Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Shen, Hongzhang ^a   Ye, Fuqiang ^b,c   Xie, Lu ^a   Yang, Jianfeng ^a   Li, Zhen ^b,c   Xu, Peisong ^d   Meng, Fei ^d   Li, Lei ^d   Chen, Ying ^b   Bo, Xiaochen ^b,c   Ni, Ming ^b,c   Zhang, Xiaofeng ^a  

^a HANGZHOU FIRST PEOPLE'S HOSPITAL   (China)

^b BEIJING INSTITUTE OF RADIATION MEDICINE   (China)

^c BEIJING INSTITUTE OF MICROBIOLOGY AND EPIDEMIOLOGY   (China)

^d Hangzhou Zhiyuan Institute of Medical Diagnostics   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AGED; BACTERIUM; BILE; CLASSIFICATION; FEMALE; GALLSTONE; GENETICS; HUMAN; MALE; METAGENOME; MICROBIAL CONSORTIUM; MICROBIOLOGY; MIDDLE AGED; VERY ELDERLY;

AGED; AGED, 80 AND OVER; BACTERIA; BILE; FEMALE; GALLSTONES; HUMANS; MALE; METAGENOME; MICROBIAL CONSORTIA; MIDDLE AGED;

EID: 84948988340     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep17450     Document Type: Article

References (59)

