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Journal of Environmental Science and Health, Part B
Pesticides, Food Contaminants, and Agricultural Wastes
Volume 59, 2024 - Issue 7
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Articles

Microbiome analyses of poultry feeds: Part I. Comparison of five different DNA extraction methods

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Pages 378-389 | Received 15 Dec 2023, Accepted 03 May 2024, Published online: 23 May 2024

References

  • Maciorowski, K. G.; Jones, F. T.; Pillai, S. D.; Ricke, S. C. Incidence and Control of Food-Borne Salmonella Spp. in Poultry feeds- A Review. World’s Poultry Sci. J. 2004, 60, 446–457. DOI: 10.1079/WPS200428.
  • Maciorowski, K. G.; Herrera, P.; Jones, F. T.; Pillai, S. D.; Ricke, S. C. Effects of Poultry and Livestock Feed with Bacteria and Fungi. Animal Feed Sci. Technol. 2007, 133, 109–136. DOI: 10.1016/j.anifeedsci.2006.08.006.
  • Ricke, S. C. Chap. 8. Feed Hygiene. In: Dewulf J.; Van Immerseel, F. (Eds.) Biosecurity in Animal Production and Veterinary Medicine – from Principles to Practice. ACCO (Academische Coöperative Vennootschap cvba), Leuven, Belgium, 2018, pp. 177–209
  • Olson, E. G.; Dittoe, D. K.; Jendza, J. A.; Stock, D. A.; Ricke, S. C. Application of Microbial Analyses to Feeds and Potential Implications for Poultry Nutrition. Poult. Sci. 2022, 101, 101789. DOI: 10.1016/j.psj.2022.101789.
  • Olson, E. G.; Grenda, T.; Ghosh, A.; Ricke, S. C. Chapter 27. Microbial Pathogen Contamination of Animal Feed. In: Present Knowledge in Food Safety: A Risk-Based Approach through the Food Chain. Anelich, L.; Boobis, A.; Knowles, M.; Popping, B. (Eds.). International Life Sciences Institute, Academic Press, Elsevier. 2023, pp. 378–393. DOI: 10/1016/B978-0-0-12-819470-6.00023-8.
  • Mackie, I. M.; Pryde, S. E.; Gonzales-Sotelo, C.; Medina, I.; Peréz-Martín, R.; Quinteiro, J.; Rey-Mendez, M.; Rehbein, H. Challenges in the Identification of Species of Canned Fish. Trends Food Sci. Technol. 1999, 10, 9–14. 1999, DOI: 10.1016/S0924-2244(99)00013-8.
  • Bossier, P. Authentication of Seafood Products by DNA Patterns. J. Food Sci. 1999, 64, 189–193. DOI: 10.1111/j.1365-2621.1999.tb15862.x.
  • Lockley, A. K.; Bardsley, R. G. DNA-Based Methods for Food Authentication. Trends Food Sci. Technol. 2000, 11, 67–77. DOI: 10.1016/S0924-2244(00)00049-2.
  • Piskata, Z.; Pospisilova, E.; Borilova, G. Comparative Study of DNA Extraction Methods from Fresh and Processed Yellowfin Tuna Muscle Tissue. Int. J. Food Prop. 2017, 20, S430–S443. DOI: 10.1080/10942912.2017.1297953.
  • Piskata, Z.; Servusova, E.; Babak, V.; Nesvadbova, M.; Borilova, G. 2019 The Quality of DNA Isolated from Processed Food and Feed via Different Extraction Procedures. Molecules 2019, 24, 1188. DOI: 10.3390/molecules24061188.
  • Maciorowski, K. G.; Pillai, S. D.; Jones, F. T.; Ricke, S. C. Polymerase Chain Reaction Detection of Foodborne Salmonella Spp. in Animal Feeds. Crit. Rev. Microbiol. 2005, 31, 45–53. DOI: 10.1080/10408410590912970.
