Advertisement

Current Microbiology

, Volume 75, Issue 6, pp 658–665 | Cite as

Metagenomic Analysis of the Jinding Duck Fecal Virome

  • Lili Zhao
  • Yinjie Niu
  • Taofeng Lu
  • Haichang Yin
  • Yuanyuan Zhang
  • Lijing Xu
  • Yiping Wang
  • Hongyan ChenEmail author
Article

Abstract

Ducks play an important role in transmitting and maintaining mammalian viruses in nature, and are a reservoir host of many animal viruses. We analyzed the fecal virome of four strains (A, B, C, and D) of ducks living in isolation by using metagenomic analysis. The feces of the ducks tested contained 18 animal virus families. The percentage values of RNA virus reads, compared to the total animal virus reads in each of the four strains were 96.96% (A), 97.30% (B), 98.01 (C), and 67.49% (D), and were mainly from Orthomyxoviridae, Mimiviridae, Bunyaviridae, Picobirnaviridae, and Reoviridae. Meanwhile, the minority of DNA virus reads were related to Herpesviridae, Adenoviridae, Iridoviridae, and other, low abundance viral families. The percentage values of Orthomyxoviridae, Mimiviridae, Bunyaviridae, Picobirnaviridae, and Herpesviridae reads were not significantly different among strains A, B, and C; however, there were marked differences in the abundance of these reads in strain D. In summary, this study provides an unbiased examination of the viral diversity in the feces of four strains of ducks in specific-pathogen-free periods, and highlights the variation in the percentage of viral families present. These results can be used as a reference for detecting duck viral pathogens and predicting zoonotic potential.

Notes

Acknowledgements

This work was supported by the National Key R&D Program of China (2016YFD0500800) and the Chinese Academy of Agricultural Sciences Fundamental Scientific Research Funds (Y2016PT41).

Compliance with Ethical Standards

Conflict of interest

The authors declare that there is no conflict of interest regarding the publication of this article.

Ethical Approval

This study was approved by Harbin Veterinary Research Institute and performed in accordance with ethics guidelines and approved protocols. The animal Ethics Committee approval number is Heilongjiang-SYXK-2006-032.

