Alterations of the human gut microbiome in liver cirrhosis
Tóm tắt
Từ khóa
Tài liệu tham khảo
Fouts, D. E., Torralba, M., Nelson, K. E., Brenner, D. A. & Schnabl, B. Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease. J. Hepatol. 56, 1283–1292 (2012)
Cesaro, C. et al. Gut microbiota and probiotics in chronic liver diseases. Digest. Liver Dis. 43, 431–438 (2011)
Wiest, R. & Garcia-Tsao, G. Bacterial translocation (BT) in cirrhosis. Hepatology 41, 422–433 (2005)
Nolan, J. P. The role of intestinal endotoxin in liver injury: a long and evolving history. Hepatology 52, 1829–1835 (2010)
Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359 (2006)
Garcia-Tsao, G. & Wiest, R. Gut microflora in the pathogenesis of the complications of cirrhosis. Best Pract. Res. Clin. Gastroenterol. 18, 353–372 (2004)
Wiest, R., Krag, A. & Gerbes, A. Spontaneous bacterial peritonitis: recent guidelines and beyond. Gut 61, 297–310 (2012)
Bass, N. M. et al. Rifaximin treatment in hepatic encephalopathy. N. Engl. J. Med. 362, 1071–1081 (2010)
Benten, D. & Wiest, R. Gut microbiome and intestinal barrier failure–the “Achilles heel” in hepatology? J. Hepatol. 56, 1221–1223 (2012)
Yan, A. W. et al. Enteric dysbiosis associated with a mouse model of alcoholic liver disease. Hepatology 53, 96–105 (2011)
De Filippo, C. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl Acad. Sci. USA 107, 14691–14696 (2010)
Cho, I. & Blaser, M. J. The human microbiome: at the interface of health and disease. Nature Rev. Genet. 13, 260–270 (2012)
Chen, Y. et al. Characterization of fecal microbial communities in patients with liver cirrhosis. Hepatology 54, 562–572 (2011)
Nelson, K. E. et al. A catalog of reference genomes from the human microbiome. Science 328, 994–999 (2010)
Ley, R. E., Turnbaugh, P. J., Klein, S. & Gordon, J. I. Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022–1023 (2006)
Turnbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031 (2006)
Ley, R. E. et al. Obesity alters gut microbial ecology. Proc. Natl Acad. Sci. USA 102, 11070–11075 (2005)
Lepage, P. et al. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 141, 227–236 (2011)
Garrett, W. S. et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 8, 292–300 (2010)
Wen, L. et al. Innate immunity and intestinal microbiota in the development of type 1 diabetes. Nature 455, 1109–1113 (2008)
Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55–60 (2012)
Vijay-Kumar, M. et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328, 228–231 (2010)
Karlsson, F. H. et al. Symptomatic atherosclerosis is associated with an altered gut metagenome. Nature Commun. 3, 1245 (2012)
The Human Microbiome Project Consortium A framework for human microbiome research. Nature 486, 215–221 (2012)
The Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012)
Le Chatelier, E. et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541–546 (2013)
Cotillard, A. et al. Dietary intervention impact on gut microbial gene richness. Nature 500, 585–588 (2013)
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010)
Nielsen, H. B. et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nature Biotechnol http://dx.doi.org/10.1038/nbt.2939 (2014)
Albertsen, M. et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnol. 31, 533–538 (2013)
Zoetendal, E. G. et al. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J. 6, 1415–1426 (2012)
Bauer, T. M. et al. Small intestinal bacterial overgrowth in human cirrhosis is associated with systemic endotoxemia. Am. J. Gastroenterol. 97, 2364–2370 (2002)
Chen, T. et al. The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database 2010, baq013 (2010)
Pagani, I. et al. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 40, D571–D579 (2012)
Saarela, M., Mogensen, G., Fonden, R., Matto, J. & Mattila-Sandholm, T. Probiotic bacteria: safety, functional and technological properties. J. Biotechnol. 84, 197–215 (2000)
Merritt, M. E. & Donaldson, J. R. Effect of bile salts on the DNA and membrane integrity of enteric bacteria. J. Med. Microbiol. 58, 1533–1541 (2009)
Marchandin, H. et al. Prosthetic joint infection due to Veillonella dispar. Eur. J Clin. Microbiol. Infect. Dis. 20, 340–342 (2001)
Hwang, J. J., Lau, Y. J., Hu, B. S., Shi, Z. Y. & Lin, Y. H. Haemophilus parainfluenzae and Fusobacterium necrophorum liver abscess: a case report. J. Microbiol. Immunol. Infect. 35, 65–67 (2002)
Xu, M. et al. Changes of fecal Bifidobacterium species in adult patients with hepatitis B virus-induced chronic liver disease. Microb. Ecol. 63, 304–313 (2012)
Greenblum, S., Turnbaugh, P. J. & Borenstein, E. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc. Natl Acad. Sci. USA 109, 594–599 (2012)
Ferenci, P., Schafer, D. F., Kleinberger, G., Hoofnagle, J. H. & Jones, E. A. Serum levels of gamma-aminobutyric-acid-like activity in acute and chronic hepatocellular disease. Lancet ii, 811–814 (1983)
Minuk, G. Y., Winder, A., Burgess, E. D. & Sarjeant, E. J. Serum gamma-aminobutyric acid (GABA) levels in patients with hepatic encephalopathy. Hepatogastroenterology 32, 171–174 (1985)
Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012)
Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 (2011)
Li, M. et al. Symbiotic gut microbes modulate human metabolic phenotypes. Proc. Natl Acad. Sci. USA 105, 2117–2122 (2008)
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009)
Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272 (2010)
Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966–1967 (2009)
Noguchi, H., Park, J. & Takagi, T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res. 34, 5623–5630 (2006)
Powell, S. et al. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res. 40, D284–D289 (2012)
Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLOS Comput. Biol. 8, e1002606 (2012)
Price, A. L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nature Genet. 38, 904–909 (2006)