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Establishment of a Standardized 16S rDNA Library Preparation to Enable Analysis of Microbiome in Poultry Processing Using Illumina MiSeq Platform

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Foodborne Bacterial Pathogens

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1918))

Abstract

The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety. This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.

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References

  1. Handley JA, Park SH, Kim SA, Ricke SC (2018) Microbiome profiles of commercial broilers through evisceration and immersion chilling during poultry slaughter and the identification of potential indicator microorganisms. Front Microbiol (9). https://doi.org/10.3389/fmicb.2018.00831

  2. FSIS compliance guideline: modernization of slaughter inspection microbiology sampling of raw poultry. Washington DC, June 2015

    Google Scholar 

  3. Oakley BB, Morales CA, Line J, Berrang ME, Meinersmann RJ, Tillman GE (2013) The poultry-associated microbiome network analysis and farm to fork characterization. PLoS One 8(2):e57190. https://doi.org/10.1371/journal.pone.0057190

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Kim SA, Park SH, Lee SI, Owens CM, Ricke SC (2017) Assessment of chicken carcass microbiome response during processing in the presence of commercial antimicrobials using a next generation sequencing approach. Sci Rep 7. https://doi.org/10.1038/srep43354

  5. Ricke SC, Hacker JC, Yearkey KL, Shi Z, Park SH, Rainwater CE (2017) Unraveling food production microbiomes: concepts and future directions. In: Ricke SC, Atungulu GG, Park SH, Rainwater CE (eds) Food and feed safety systems and analysis. Elsevier Inc, San Diego, CA, pp 347–374

    Google Scholar 

  6. FSIS Notice: 35–16: raw chicken parts sampling program. 1 July 2016

    Google Scholar 

  7. FSIS Notice: 72–16: other raw chicken parts sampling program. 21 Sep 2016

    Google Scholar 

  8. Golob JL, Margolis E, Hoffman NG, Fredricks DN (2017) Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities. BMC Bioinformatics 18:283. https://doi.org/10.1186/s12859-017-1690-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Hiergeist A, Glasner J, Reischl U, Gessner A (2015) Analyses of intestinal microbial: culture verses sequencing. ILAR J 56(2):228–240. https://doi.org/10.1093/ilar/ilv017

    Article  CAS  PubMed  Google Scholar 

  10. Knight R, Maxwell P, Birmingham A, Carnes J, Caporasco JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, Huttley GA (2007) PyCogent: a toolkit for making sense from sequence. Genome Biol 8(8):R171. https://doi.org/10.1186/gb-2007-8-8-r171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Park SH, Lee SI, Ricke SC (2016) Microbial populations in naked neck chicken ceca raised on pasture flock fed with commercial yeast cell wall prebiotics via an Illumina MiSeq platform. PLoS One 11(3):e0151944. https://doi.org/10.1371/journal.pone.0151944

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Plummer E, Twin J, Bulach DM, Garland SM, Tabrizi SN (2015) A comparison of three bioinformatics pipelines for the analysis of preterm gut microbiota using 16s rRNA gene sequencing data. J Proteomics Bioinform 8:283–291. https://doi.org/10.4172/jbp.1000381

    Article  Google Scholar 

  13. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewsky RA, Oakley BB, Park DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mother: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    Article  CAS  Google Scholar 

  14. Kim YK, Jinah Y, Kim B, Ha M, Kim VN (2012) Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells. Cell 46(6):893–895. https://doi.org/10.1016/j.molcell.2012.05.036

    Article  CAS  Google Scholar 

  15. Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis K (2012) Direct comparisons of Illumina vs. Roche. PLoS One 7(2):e30087. https://doi.org/10.1371/journal.pone.0030087

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Thompson DR, Rainwater C, Di J, Ricke SC (2017) Student cross-training opportunities for combining food, transportation, and critical infrastructure cybersecurity into an academic food systems education program. In: Ricke SC, Atungulu GG, Park SH, Rainwater CE (eds) Food and feed safety systems and analysis. Elsevier Inc, San Diego, CA, pp 375–391

    Google Scholar 

  17. Allender HD, Rogers J, Dessai U (2012) FSIS nationwide raw chicken parts microbiological baseline. FSIS

    Google Scholar 

  18. Rothrock MJ, Hiett KL, Gamble J, Caudill AC, Cicconi-Hogan KM, Caporasco JG (2014) A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples. J Vis Exp (94). https://doi.org/10.3791/52161

  19. (2018) Qiagen fast DNA stool kit manual. Qiagen Corporation, Hilden. Dec 2015

    Google Scholar 

  20. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79:5112–5120

    Article  CAS  Google Scholar 

  21. (2018) Accuprime Pfx DNA polymerase manual. Invitrogen, Carlsbad, CA

    Google Scholar 

  22. (2018) SequalPrep normalization kit. Invitrogen, Carlsbad, CA

    Google Scholar 

  23. (2018) Qbit fluorometer 2.0 manual. Invitrogen, Carlsbad, CA

    Google Scholar 

  24. (2018) Agilent bioanalyzer user manual. Agilent Corporation Santa, Clara, CA

    Google Scholar 

  25. (2018) KAPA library quantification kit KR0405-v8.17. Kappa Biosciences, Wilmington, MA

    Google Scholar 

  26. Becker L, Steglich M, Fuchs S, Werner G, Nubel U (2016) Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing. Sci Rep 6(1):28063. https://doi.org/10.1038/srep280632

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA

    Kristina M. Feye & Steven C. Ricke

Authors
  1. Kristina M. Feye
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  2. Steven C. Ricke
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Corresponding author

Correspondence to Steven C. Ricke .

Editor information

Editors and Affiliations

  1. Fougères Laboratory, ANSES, Fougères, France

    Arnaud Bridier

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Feye, K.M., Ricke, S.C. (2019). Establishment of a Standardized 16S rDNA Library Preparation to Enable Analysis of Microbiome in Poultry Processing Using Illumina MiSeq Platform. In: Bridier, A. (eds) Foodborne Bacterial Pathogens. Methods in Molecular Biology, vol 1918. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9000-9_18

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  • DOI: https://doi.org/10.1007/978-1-4939-9000-9_18

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-8999-7

  • Online ISBN: 978-1-4939-9000-9

  • eBook Packages: Springer Protocols

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