References

  1. 1.
    Firdous AD, Maya S, Massarat K, Baba MA (2016) Developmental ossification sequences of the appendicular and axial skeleton in Kuttanad duck embryos (Anas platyrhynchos domesticus). Open Vet J 6(1):1–5CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Hill NJ, Runstadler JA (2016) A bird’s eye view of influenza A virus transmission: challenges with characterizing both sides of a co-evolutionary dynamic. Integr Comp Biol 56(2):304–316CrossRefPubMedGoogle Scholar
  3. 3.
    Chen GQ, Zhuang QY, Wang KC, Liu S, Shao JZ, Jiang WM, Hou GY, Li JP, Yu JM, Li YP, Chen JM (2013) Identification and survey of a novel avian coronavirus in ducks. PLoS ONE 8(8):e72918CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y (1992) Evolution and ecology of influenza A viruses. Microbiol Rev 56(1):152–179PubMedPubMedCentralGoogle Scholar
  5. 5.
    Costa TP, Brown JD, Howerth EW, Stallknecht DE (2011) Variation in viral shedding patterns between different wild bird species infected experimentally with low-pathogenicity avian influenza viruses that originated from wild birds. Avian Pathol 40(2):119–124CrossRefPubMedGoogle Scholar
  6. 6.
    Stallknecht DE, Brown JD (2008) Ecology of avian influenza in wild birds. In: Swayne D (ed) Blackwell, IowaCrossRefGoogle Scholar
  7. 7.
    Stallknecht DE, Brown JD (2009) Tenacity of avian influenza viruses. Rev Sci Tech 28(1):59–67CrossRefPubMedGoogle Scholar
  8. 8.
    Victoria JG, Kapoor A, Li L, Blinkova O, Slikas B, Wang C, Naeem A, Zaidi S, Delwart E (2009) Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J Virol 83(9):4642–4651CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Li L, Victoria JG, Wang C, Jones M, Fellers GM, Kunz TH, Delwart E (2010) Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. J Virol 84(14):6955–6965CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Day JM, Ballard LL, Duke MV, Scheffler BE, Zsak L (2010) Metagenomic analysis of the turkey gut RNA virus community. Virol J 7:313CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Shan T, Li L, Simmonds P, Wang C, Moeser A, Delwart E (2011) The fecal virome of pigs on a high-density farm. J Virol 85(22):11697–11708CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Phan TG, Vo NP, Ak B, Pankovics P, Reuter G, Li OT, Wang C, Deng X, Poon LL, Delwart E (2013) The viruses of wild pigeon droppings. PLoS ONE 8(9):e72787CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Fawaz M, Vijayakumar P, Mishra A, Gandhale PN, Dutta R, Kamble NM, Sudhakar SB, Roychoudhary P, Kumar H, Kulkarni DD, Raut AA (2016) Duck gut viral metagenome analysis captures snapshot of viral diversity. Gut Pathog 8:30CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Morgan RW, Cantello JL, McDermott CH (1990) Transfection of chicken embryo fibroblasts with Marek’s disease virus DNA. Avian Dis 34(2):345–351CrossRefPubMedGoogle Scholar
  15. 15.
    Wang H, Song S, Zeng J, Zhou G, Yang D, Liang T, Yu L (2014) Single amino acid substitution of VP1 N17D or VP2 H145Y confers acid-resistant phenotype of type Asia1 foot-and-mouth disease virus. Virol Sin 29(2):103–111CrossRefPubMedGoogle Scholar
  16. 16.
    Allander T, Emerson SU, Engle RE, Purcell RH, Bukh J (2001) A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci USA 98(20):11609–11614CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Cheng WX, Li JS, Huang CP, Yao DP, Liu N, Cui SX, Jin Y, Duan ZJ (2010) Identification and nearly full-length genome characterization of novel porcine bocaviruses. PLoS ONE 5(10):e13583CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Chrzastek K, Lee DH, Smith D, Sharma P, Suarez DL, Pantin-Jackwood M, Kapczynski DR (2017) Use of sequence-independent, single-primer-amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses. Virology 509:159–166CrossRefPubMedGoogle Scholar
  19. 19.
    Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform 9:386CrossRefGoogle Scholar
  20. 20.
    Richard M, Fouchier RA (2016) Influenza A virus transmission via respiratory aerosols or droplets as it relates to pandemic potential. FEMS Microbiol Rev 40(1):68–85CrossRefPubMedGoogle Scholar
  21. 21.
    Talker SC, Stadler M, Koinig HC, Mair KH, Rodriguez-Gomez IM, Graage R, Zell R, Durrwald R, Starick E, Harder T, Weissenbock H, Lamp B, Hammer SE, Ladinig A, Saalmuller A, Gerner W (2016) Influenza A virus infection in pigs attracts multifunctional and cross-reactive T cells to the lung. J Virol 90(20):9364–9382CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Li Y, Huang B, Ma X, Wu J, Li F, Ai W, Song M, Yang H (2009) Molecular characterization of the genome of duck enteritis virus. Virology 391(2):151–161CrossRefPubMedGoogle Scholar
  23. 23.
    Dhama K, Kumar N, Saminathan M, Tiwari R, Karthik K, Kumar MA, Palanivelu M, Shabbir MZ, Malik YS, Singh RK (2017) Duck virus enteritis (duck plague)—a comprehensive update. Vet Q 37(1):57–80CrossRefPubMedGoogle Scholar
  24. 24.
    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(5):367–373CrossRefPubMedGoogle Scholar
  25. 25.
    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(20):6220–6223CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Cann AJ, Fandrich SE, Heaphy S (2005) Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes. Virus Genes 30(2):151–156CrossRefPubMedGoogle Scholar
  27. 27.
    Li L, Shan T, Wang C, Cote C, Kolman J, Onions D, Gulland FM, Delwart E (2011) The fecal viral flora of California sea lions. J Virol 85(19):9909–9917CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Li L, Kapoor A, Slikas B, Bamidele OS, Wang C, Shaukat S, Masroor MA, Wilson ML, Ndjango JB, Peeters M, Gross-Camp ND, Muller MN, Hahn BH, Wolfe ND, Triki H, Bartkus J, Zaidi SZ, Delwart E (2010) Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol 84(4):1674–1682CrossRefPubMedGoogle Scholar
  29. 29.
    Manteufel J, Truyen U (2008) Animal bocaviruses: a brief review. Intervirology 51(5):328–334CrossRefPubMedGoogle Scholar
  30. 30.
    Cagle C, To TL, Nguyen T, Wasilenko J, Adams SC, Cardona CJ, Spackman E, Suarez DL, Pantin-Jackwood MJ (2011) Pekin and Muscovy ducks respond differently to vaccination with a H5N1 highly pathogenic avian influenza (HPAI) commercial inactivated vaccine. Vaccine 29(38):6549–6557CrossRefPubMedGoogle Scholar
  31. 31.
    Cagle C, Wasilenko J, Adams SC, Cardona CJ, To TL, Nguyen T, Spackman E, Suarez DL, Smith D, Shepherd E, Roth J, Pantin-Jackwood MJ (2012) Differences in pathogenicity, response to vaccination, and innate immune responses in different types of ducks infected with a virulent H5N1 highly pathogenic avian influenza virus from Vietnam. Avian Dis 56(3):479–487CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research InstituteThe Chinese Academy of Agriculture SciencesHarbinPeople’s Republic of China

Personalised recommendations