Functional gene arrays-based analysis of fecal microbiomes in patients with liver cirrhosis
详细信息 查看全文
- 作者：Yanfei Chen (1)
Nan Qin (1)
Jing Guo (1)
Guirong Qian (1)
Daiqiong Fang (1)
Ding Shi (1)
Min Xu (1)
Fengling Yang (1)
Zhili He (2)
Joy D Van Nostrand (2)
Tong Yuan (2)
Ye Deng (2)
Jizhong Zhou (2) (3) (4)
Lanjuan Li (1)
1. State Key Laboratory for Diagnosis and Treatment of Infectious Disease ; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases ; The First Affiliated Hospital ; Zhejiang University ; Hangzhou ; 310003 ; PR China
2. Institute for Environmental Genomics ; Department of Microbiology and Plant Biology ; University of Oklahoma ; Norman ; OK ; 73019 ; USA
3. State Key Joint Laboratory of Environment Simulation and Pollution Control ; School of Environment ; Tsinghua University ; Beijing ; 100084 ; China
4. Earth Sciences Division ; Lawrence Berkeley National Laboratory ; Berkeley ; CA ; 94720 ; USA - 关键词：End ; stage liver disease ; Intestines ; Microbial communities ; Alcohol ; Microarray
- 刊名：BMC Genomics
- 出版年：2014
- 出版时间：December 2014
- 年：2014
- 卷：15
- 期：1
- 全文大小：1,677 KB
- 参考文献：1. Garcia-Tsao, G, Wiest, R (2004) Gut microflora in the pathogenesis of the complications of cirrhosis. Best Pract Res Clin Gastroenterol 18: pp. 353-372 CrossRef
2. Wiest, R, Garcia-Tsao, G (2005) Bacterial translocation (BT) in cirrhosis. Hepatology 41: pp. 422-433 CrossRef
3. Guarner, C, Soriano, G (2005) Bacterial translocation and its consequences in patients with cirrhosis. Eur J Gastroenterol Hepatol 17: pp. 27-31 CrossRef
4. Chen, Y, Yang, F, Lu, H, Wang, B, Lei, D, Wang, Y, Zhu, B, Li, L (2011) Characterization of fecal microbial communities in patients with liver cirrhosis. Hepatology 54: pp. 562-572 CrossRef
5. Wei, X, Yan, X, Zou, D, Yang, Z, Wang, X, Liu, W, Wang, S, Li, X, Han, J, Huang, L, Jing, Y (2013) Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach. BMC Gastroenterol 13: pp. 175 CrossRef
6. Grice, EA, Segre, JA (2012) The human microbiome: our second genome. Annu Rev Genomics Hum Genet 13: pp. 151-170 CrossRef
7. Gill, SR, Pop, M, Deboy, RT, Eckburg, PB, Turnbaugh, PJ, Samuel, BS, Gordon, JI, Relman, DA, Fraser-Liggett, CM, Nelson, KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: pp. 1355-1359 CrossRef
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 (2009) A core gut microbiome in obese and lean twins. Nature 457: pp. 480-484 CrossRef
9. Kurokawa, K, Itoh, T, Kuwahara, T, Oshima, K, Toh, H, Toyoda, A, Takami, H, Morita, H, Sharma, VK, Srivastava, TP (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14: pp. 169-181 CrossRef
10. Yatsunenko, T, Rey, FE, Manary, MJ, Trehan, I, Dominguez-Bello, MG, Contreras, M, Magris, M, Hidalgo, G, Baldassano, RN, Anokhin, AP (2012) Human gut microbiome viewed across age and geography. Nature 486: pp. 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 (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490: pp. 55-60 CrossRef
12. Zhou, J (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6: pp. 288-294 CrossRef
13. He, Z, Deng, Y, Zhou, J (2012) Development of functional gene microarrays for microbial community analysis. Curr Opin Biotechnol 23: pp. 49-55 CrossRef
14. He, Z, Van Nostrand, JD, Zhou, J (2012) Applications of functional gene microarrays for profiling microbial communities. Curr Opin Biotechnol 23: pp. 460-466 CrossRef
15. He, Z, Nostrand, J, Deng, Y, Zhou, J (2011) 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 5: pp. 1-20 CrossRef
16. Topping, DL, Clifton, PM (2001) Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol Rev 81: pp. 1031-1064
17. Ridlon, JM, Kang, DJ, Hylemon, PB (2006) Bile salt biotransformations by human intestinal bacteria. J Lipid Res 47: pp. 241-259 CrossRef
