دورية أكاديمية
Assessment of Inter-Laboratory Variation in the Characterization and Analysis of the Mucosal Microbiota in Crohn's Disease and Ulcerative Colitis.
| العنوان: | Assessment of Inter-Laboratory Variation in the Characterization and Analysis of the Mucosal Microbiota in Crohn's Disease and Ulcerative Colitis. |
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| المؤلفون: | Szamosi JC; Department of Medicine, McMaster University, Hamilton, ON, Canada., Forbes JD; Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada.; IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada.; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Copeland JK; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada., Knox NC; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada., Shekarriz S; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada., Rossi L; Department of Medicine, McMaster University, Hamilton, ON, Canada., Graham M; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada., Bonner C; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Guttman DS; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada., Van Domselaar G; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada., Surette MG; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada., Bernstein CN; Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada.; IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada. |
| المصدر: | Frontiers in microbiology [Front Microbiol] 2020 Aug 21; Vol. 11, pp. 2028. Date of Electronic Publication: 2020 Aug 21 (Print Publication: 2020). |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Frontiers Research Foundation Country of Publication: Switzerland NLM ID: 101548977 Publication Model: eCollection Cited Medium: Print ISSN: 1664-302X (Print) Linking ISSN: 1664302X NLM ISO Abbreviation: Front Microbiol Subsets: PubMed not MEDLINE |
| أسماء مطبوعة: | Original Publication: Lausanne : Frontiers Research Foundation |
| مستخلص: | Background: In studies evaluating the microbiome, numerous factors can contribute to technical variability. These factors include DNA extraction methodology, sequencing protocols, and data analysis strategies. We sought to evaluate the impact these factors have on the results obtained when the sequence data are independently generated and analyzed by different laboratories. Methods: To evaluate the effect of technical variability, we used human intestinal biopsy samples resected from individuals diagnosed with an inflammatory bowel disease (IBD), including Crohn's disease ( n = 12) and ulcerative colitis ( n = 10), and those without IBD ( n = 10). Matched samples from each participant were sent to three laboratories and studied using independent protocols for DNA extraction, library preparation, targeted-amplicon sequencing of a 16S rRNA gene hypervariable region, and processing of sequence data. We looked at two measures of interest - Bray-Curtis PERMANOVA R 2 values and log2 fold-change estimates of the 25 most-abundant taxa - to assess variation in the results produced by each laboratory, as well the relative contribution to variation from the different extraction, sequencing, and analysis steps used to generate these measures. Results: The R 2 values and estimated differential abundance associated with diagnosis were consistent across datasets that used different DNA extraction and sequencing protocols, and within datasets that pooled samples from multiple protocols; however, variability in bioinformatic processing of sequence data led to changes in R 2 values and inconsistencies in taxonomic assignment and abundance estimates. Conclusion: Although the contribution of DNA extraction and sequencing methods to variability were observable, we find that results can be robust to the various extraction and sequencing approaches used in our study. Differences in data processing methods have a larger impact on results, making comparison among studies less reliable and the combined analysis of bioinformatically processed samples nearly impossible. Our results highlight the importance of making raw sequence data available to facilitate combined and comparative analyses of published studies using common data processing protocols. Study methodologies should provide detailed data processing methods for validation, interpretability, reproducibility, and comparability. (Copyright © 2020 Szamosi, Forbes, Copeland, Knox, Shekarriz, Rossi, Graham, Bonner, Guttman, Van Domselaar, Surette and Bernstein.) |
| References: | Int J Med Microbiol. 2016 Aug;306(5):334-342. (PMID: 27052158) ISME J. 2015 May;9(5):1246-59. (PMID: 25575312) Am J Gastroenterol. 2011 Apr;106(4):661-73. (PMID: 21407187) Bioinformatics. 2019 Feb 1;35(3):526-528. (PMID: 30016406) mSystems. 2016 May 3;1(3):. (PMID: 27822526) Future Microbiol. 2015;10(9):1485-504. (PMID: 26347019) Sci Rep. 2015 Nov 17;5:16350. (PMID: 26572876) BMC Res Notes. 2016 Jul 26;9:365. (PMID: 27456340) Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5. (PMID: 19004872) Genome Biol. 2015 Dec 09;16:276. (PMID: 26653756) Appl Environ Microbiol. 2011 Jun;77(11):3846-52. (PMID: 21460107) Nat Biotechnol. 2016 Sep;34(9):942-9. (PMID: 27454739) Nucleic Acids Res. 2016 Jul 8;44(W1):W242-5. (PMID: 27095192) Sci Rep. 2018 Nov 5;8(1):16321. (PMID: 30397210) Gastroenterology. 2014 May;146(6):1449-58. (PMID: 24486050) Nat Methods. 2016 Jul;13(7):581-3. (PMID: 27214047) Appl Environ Microbiol. 2009 Dec;75(23):7537-41. (PMID: 19801464) PLoS One. 2013 Apr 22;8(4):e61217. (PMID: 23630581) Semin Immunopathol. 2015 Jan;37(1):47-55. (PMID: 25420450) Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):14024-9. (PMID: 26512100) ISME J. 2012 Aug;6(8):1621-4. (PMID: 22402401) Nat Methods. 2013 Oct;10(10):996-8. (PMID: 23955772) Nat Biotechnol. 2017 Nov;35(11):1069-1076. (PMID: 28967887) Primates. 2018 Sep;59(5):423-436. (PMID: 29942984) Appl Environ Microbiol. 2007 Aug;73(16):5261-7. (PMID: 17586664) Bioinformatics. 2010 Oct 1;26(19):2460-1. (PMID: 20709691) Nucleic Acids Res. 2007;35(21):7188-96. (PMID: 17947321) Microbiome. 2016 Jul 30;4(1):40. (PMID: 27473284) Clin Nutr. 2018 Jun;37(3):797-807. (PMID: 28410921) Nature. 2012 Sep 13;489(7415):220-30. (PMID: 22972295) Microbiome. 2014 Jun 05;2:19. (PMID: 24949196) PLoS Comput Biol. 2014 Apr 03;10(4):e1003531. (PMID: 24699258) BMC Bioinformatics. 2017 May 30;18(1):283. (PMID: 28558684) Nat Methods. 2010 May;7(5):335-6. (PMID: 20383131) J Formos Med Assoc. 2019 Feb;118(2):545-555. (PMID: 29490879) Bioinformatics. 2011 Aug 15;27(16):2194-200. (PMID: 21700674) BMC Microbiol. 2014 May 01;14:112. (PMID: 24884524) |
| فهرسة مساهمة: | Keywords: 16S rRNA; inflammatory bowel diseases; intestinal biopsies; microbiome; replicability; standards; technical variability |
| تواريخ الأحداث: | Date Created: 20200925 Latest Revision: 20220417 |
| رمز التحديث: | 20240628 |
| مُعرف محوري في PubMed: | PMC7472644 |
| DOI: | 10.3389/fmicb.2020.02028 |
| PMID: | 32973734 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1664-302X |
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| DOI: | 10.3389/fmicb.2020.02028 |