-602, 1998.
30. Probert HM, Gibson GR. Bacterial biofilms in the human gastrointestinal tract. Current issues in intestinal microbiology 3: 23-27, 2002.
31. Rimola A. Infections in liver disease. Oxford, England: Oxford University Press, 1991.
32. Riordan SM, Skinner N, Nagree A, McCallum H, McIver CJ, Kurtovic J, Hamilton JA, Bengmark S, Williams R, Visvanathan K. Peripheral blood mononuclear cell expression of toll-like receptors and relation to cytokine levels in cirrhosis. Hepatology 37: 1154-1164, 2003.
33. Sharara AI, Rockey DC. Gastroesophageal variceal hemorrhage. The New England journal of medicine 345: 669-681, 2001.
34. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. A core gut microbiome in obese and lean twins. Nature 457: 480-484, 2009.
35. van de Wiel A. Diabetes mellitus and alcohol. Diabetes/metabolism research and reviews 20: 263-267, 2004.
36. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and environmental microbiology 73: 5261-5267, 2007.
37. White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS computational biology 5: e1000352, 2009.
38. Whittaker RH. Evolution and measurement of species diversity. Taxon 21: 213-251, 1972.