  • Yuan, S.; Cohen, D. B.; Ravel, J.; Abdo, Z.; Forney, L. J. Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome. PLoS One. 2012, 7, e33865. 2012, DOI: 10.1371/journal.pone.0033865.
  • Olson, E. G.; Dittoe, D. K.; Micciche, A. C.; Stock, D. A.; Rubinelli, P. M.; Rothrock, M. J.; Jr.; Ricke, S. C. Microbiome Analyses of Poultry Feeds: Part II. Comparison of Different Poultry Feeds. J. Environ. Sci. Health B 1923, (Submitted).
  • Rothrock, M. J.; Jr., Hiett, K. L.; Gamble, J.; Caudill, A. C.; Cicconi-Hogan, K. M.; Caporaso, J. G. A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples. J. Vis. Exp. 2014, 94, e52161. 2014 DOI: 10.3791/52161.
  • Boom, R.; Sol, C. J.; Salimans, M. M.; Jansen, C. L.; Wertheim-van Dillen, P. M.; van der Noordaa, J. Rapid and Simple Method for Purification of Nucleic Acids. J. Clin. Microbiol. 1990, 1990, 28, 495–503. DOI: 10.1128/jcm.28.3.495-503.1990.
  • Porteous, L. A.; Armstrong, J. L.; R, J.; Seidler, R. J.; Watrud, L. S. An Effective Method to Extract DNA from Environmental Samples for Polymerase Chain Reaction Amplification and DNA Fingerprint Analysis. Curr. Microbiol. 1994, 29, 301–307. DOI: 10.1007/BF01577445.
  • Widmer, F.; Seidler, R. J.; Watrud, L. S. Sensitive Detection of Transgenic Plant Marker Gene Persistence in Soil Microcosms. Mol. Ecol. 1996, 5, 603–613. DOI: 10.1111/j.1365-294X.1996.tb00356.x.
  • Kozich, J. J.; Westcott, S. L.; Baxter, N. T.; Highlander, S. K.; Schloss, P. D. Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform. Appl. Environ. Microbiol. 2013, 79, 5112–5120. DOI: 10.1128/AEM.01043-13.
  • Wages, J. A.; Dittoe, D. K.; Feye, K. M.; Ricke, S. C. Consequences of Implementing Neutralizing Buffered Peptone Water in Commercial Poultry Processing on the Microbiota of Whole Bird Carcass Rinses and the Subsequent Microbiological Analyses. Front. Microbiol. 2022, 13, 813461. DOI: 10.3389/fmicb.2022.813461.
  • Bolyen, E.; Rideout, J. R.; Dillon, M. R.; Bokulich, N. A.; Abnet, C. C.; Al-Ghalith, G. A.; Alexander, H.; Alm, E. J.; Arumugam, M.; Asnicar, F.; et al. Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2. Nat. Biotechnol. 2019, 37, 852–857. DOI: 10.1038/s41587-019-0209-9.
  • Callahan, B. J.; McMurdie, P. J.; Rosen, M. J.; Han, A. W.; Johnson, A. J. A.; Holmes, S. P. DADA2: High Resolution Sample Inference from Illumina Amplicon Data. Nat. Methods. 2016, 13, 581–583. DOI: 10.1038/nmeth.3869.
  • Katoh, K.; Misawa, K.; Kuma, K.; Miyata, T. MAFFT: A Novel Method for Rapid Multiple Sequence Alignment Based on Fast Fourier Transform. Nucleic Acids Res. 2002, 30, 3059–3066. DOI: 10.1093/nar/gkf436.
  • Price, M. N.; Dehal, P. S.; Arkin, A. P. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One. 2010, 5, e9490. DOI: 10.1371/journal.pone.0009490.
  • Bokulich, N. A.; Kaehler, B. D.; Rideout, J. R.; Dillon, M.; Bolyen, E.; Knight, R.; Huttley, G. A.; Gregory Caporaso, J. Optimizing Taxonomic Classification of Marker-Gene Amplicon Sequences with QIIME 2’s q2-Feature-Classifier Plugin. Microbiome 2018, 6, 90. DOI: 10.1186/s40168-018-0470-z.
  • Quast, C.; Pruesse, E.; Yilmaz, P.; Gerken, J.; Schweer, T.; Yarza, P.; Peplies, J.; Glöckner, F. O. The SILVA Ribosomal RNA Gene Database Project: Improved Data Processing and Web-Based Tools. Nucleic Acids Res. 2013, 41, D590–D596. DOI: 10.1093/nar/gks1219.
