Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Chen, Yanfei ^a   Qin, Nan ^a   Guo, Jing ^a   Qian, Guirong ^a   Fang, Daiqiong ^a   Shi, Ding ^a   Xu, Min ^a   Yang, Fengling ^a   He, Zhili ^b   Van Nostrand, Joy D ^b   Yuan, Tong ^b   Deng, Ye ^b   Zhou, Jizhong ^b,c,d   Li, Lanjuan ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b UNIVERSITY OF OKLAHOMA   (United States)

^c TSINGHUA UNIVERSITY   (China)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Alcohol; End stage liver disease; Intestines; Microarray; Microbial communities

Indexed keywords

ADENYLOSUCCINATE SYNTHASE; AMINO ACID; ASPARTATE AMMONIA LIGASE; DNA; INOSINATE DEHYDROGENASE; ISOPRENOID; LIPID; TRANSALDOLASE; ALCOHOL DERIVATIVE;

ADULT; ALCOHOL LIVER CIRRHOSIS; AMINO ACID METABOLISM; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL VIRULENCE; BIOSYNTHESIS; CHILD PUGH SCORE; CLINICAL ARTICLE; CONTROLLED STUDY; DNA EXTRACTION; FEMALE; GENETIC VARIABILITY; HEPATITIS B VIRUS RELATED CIRRHOSIS; HUMAN; INTESTINE FLORA; LIPID METABOLISM; LIVER CIRRHOSIS; MALE; MICROBIAL COMMUNITY; MICROBIOME; MONITORING; NUCLEOTIDE METABOLISM; STRESS; AGED; BIODIVERSITY; CLUSTER ANALYSIS; DRUG EFFECTS; FECES; GENOTYPE ENVIRONMENT INTERACTION; METAGENOME; METAGENOMICS; MICROBIOLOGY; MICROFLORA; MIDDLE AGED; PROCEDURES;

ADULT; AGED; ALCOHOLS; BIODIVERSITY; CLUSTER ANALYSIS; FECES; FEMALE; GENE-ENVIRONMENT INTERACTION; GENETIC VARIATION; HUMANS; LIVER CIRRHOSIS; MALE; METAGENOME; METAGENOMICS; MICROBIOTA; MIDDLE AGED;

EID: 84907292257     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-753     Document Type: Article

References (49)