1. Shaffer, E. A. Epidemiology and risk factors for gallstone disease: has the paradigm changed in the 21st century? Curr. Gastroenterol. Rep. 7, 132-140 (2005).
2. Stinton, L. & Shaffer, E. Epidemiology of gallbladder disease: cholelithiasis and cancer. Gut Liver 6, 172-187 (2012).
3. Stinton, L. M., Myers, R. P. & Shaffer, E. A. Epidemiology of gallstones. Gastroenterol. Clin. North Am. 39, 157-169 (2010).
4. Maki, T. Pathogenesis of calcium bilirubinate gallstone: role of E. coli, beta-glucuronidase and coagulation by inorganic ions, polyelectrolytes and agitation. Ann. Surg. 164, 90-100 (1966).
5. Swidsinski, A. & Lee, S. P. The role of bacteria in gallstone pathogenesis. Front. Biosci. 6, 93-103 (2001).
6. Stewart, L., Oesterle, A. L., Erdan, I., Griffiss, J. M. & Way, L. W. Pathogenesis of pigment gallstones in Western societies: the central role of bacteria. J. Gastrointest. Surg. 6, 891-904 (2002).
7. Stewart, L., Grifiss, J. M., Jarvis, G. A. & Way, L. W. Biliary bacterial factors determine the path of gallstone formation. Am. J. Surg. 192, 598-603 (2006).
8. Begley, M., Gahan, C. G. & Hill, C. The interaction between bacteria and bile. Fems Microbiol. Rev. 29, 625-651 (2005).
9. Kaufman, H. S., Magnuson, T. H., Lillemoe, K. D., Frasca, P. & Pitt, H. A. The role of bacteria in gallbladder and common duct stone formation. Ann. Surg. 209, 584-592 (1989).
10. Tabata, M. Bacteria and gallstones. Dig. Dis. Sci. 26, 218-224 (1981).
11. Salvador, V. B. D., Lozada, M. C. H. & Consunji, R. J. Microbiology and antibiotic susceptibility of organisms in bile cultures from patients with and without cholangitis at an Asian academic medical center. Surg. Infect. 12, 105-111 (2011).
12. Chang, W.-T. et al. Bacteriology and antimicrobial susceptibility in biliary tract disease: an audit of 10-year's experience. Kaohsiung J. Med. Sci. 18, 221-228 (2002).
13. Tanaka, A. et al. Antimicrobial therapy for acute cholangitis: Tokyo Guidelines. J. Hepatobiliary Pancreat. Surg. 14, 59-67 (2007).
14. Theron, J. & Cloete, T. Molecular techniques for determining microbial diversity and community structure in natural environments. Crit. Rev. Microbiol. 26, 37-57 (2000).
15. Segata, N. et al. Computational meta'omics for microbial community studies. Mol. Syst. Biol. 9, 666 (2013).
16. Wu, T. et al. Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study. BMC Genomics 14, 669 (2013).
17. Consortium, H. M. P. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012).
18. Consortium, H. M. P. A framework for human microbiome research. Nature 486, 215-221 (2012).
19. Aagaard, K. et al. The placenta harbors a unique microbiome. Sci. Transl. Med. 6, 237ra265-237ra265 (2014).
20. 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).
21. Downes, J. et al. Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum 'Synergistetes' isolated from the human oral cavity. Int. J. Syst. Evol. Microbiol. 59, 972-980 (2009).
22. Rôças, I. N. & Siqueira, J. F. Identification of bacteria enduring endodontic treatment procedures by a combined Reverse Transcriptase-Polymerase Chain reaction and Reverse-Capture Checkerboard approach. J. Endod. 36, 45-52 (2010).
23. Tomazinho, L. F. & Avila-Campos, M. J. Detection of Porphyromonas gingivalis, Porphyromonas endodontalis, Prevotella intermedia, and Prevotella nigrescens in chronic endodontic infection. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 103, 285-288 (2007).
24. Göker, M. et al. Complete genome sequence of Olsenella uli type strain (VPI D76D-27C T). Stand. Genomic Sci. 3, 76-84 (2010).
25. Brown, J. M. et al. Characterization of clinical isolates previously identified as Oerskovia turbata: proposal of Cellulosimicrobium funkei sp. nov. and emended description of the genus Cellulosimicrobium. Int. J. Syst. Evol. Microbiol. 56, 801-804 (2006).
26. Magro-Checa, C. et al. Septic Arthritis due to Cellulosimicrobium cellulans. J. Clin. Microbiol. 49, 4391-4393 (2011).
27. Rowlinson, M.-C., Bruckner, D. A., Hinnebusch, C., Nielsen, K. & Deville, J. G. Clearance of Cellulosimicrobium cellulans bacteremia in a child without central venous catheter removal. J. Clin. Microbiol. 44, 2650-2654 (2006).
28. Hadano, Y. et al. Raoultella ornithinolytica bacteremia in cancer patients: report of three cases. Intern. Med. 51, 3193-3195 (2012).
29. Sng, L.-H. et al. Bacteremia caused by Gordonia bronchialis in a patient with sequestrated lung. J. Clin. Microbiol. 42, 2870-2871 (2004).
30. Renvoise, A., Harle, J., Raoult, D. & Roux, V. Gordonia sputi bacteremia. Emerg. Infect. Dis 15, 1535-1537 (2009).