18. Bajaj, JS, Ridlon, JM, Hylemon, PB, Thacker, LR, Heuman, DM, Smith, S, Sikaroodi, M, Gillevet, PM (2012) Linkage of Gut Microbiome with Cognition in Hepatic Encephalopathy. Am J Physiol Gastrointest Liver Physiol 302: pp. G168-G175 CrossRef
19. Nikolaki, S, Tsiamis, G (2013) Microbial diversity in the era of omic technologies. Biomed Res Int 2013: pp. e958719 CrossRef
20. Paliy, O, Agans, R (2012) Application of phylogenetic microarrays to interrogation of human microbiota. FEMS Microbiol Ecol 79: pp. 2-11 CrossRef
21. Huang, HJ, Zhang, AY, Cao, HC, Lu, HF, Wang, BH, Xie, Q, Xu, W, Li, LJ (2013) Metabolomic analyses of faeces reveals malabsorption in cirrhotic patients. Dig Liver Dis 45: pp. 677-682 CrossRef
22. Cabral, CM, Burns, DL (2011) Low-protein diets for hepatic encephalopathy debunked: let them eat steak. Nutr Clin Pract 26: pp. 155-159 CrossRef
23. Turnbaugh, PJ, Ridaura, VK, Faith, JJ, Rey, FE, Knight, R, Gordon, JI (2009) The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1: pp. 6ra-14ra CrossRef
24. Shanks, OC, Kelty, CA, Archibeque, S, Jenkins, M, Newton, RJ, McLellan, SL, Huse, SM, Sogin, ML (2011) Community structures of fecal bacteria in cattle from different animal feeding operations. Appl Environ Microbiol 77: pp. 2992-3001 CrossRef
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 (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334: pp. 105-108 CrossRef
26. Singh, KM, Shah, TM, Reddy, B, Deshpande, S, Rank, DN, Joshi, CG (2014) Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers. J Appl Genet 55: pp. 145-154 CrossRef
27. Deusch, O, O鈥橣lynn, C, Colyer, A, Morris, P, Allaway, D, Jones, PG, Swanson, KS (2014) Deep illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens. PLoS One 9: pp. e101021 CrossRef
28. Tsiaousi, ET, Hatzitolios, AI, Trygonis, SK, Savopoulos, CG (2008) Malnutrition in end stage liver disease: recommendations and nutritional support. J Gastroenterol Hepatol 23: pp. 527-533 CrossRef
29. Kokavec, A (2008) Is decreased appetite for food a physiological consequence of alcohol consumption?. Appetite 51: pp. 233-243 CrossRef
30. Lindenbaum, J, Lieber, CS (1975) Effects of chronic ethanol administration on intestinal absorption in man in the absence of nutritional deficiency. Ann N Y Acad Sci 252: pp. 228-234 CrossRef
31. Raux, E, Schubert, HL, Warren, MJ (2000) Biosynthesis of cobalamin (vitamin B12): a bacterial conundrum. Cell Mol Life Sci 57: pp. 1880-1893 CrossRef
32. Zeuzem, S (2000) Gut-liver axis. Int J Colorectal Dis 15: pp. 59-82 CrossRef
33. Jones, BV, Begley, M, Hill, C, Gahan, CG, Marchesi, JR (2008) Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A 105: pp. 13580-13585 CrossRef
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 (2013) Modulation of the fecal bile acid profile by gut microbiota in cirrhosis. J Hepatol 58: pp. 949-955 CrossRef
35. Bajaj, JS, Hylemon, PB, Ridlon, JM, Heuman, DM, Daita, K, White, MB, Monteith, P, Noble, NA, Sikaroodi, M, Gillevet, PM (2012) 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 303: pp. G675-G685 CrossRef
36. Hamer, HM, Jonkers, D, Venema, K, Vanhoutvin, S, Troost, FJ, Brummer, RJ (2008) Review article: the role of butyrate on colonic function. Aliment Pharmacol Ther 27: pp. 104-119 CrossRef
37. Norman, K, Pirlich, M (2008) Gastrointestinal tract in liver disease: which organ is sick?. Curr Opin Clin Nutr Metab Care 11: pp. 613-619 CrossRef
38. Thomas, F, Hehemann, JH, Rebuffet, E, Czjzek, M, Michel, G (2011) Environmental and gut bacteroidetes: the food connection. Front Microbiol 2: pp. 93 CrossRef
39. Zapparoli, G, Fracchetti, F, Stefanelli, E, Torriani, S (2012) Genetic and phenotypic strain heterogeneity within a natural population of Oenococcus oeni from Amarone wine. J Appl Microbiol 113: pp. 1087-1096 CrossRef
40. Levitt, MD, Doizaki, W, Levine, AS (1982) Hypothesis: metabolic activity of the colonic bacteria influences organ injury from ethanol. Hepatology 2: pp. 598-600 CrossRef
