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Williamson KM, Wagner BD, Robertson CE, et al. Impact of enzymatic digestion on bacterial community composition in CF airway samples. PeerJ. 2017;5:e3362doi: 10.7717/peerj.3362.
Williamson, K. M., Wagner, B. D., Robertson, C. E., Johnson, E. J., Zemanick, E. T., & Harris, J. K. (2017). Impact of enzymatic digestion on bacterial community composition in CF airway samples. PeerJ, 5e3362. https://doi.org/10.7717/peerj.3362
Williamson, Kayla M, et al. "Impact of enzymatic digestion on bacterial community composition in CF airway samples." PeerJ vol. 5 (2017): e3362. doi: https://doi.org/10.7717/peerj.3362
Williamson KM, Wagner BD, Robertson CE, Johnson EJ, Zemanick ET, Harris JK. Impact of enzymatic digestion on bacterial community composition in CF airway samples. PeerJ. 2017 May 30;5:e3362. doi: 10.7717/peerj.3362. eCollection 2017. PMID: 28584706; PMCID: PMC5452939.
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PeerJ. 2017 May 30;5:e3362. doi: 10.7717/peerj.3362. eCollection 2017.

Impact of enzymatic digestion on bacterial community composition in CF airway samples.

PeerJ

Kayla M Williamson, Brandie D Wagner, Charles E Robertson, Emily J Johnson, Edith T Zemanick, J Kirk Harris

Affiliations

  1. Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, United States of America.
  2. Department of Pediatrics, School of Medicine, University of Colorado, Aurora, CO, United States of America.
  3. Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, CO, United States of America.
  4. Multicare Tacoma Family Medicine, Tacoma, WA, United States of America.

PMID: 28584706 PMCID: PMC5452939 DOI: 10.7717/peerj.3362

Abstract

BACKGROUND: Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of

METHODS: DNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD.

RESULTS: Shannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera

DISCUSSION: We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of

Keywords: 16s Sequencing; Beta diversity; DNA extraction; Gram positive; Microbiome; Sputum

Conflict of interest statement

The authors declare there are no competing interests.

References

  1. Bioinformatics. 2012 Jul 15;28(14):1823-9 - PubMed
  2. Appl Environ Microbiol. 2011 May;77(10):3219-26 - PubMed
  3. PLoS One. 2012;7(4):e34605 - PubMed
  4. Science. 2013 Mar 1;339(6123):1084-8 - PubMed
  5. Proc Natl Acad Sci U S A. 1964 Mar;51:414-21 - PubMed
  6. J Biol Chem. 1970 Sep 25;245(18):4842-6 - PubMed
  7. J Clin Microbiol. 1995 Apr;33(4):1022-4 - PubMed
  8. Clin Microbiol Rev. 2010 Apr;23(2):299-323 - PubMed
  9. Pediatr Pulmonol. 1996 May;21(5):267-75 - PubMed
  10. PLoS One. 2012;7(3):e33865 - PubMed
  11. Biotechnol Lett. 2007 Jul;29(7):985-94 - PubMed
  12. PLoS One. 2016 Jan 25;11(1):e0147643 - PubMed
  13. Genome Res. 1998 Mar;8(3):186-94 - PubMed
  14. Bioinformatics. 2011 Aug 15;27(16):2194-200 - PubMed
  15. J Clin Microbiol. 2001 Oct;39(10):3520-3 - PubMed
  16. Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6 - PubMed
  17. Pediatr Pulmonol. 2015 Jul;50(7):638-46 - PubMed
  18. J Cyst Fibros. 2005 Aug;4 Suppl 2:3-5 - PubMed
  19. PLoS One. 2012;7(3):e33127 - PubMed
  20. Biochem Biophys Res Commun. 1965 Apr 23;19:383-9 - PubMed
  21. Clin Infect Dis. 1998 Jul;27(1):158-63 - PubMed
  22. Clin Infect Dis. 2013 Aug;57(3):384-91 - PubMed
  23. J Immunol. 2012 Oct 15;189(8):3805-14 - PubMed
  24. Clin Chem. 2016 Nov;62(11):1465-1473 - PubMed
  25. Genome Res. 2013 Oct;23(10):1704-14 - PubMed
  26. Bioinformatics. 2013 Dec 1;29(23):3100-1 - PubMed
  27. Ann Am Thorac Soc. 2015 Feb;12(2):221-9 - PubMed
  28. Pediatr Pulmonol. 2010 Jun;45(6):569-77 - PubMed
  29. Genome Res. 1998 Mar;8(3):175-85 - PubMed
  30. Appl Environ Microbiol. 2005 Jul;71(7):3420-6 - PubMed

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