Viral metagenomics analysis of feces from coronary heart disease patients reveals the genetic diversity of the Microviridae

Virologica Sinica

Volumn 32, Issue 2, 2017, Pages 130-138

  Guo, Lianghua ^a   Hua, Xiuguo ^a   Zhang, Wen ^b   Yang, Shixing ^b   Shen, Quan ^b   Hu, Haibing ^a   Li, Jingjiao ^a   Liu, Zhijian ^b   Wang, Xiaochun ^b   Wang, Hua ^b   Zhou, Chenglin ^c   Cui, Li ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b JIANGSU UNIVERSITY   (China)

^c Department of Thoracic Surgery Jiangsu Taizhou People's Hospital   (China)

Author keywords

coronary heart disease (CHD); Gokushovirinae; gut virome; Microviridae; viral metagenomics

Indexed keywords

ADULT; AGED; ARTICLE; CARDIAC PATIENT; CLINICAL ARTICLE; CONTROLLED STUDY; FECES ANALYSIS; GENETIC VARIABILITY; GENOME ANALYSIS; GOKUSHOVIRINAE; HUMAN; ISCHEMIC HEART DISEASE; METAGENOMICS; MICROVIRIDAE; NONHUMAN; PHYLOGENY; SEQUENCE ANALYSIS; VIRGAVIRIDAE; VIRUS GENOME; BIODIVERSITY; CLASSIFICATION; CORONARY ARTERY DISEASE; FECES; GENETICS; MIDDLE AGED; VERY ELDERLY; VIROLOGY; VIRUS;

AGED; AGED, 80 AND OVER; BIODIVERSITY; CORONARY DISEASE; FECES; HUMANS; METAGENOMICS; MIDDLE AGED; VIRUSES;

EID: 85018732376     PISSN: 16740769     EISSN: 1995820X     Source Type: Journal    
DOI: 10.1007/s12250-016-3896-0     Document Type: Article

References (29)

1. Adams MJ, Antoniw JF, Kreuze J. 2009. Virgaviridae: a new family of rod-shaped plant viruses. Arch Virol, 154: 1967–1972.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25: 3389–3402.
3. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, Mahaffy JM, Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F. 2006. The marine viromes of four oceanic regions. PLoS Biol, 4: e368.
4. Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, Felts B, Mahaffy JM, Mueller J, Nulton J, Rayhawk S, Rodriguez-Brito B, Salamon P, Rohwer F. 2008. Viral diversity and dynamics in an infant gut. Res Microbiol, 159: 367–373.
5. Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, Salamon P, Rohwer F. 2003. Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol, 185: 6220–6223.
6. Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F. 2002. Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A, 99: 14250–14255.
7. Brentlinger KL, Hafenstein S, Novak CR, Fane BA, Borgon R, McKenna R, Agbandje- McKenna M. 2002. Microviridae, a family divided: isolation, characterization, and genome sequence of phiMH2K, a bacteriophage of the obligate intracellular parasitic bacterium Bdellovibrio bacteriovorus. J Bacteriol, 184: 1089–1094.
8. Deng X, Naccache SN, Ng T, Federman S, Li L, Chiu CY, Delwart EL. 2015. An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data. Nucleic Acids Res, 43: e46.
9. Desnues C, Rodriguez-Brito B, Rayhawk S, Kelley S, Tran T, Haynes M, Liu H, Furlan M, Wegley L, Chau B, Ruan Y, Hall D, Angly FE, Edwards RA, Li L, Thurber RV, Reid RP, Siefert J, Souza V, Valentine DL, Swan BK, Breitbart M, Rohwer F. 2008. Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature, 452: 340–343.
10. Emoto T, Yamashita T, Sasaki N, Hirota Y, Hayashi T, So A, Kasahara K, YodoiK, Matsumoto T, Mizoguchi T, Ogawa W, Hirata KI. 2016. Analysis of Gut Microbiota in Coronary Artery Disease Patients: a Possible Link between Gut Microbiota and Coronary Artery Disease. J Atheroscler Thromb.
11. Feng Q, Liu Z, Zhong S, Li R, Xia H, Jie Z, Wen B, Chen X, Yan W, Fan Y, Guo Z, Meng N, Chen J, Yu X, Zhang Z, Kristiansen K, Wang J, Xu X, He K, Li G. 2016. Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease. Sci Rep, 6: 22525.
12. Kim MS, Park EJ, Roh SW, Bae JW. 2011. Diversity and abundance of single-stranded DNA viruses in human feces. Appl Environ Microbiol, 77: 8062–8070.
13. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods, 9: 357–359.
14. Lopez-Bueno A, Tamames J, Velazquez D, Moya A, Quesada A, Alcami A. 2009. High diversity of the viral community from an Antarctic lake. Science, 326: 858–861.
15. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 1: 18.
16. Marais A, Faure C, Mustafayev E, Candresse T. 2015. Characterization of New Isolates of Apricot vein clearing-associated virus and of a New Prunus-Infecting Virus: Evidence for Recombination as a Driving Force in Betaflexiviridae Evolution. PLoS One, 10: e0129469.
17. Martinez C. 2016. Cut intake of saturated fats to stave off coronary heart disease. Nurs Stand, 31: 18.
18. Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD. 2011. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res, 21: 1616–1625.
19. Phan TG, Kapusinszky B, Wang C, Rose RK, Lipton HL, Delwart EL. 2011. The fecal viral flora of wild rodents. PLoS Pathog, 7: e1002218.
20. Quaiser A, Dufresne A, Ballaud F, Roux S, Zivanovic Y, Colombet J, Sime-Ngando T, Francez AJ. 2015. Diversity and comparative genomics of Microviridae in Sphagnum-dominated peatlands. Front Microbiol, 6: 375.
21. Reyes A, Semenkovich NP, Whiteson K, Rohwer F, Gordon JI. 2012. Going viral: next-generation sequencing applied to phage populations in the human gut. Nat Rev Microbiol, 10: 607–617.
22. Roux S, Enault F, Robin A, Ravet V, Personnic S, Theil S, Colombet J, Sime-Ngando T, Debroas D. 2012a. Assessing the diversity and specificity of two freshwater viral communities through metagenomics. PLoS One, 7: e33641.
23. Roux S, Krupovic M, Poulet A, Debroas D, Enault F. 2012b. Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads. PLoS One, 7: e40418.
24. Scarpellini E, Ianiro G, Attili F, Bassanelli C, De Santis A, Gasbarrini A. 2015. The human gut microbiota and virome: Potential therapeutic implications. Dig Liver Dis, 47: 1007–1012.
25. Schroder SL, Richter M, Schroder J, Frantz S, Fink A. 2016. Socioeconomic inequalities in access to treatment for coronary heart disease: A systematic review. Int J Cardiol, 219: 70–78.
26. Tucker KP, Parsons R, Symonds EM, Breitbart M. 2011. Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean. Isme j, 5: 822–830.
27. Wommack KE, Colwell RR. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev, 64: 69–114.
28. Wong JM, Esfahani A, Singh N, Villa CR, Mirrahimi A, Jenkins DJ, Kendall CW. 2012. Gut microbiota, diet, and heart disease. J AOAC Int, 95: 24–30.
29. Zhang T, Breitbart M, Lee WH, Run JQ, Wei CL, Soh SW, Hibberd ML, Liu ET, Rohwer F, Ruan Y. 2006. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol, 4: e3.