41. Tillonen, J, Homann, N, Rautio, M, Jousimies-Somer, H, Salaspuro, M (1999) Ciprofloxacin decreases the rate of ethanol elimination in humans. Gut 44: pp. 347-352 CrossRef
42. Korem, M, Gov, Y, Rosenberg, M (2010) Global gene expression in Staphylococcus aureus following exposure to alcohol. Microb Pathog 48: pp. 74-84 CrossRef
43. Redelman, CV, Maduakolam, C, Anderson, GG (2012) Alcohol treatment enhances Staphylococcus aureus biofilm development. FEMS Immunol Med Microbiol 66: pp. 411-418 CrossRef
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 (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: pp. 59-65 CrossRef
45. Chou, K, Wright, RO (2006) Phthalates in food and medical devices. J Med Toxicol 2: pp. 126-135 CrossRef
46. Leitz, J, Kuballa, T, Rehm, J, Lachenmeier, DW (2009) Chemical analysis and risk assessment of diethyl phthalate in alcoholic beverages with special regard to unrecorded alcohol. PLoS One 4: pp. e8127 CrossRef
47. Kitko, RD, Cleeton, RL, Armentrout, EI, Lee, GE, Noguchi, K, Berkmen, MB, Jones, BD, Slonczewski, JL (2009) Cytoplasmic acidification and the benzoate transcriptome in Bacillus subtilis. PLoS One 4: pp. e8255 CrossRef
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 (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330: pp. 204-208 CrossRef
49. Lu, Z, He, Z, Parisi, VA, Kang, S, Deng, Y, Van Nostrand, JD, Masoner, JR, Cozzarelli, IM, Suflita, JM, Zhou, J (2012) GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer. Environ Sci Technol 46: pp. 5824-5833 CrossRef - 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
- 出版者：BioMed Central
- ISSN：1471-2164
文摘
Background Human gut microbiota plays an important role in the pathogenesis of cirrhosis complications. Although the phylogenetic diversity of intestinal microbiota in patients with liver cirrhosis has been examined in several studies, little is known about their functional composition and structure. Results To characterize the functional gene diversity of the gut microbiome in cirrhotic patients, we recruited a total of 42 individuals, 12 alcoholic cirrhosis patients, 18 hepatitis B virus (HBV)-related cirrhosis patients, and 12 normal controls. We determined the functional structure of these samples using a specific functional gene array, which is a combination of GeoChip for monitoring biogeochemical processes and HuMiChip specifically designed for analyzing human microbiomes. Our experimental data showed that the microbial community functional composition and structure were dramatically distinctive in the alcoholic cirrhosis. Various microbial functional genes involved in organic remediation, stress response, antibiotic resistance, metal resistance, and virulence were highly enriched in the alcoholic cirrhosis group compared to the control group and HBV-related cirrhosis group. Cirrhosis may have distinct influences on metabolic potential of fecal microbial communities. The abundance of functional genes relevant to nutrient metabolism, including amino acid metabolism, lipid metabolism, nucleotide metabolism, and isoprenoid biosynthesis, were significantly decreased in both alcoholic cirrhosis group and HBV-related cirrhosis group. Significant correlations were observed between functional gene abundances and Child-Pugh scores, such as those encoding aspartate-ammonia ligase, transaldolase, adenylosuccinate synthetase and IMP dehydrogenase. Conclusions Functional gene array was utilized to study the gut microbiome in alcoholic and HBV-related cirrhosis patients and controls in this study. Our array data indicated that the functional composition of fecal microbiomes was heavily influenced by cirrhosis, especially by alcoholic cirrhosis. This study provides new insights into the functional potentials and activity of gut microbiota in cirrhotic patients with different etiologies.