  • Faith, D. P. Conservation Evaluation and Phylogenetic Diversity. Biol. Conserv. 1992, 61, 1–10. DOI: 10.1016/0006-3207(92)91201-3.
  • Kruskal, W. H.; Wallis, W. A. Use of Ranks in One-Criterion Variance Analysis. J. Am. Stat. Assoc. 1952, 47, 583–621. DOI: 10.2307/2280779.
  • Lozupone, C. A.; Hamady, M.; Kelley, S. T.; Knight, R. Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities. Appl. Environ. Microbiol. 2007, 73, 1576–1585. DOI: 10.1128/AEM.01996-06.
  • Anderson, M. J. A New Method for Non-Parametric Multivariate Analysis of Variance. Austral. Ecol. 2001, 26, 32–46. DOI: 10.1111/j.1442-9993.2001.01070.
  • Mandal, S.; Van Treuren, W.; White, R. A.; Eggesbø, M.; Knight, R.; Peddada, S. D. Analysis of Composition of Microbiomes: A Novel Method for Studying Microbial Composition. Microb. Ecol. Health Dis. 2015, 26, 1, 27663. DOI: 10.3402/mehd.v26.27663.
  • Oliveros, J. C. 2007-2015 Venny. An interactive tool for comparing lists with Venn’s diagrams. https://bioinfogp.cnb.csic.es/tools/venny/index.html.
  • Wu, G. D.; Lewis, J. D.; Hoffmann, C.; Chen, Y.-Y.; Knight, R.; Bittinger, K.; Hwang, J.; Chen, J.; Berkowsky, R.; Nessel, L.; et al. Sampling and Pyrosequencing Methods for Characterizing Bacterial Communities in the Human Gut Using 16S Sequence Tags. BMC Microbiol. 2010, 10, 206. http://www.biomedcentral.com/1471-2180/10/206. DOI: 10.1186/1471-2180-10-206.
  • Ariefdjohan, M. W.; Savaiano, D. A.; Nakatsu, C. H. Comparison of DNA Extraction Kits for PCR-DGGE Analysis of Human Intestinal Microbial Communities from Fecal Specimens. Nutr. J. 2010, 9, 23. http://www.nutritionj.com/content/9/1/23. DOI: 10.1186/1475-2891-9-23.
  • Vandeventer, P. E.; Weigel, K. M.; Salazar, J.; Erwin, B.; Irvine, B.; Doebler, R.; Nadim, A.; Cangelosi, G. A.; Niemz, A. Mechanical Disruption of Lysis-Resistant Bacterial Cells by Use of a Miniature, Low-Power, Disposable Device. J. Clin. Microbiol. 2011, 49, 2533–2539. DOI: 10.1128/JCM.02171-10.
  • De Backer, E.; Verhelst, R.; Verstraelen, H.; Alqumber, M. A.; Burton, J. P.; Tagg, J. R.; Temmerman, M.; Vaneechoutte, M. Quantitative Determination by Real-Time PCR of Four Vaginal Lactobacillus Species, Gardnerella vaginalis and Atopobium vaginae Indicates an Inverse Relationship between L. gasseri and L. iners. BMC Microbiol. 2007, 7, 115. DOI: 10.1186/1471-2180-7-115.
  • Bhogoju, S.; Khwatenge, C. N.; Taylor-Bowden, T.; Akerele, G.; Kimathi, B. M.; Donkor, J.; Nahashon, S. N. Effects of Lactobacillus reuteri and Streptomyces coelicolor on Growth Performance of Broiler Chickens. Microorganisms 2021, 9, 1341. DOI: 10.3390/microorganisms9061341.
  • Kumar, J. K. Lysostaphin: An Antistaphylococcal Agent. Appl. Microbiol. Biotechnol. 2008, 80, 555–561. DOI: 10.1007/s00253-008-1579-y.
  • Morgan, J. L.; Darling, A. E.; Eisen, J. A. Metagenomic Sequencing of an in Vitro-Simulated Microbial Community. PLoS One. 2010, 5, e10209. DOI: 10.1371/journal.pone.0010209.

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