The effect of DNA extraction methodology on gut microbiota research applications

BMC Research Notes

Volumn 9, Issue 1, 2016, Pages

  Gerasimidis, Konstantinos ^a   Bertz, Martin ^a   Quince, Christopher ^b   Brunner, Katja ^a   Bruce, Alanna ^a   Combet, Emilie ^a   Calus, Szymon ^a   Loman, Nick ^c   Ijaz, Umer Zeeshan ^a  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

^b UNIVERSITY OF WARWICK   (United Kingdom)

^c UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

16S rRNA gene; Benchmarking; Diversity; DNA extraction; Metagenomics; PCR

Indexed keywords

BACTERIAL DNA; CHLOROFORM; DNA; PHENOL; RNA 16S;

BENCHMARKING; CHEMISTRY; DNA BARCODING; DRUG EFFECTS; FECES; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INTESTINE FLORA; ISOLATION AND PURIFICATION; LIQUID PHASE MICROEXTRACTION; MICROBIOLOGY; PROCEDURES; REAL TIME POLYMERASE CHAIN REACTION; STANDARDS;

BENCHMARKING; CHLOROFORM; DNA; DNA BARCODING, TAXONOMIC; DNA, BACTERIAL; FECES; GASTROINTESTINAL MICROBIOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LIQUID PHASE MICROEXTRACTION; PHENOL; REAL-TIME POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S;

EID: 84979561720     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/s13104-016-2171-7     Document Type: Article

References (21)

1. Kennedy NA, Walker AW, Berry SH, et al. The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing. PLoS ONE. 2014;9:e88982.
2. Salonen A, Nikkila J, Jalanka-Tuovinen J, et al. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods. 2010;81:127-34.
3. de Boer R, Peters R, Gierveld S, et al. Improved detection of microbial DNA after bead-beating before DNA isolation. J Microbiol Methods. 2010;80:209-11.
4. McOrist AL, Jackson M, Bird AR. A comparison of five methods for extraction of bacterial DNA from human faecal samples. J Microbiol Methods. 2002;50:131-9.
5. Nechvatal JM, Ram JL, Basson MD, et al. Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces. J Microbiol Methods. 2008;72:124-32.
6. D'Amore R, Ijaz UZ, Schirmer M, et al. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genom. 2016;17:55.
7. Quince C, Ijaz UZ, Loman N, et al. Extensive modulation of the fecal metagenome in children with crohn's disease during exclusive enteral nutrition. Am J Gastroenterol. 2015;110:1718-29.
8. Reichardt N, Barclay AR, Weaver LT, et al. Use of stable isotopes to measure the metabolic activity of the human intestinal microbiota. Appl Environ Microbiol. 2011;77:8009-14.
9. Godon JJ, Zumstein E, Dabert P, et al. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol. 1997;63:2802-13.
10. Gerasimidis K, Bertz M, Hanske L, et al. Decline in presumptively protective gut bacterial species and metabolites are paradoxically associated with disease improvement in pediatric Crohn's disease during enteral nutrition. Inflamm Bowel Dis. 2014;20:861-71.
11. Caporaso JG, Lauber CL, Walters WA, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA. 2011;108(Suppl 1):4516-22.
12. Joshi NA, Fass JN. Sickle: A sliding-window, adaptive, quality-based trimming tool for fastq files. Version 1.21; 2011.
13. Masella AP, Bartram AK, Truszkowski JM, et al. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics. 2012;13:31.
14. Wang Q, Garrity GM, Tiedje JM, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261-7.
15. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772-80.
16. Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490.
17. Oksanen J, Blanchet F G, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H. vegan: Community Ecology Package, R Package version 2.2-1, version 2.2-1 ed; 2015.
18. McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.
19. Paradis E, Claude J, Strimmer K. APE: analyses of Phylogenetics and Evolution in R language. Bioinformatics (Oxford, England). 2004;20:289-90.
20. Schliep KP. phangorn: phylogenetic analysis in R. Bioinformatics (Oxford, England). 2011;27:592-3.
21. Cardoso P, Rigal F, Borges PAV, et al. A new frontier in biodiversity inventory: a proposal for estimators of phylogenetic and functional diversity. Methods Ecol Evol. 2014;5:452-61.