31. Rajagopal, T. et al. Gemella haemolysans spondylodiscitis A report of two cases. J. Bone Joint Surg.-Br. Vol. 94, 825-828 (2012).
32. Rapeport, K. B., Giron, J. A. & Rosner, F. Streptococcus mitis endocarditis: report of 17 cases. Arch. Intern. Med. 146, 2361-2363 (1986).
33. Bhatti, M. A. & Frank, M. O. Veillonella parvula meningitis: case report and review of Veillonella infections. Clin. Infect. Dis. 31, 839-840 (2000).
34. Odeh, M., Oliven, A., Potasman, I., Solomon, H. & Srugo, I. Pyomyositis of the thigh due to Prevotella melaninogenica. Infection 28, 49-50 (2000).
35. Janda, W. et al. Neisseria in Manual of clinical microbiology Volume 1 (eds Murray, P. R. et al.) 601-620 (ASM Press, 2006).
36. Maurer, K. J., Carey, M. C. & Fox, J. G. Roles of infection, inflammation, and the immune system in cholesterol gallstone formation. Gastroenterology 136, 425-440 (2009).
37. Pattinson, N. & Willis, K. Effect of phospholipase C on cholesterol solubilization in model bile. A concanavalin A-binding nucleation-promoting factor from human gallbladder bile. Gastroenterology 101, 1339-1344 (1991).
38. Belzer, C., Kusters, J., Kuipers, E. & Van Vliet, A. Urease induced calcium precipitation by Helicobacter species may initiate gallstone formation. Gut 55, 1678-1679 (2006).
39. Guaglianone, E. et al. Microbial biofilms associated with biliary stent clogging. FEMS Immunol. Med. Microbiol. 59, 410-420 (2010).
40. Ruiz, L., Margolles, A. & Sánchez, B. Bile resistance mechanisms in Lactobacillus and Bifidobacterium. Front. Microbiol. 4, 396 (2013).
41. Stewart, L., Ponce, R., Oesterk, A. L., Griffiss, J. M. & Way, L. W. Pigment gallstone pathogenesis: slime production by biliary bacteria is more important than beta-glucuronidase production. J. Gastrointest. Surg. 4, 547-553 (2000).
42. Sung, J., Leung, J., Shaffer, E., Lam, K. & Costerton, J. Bacterial biofilm, brown pigment stone and blockage of biliary stents. J. Gastroenterol. Hepatol. 8, 28-34 (1993).
43. Prouty, A., Schwesinger, W. & Gunn, J. Biofilm Formation and Interaction with the Surfaces of Gallstones by Salmonella spp. Infect. Immun. 70, 2640-2649 (2002).
44. Pratt, L. A. & Kolter, R. Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili. Mol. Microbiol. 30, 285-293 (1998).
45. O'Toole, G. A. & Kolter, R. Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol. Microbiol. 30, 295-304 (1998).
46. Yamada, T., Letunic, I., Okuda, S., Kanehisa, M. & Bork, P. iPath2. 0: interactive pathway explorer. Nucleic Acids Res. 39, W412-W415 (2011).
47. Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8, e1002358 (2012).
48. Morita, H., Nakanishi, K., Dohi, T., Yasugi, E. & Oshima, M. Phospholipid turnover in the inflamed intestinal mucosa: arachidonic acid-rich phosphatidyl/plasmenyl-ethanolamine in the mucosa in inflammatory bowel disease. J. Gastroenterol. 34, 46-53 (1999).
49. Morgan, X. C. et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13, R79 (2012).
50. Wadhams, G. H. & Armitage, J. P. Making sense of it all: bacterial chemotaxis. Nat. Rev. Mol. Cell Biol. 5, 1024-1037 (2004).
51. Martens, E. C., Chiang, H. C. & Gordon, J. I. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4, 447-457 (2008).
52. Ding, J., Li, F., Zhu, H. & Zhang, X. Endoscopic treatment of difficult extrahepatic bile duct stones, EPBD or EST: An anatomic view. World J. Gastrointest. Endosc. 7, 274-277 (2015).
53. Xu, L., Kyaw, M., Tse, Y. & Lau, J. Endoscopic Sphincterotomy with Large Balloon Dilation versus Endoscopic Sphincterotomy for Bile Duct Stones: A Systematic Review and Meta-Analysis. Biomed Res. Int. 2015, 673103 (2015).
54. Natsui, M., Honma, T., Genda, T. & Nakadaira, H. Effects of endoscopic papillary balloon dilation and endoscopic sphincterotomy on bacterial contamination of the biliary tract. Eur. J. Gastroenterol. Hepatol. 23, 818-824 (2011).
55. dos Santos, J. S., Júnior, W. S., Modena, J., Brunaldi, J. E. & Ceneviva, R. Effect of preoperative endoscopic decompression on malignant biliary obstruction and postoperative infection. Hepatogastroenterology 52, 45-47 (2005).
56. Ipek, S. et al. Evaluation of the effectiveness of endoscopic retrograde cholangiopancreatography in patients with perihilar cholangiocarcinoma and its effect on development of cholangitis. Gastroenterol. Res. Pract. 2014, 508286 (2014).
57. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010).
58. Qin, N. et al. Alterations of the human gut microbiome in liver cirrhosis. Nature 513, 59-64 (2014).
59. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. B 57, 289-300 (1995).