1. Garcia-Tsao G, Wiest R. Gut microflora in the pathogenesis of the complications of cirrhosis. Best Pract Res Clin Gastroenterol 2004, 18(2):353-372.
2. Wiest R, Garcia-Tsao G. Bacterial translocation (BT) in cirrhosis. Hepatology 2005, 41(3):422-433.
3. Guarner C, Soriano G. Bacterial translocation and its consequences in patients with cirrhosis. Eur J Gastroenterol Hepatol 2005, 17(1):27-31.
4. Chen Y, Yang F, Lu H, Wang B, Lei D, Wang Y, Zhu B, Li L. Characterization of fecal microbial communities in patients with liver cirrhosis. Hepatology 2011, 54(2):562-572.
5. Wei X, Yan X, Zou D, Yang Z, Wang X, Liu W, Wang S, Li X, Han J, Huang L, Jing Y. Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach. BMC Gastroenterol 2013, 13(1):175.
6. Grice EA, Segre JA. The human microbiome: our second genome. Annu Rev Genomics Hum Genet 2012, 13:151-170.
7. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. Metagenomic analysis of the human distal gut microbiome. Science 2006, 312(5778):1355-1359.
8. 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 2009, 457(7228):480-484.
9. Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 2007, 14(4):169-181.
10. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, et al. Human gut microbiome viewed across age and geography. Nature 2012, 486(7402):222-227.
11. Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, Peng Y, Zhang D, Jie Z, Wu W, Qin Y, Xue W, Li J, Han L, Lu D, Wu P, Dai Y, Sun X, Li Z, Tang A, Zhong S, Li X, Chen W, Xu R, Wang M, Feng Q, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 2012, 490(7418):55-60.
12. Zhou J. Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 2003, 6(3):288-294.
13. He Z, Deng Y, Zhou J. Development of functional gene microarrays for microbial community analysis. Curr Opin Biotechnol 2012, 23(1):49-55.
14. He Z, Van Nostrand JD, Zhou J. Applications of functional gene microarrays for profiling microbial communities. Curr Opin Biotechnol 2012, 23(3):460-466.
15. He Z, Nostrand J, Deng Y, Zhou J. Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities. Front Environ Sci Eng China 2011, 5(1):1-20.
16. Topping DL, Clifton PM. Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol Rev 2001, 81(3):1031-1064.
17. Ridlon JM, Kang DJ, Hylemon PB. Bile salt biotransformations by human intestinal bacteria. J Lipid Res 2006, 47(2):241-259.
18. Bajaj JS, Ridlon JM, Hylemon PB, Thacker LR, Heuman DM, Smith S, Sikaroodi M, Gillevet PM. Linkage of Gut Microbiome with Cognition in Hepatic Encephalopathy. Am J Physiol Gastrointest Liver Physiol 2012, 302(1):G168-G175.
19. Nikolaki S, Tsiamis G. Microbial diversity in the era of omic technologies. Biomed Res Int 2013, 2013:e958719.
20. Paliy O, Agans R. Application of phylogenetic microarrays to interrogation of human microbiota. FEMS Microbiol Ecol 2012, 79(1):2-11.
21. Huang HJ, Zhang AY, Cao HC, Lu HF, Wang BH, Xie Q, Xu W, Li LJ. Metabolomic analyses of faeces reveals malabsorption in cirrhotic patients. Dig Liver Dis 2013, 45(8):677-682.
22. Cabral CM, Burns DL. Low-protein diets for hepatic encephalopathy debunked: let them eat steak. Nutr Clin Pract 2011, 26(2):155-159.
23. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 2009, 1(6):6ra-14ra.
24. Shanks OC, Kelty CA, Archibeque S, Jenkins M, Newton RJ, McLellan SL, Huse SM, Sogin ML. Community structures of fecal bacteria in cattle from different animal feeding operations. Appl Environ Microbiol 2011, 77(9):2992-3001.
25. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011, 334(6052):105-108.
26. Singh KM, Shah TM, Reddy B, Deshpande S, Rank DN, Joshi CG. Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers. J Appl Genet 2014, 55(1):145-154.
27. Deusch O, O'Flynn C, Colyer A, Morris P, Allaway D, Jones PG, Swanson KS. Deep illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens. PLoS One 2014, 9(7):e101021.
28. Tsiaousi ET, Hatzitolios AI, Trygonis SK, Savopoulos CG. Malnutrition in end stage liver disease: recommendations and nutritional support. J Gastroenterol Hepatol 2008, 23(4):527-533.
29. Kokavec A. Is decreased appetite for food a physiological consequence of alcohol consumption?. Appetite 2008, 51(2):233-243.
30. Lindenbaum J, Lieber CS. Effects of chronic ethanol administration on intestinal absorption in man in the absence of nutritional deficiency. Ann N Y Acad Sci 1975, 252:228-234.
31. Raux E, Schubert HL, Warren MJ. Biosynthesis of cobalamin (vitamin B12): a bacterial conundrum. Cell Mol Life Sci 2000, 57(13-14):1880-1893.
32. Zeuzem S. Gut-liver axis. Int J Colorectal Dis 2000, 15(2):59-82.
33. Jones BV, Begley M, Hill C, Gahan CG, Marchesi JR. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A 2008, 105(36):13580-13585.
34. Kakiyama G, Pandak WM, Gillevet PM, Hylemon PB, Heuman DM, Daita K, Takei H, Muto A, Nittono H, Ridlon JM, White MB, Noble NA, Monteith P, Fuchs M, Thacker LR, Sikaroodi M, Bajaj JS. Modulation of the fecal bile acid profile by gut microbiota in cirrhosis. J Hepatol 2013, 58(5):949-955.
35. Bajaj JS, Hylemon PB, Ridlon JM, Heuman DM, Daita K, White MB, Monteith P, Noble NA, Sikaroodi M, Gillevet PM. Colonic mucosal microbiome differs from stool microbiome in cirrhosis and hepatic encephalopathy and is linked to cognition and inflammation. Am J Physiol Gastrointest Liver Physiol 2012, 303(6):G675-G685.
36. Hamer HM, Jonkers D, Venema K, Vanhoutvin S, Troost FJ, Brummer RJ. Review article: the role of butyrate on colonic function. Aliment Pharmacol Ther 2008, 27(2):104-119.
37. Norman K, Pirlich M. Gastrointestinal tract in liver disease: which organ is sick?. Curr Opin Clin Nutr Metab Care 2008, 11(5):613-619.
38. Thomas F, Hehemann JH, Rebuffet E, Czjzek M, Michel G. Environmental and gut bacteroidetes: the food connection. Front Microbiol 2011, 2:93.
39. Zapparoli G, Fracchetti F, Stefanelli E, Torriani S. Genetic and phenotypic strain heterogeneity within a natural population of Oenococcus oeni from Amarone wine. J Appl Microbiol 2012, 113(5):1087-1096.
40. Levitt MD, Doizaki W, Levine AS. Hypothesis: metabolic activity of the colonic bacteria influences organ injury from ethanol. Hepatology 1982, 2(5):598-600.
41. Tillonen J, Homann N, Rautio M, Jousimies-Somer H, Salaspuro M. Ciprofloxacin decreases the rate of ethanol elimination in humans. Gut 1999, 44(3):347-352.
42. Korem M, Gov Y, Rosenberg M. Global gene expression in Staphylococcus aureus following exposure to alcohol. Microb Pathog 2010, 48(2):74-84.
43. Redelman CV, Maduakolam C, Anderson GG. Alcohol treatment enhances Staphylococcus aureus biofilm development. FEMS Immunol Med Microbiol 2012, 66(3):411-418.
44. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464(7285):59-65.
45. Chou K, Wright RO. Phthalates in food and medical devices. J Med Toxicol 2006, 2(3):126-135.
46. Leitz J, Kuballa T, Rehm J, Lachenmeier DW. Chemical analysis and risk assessment of diethyl phthalate in alcoholic beverages with special regard to unrecorded alcohol. PLoS One 2009, 4(12):e8127.
47. Kitko RD, Cleeton RL, Armentrout EI, Lee GE, Noguchi K, Berkmen MB, Jones BD, Slonczewski JL. Cytoplasmic acidification and the benzoate transcriptome in Bacillus subtilis. PLoS One 2009, 4(12):e8255.
48. Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'Haeseleer P, Holman HY, Osman S, Lu Z, Van Nostrand JD, Deng Y, et al. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 2010, 330(6001):204-208.
49. Lu Z, He Z, Parisi VA, Kang S, Deng Y, Van Nostrand JD, Masoner JR, Cozzarelli IM, Suflita JM, Zhou J. GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer. Environ Sci Technol 2012, 46(11):5824-5833.