High-throughput sequencing of 16s rRNA gene amplicons: Effects of extraction procedure, primer length and annealing temperature

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Sergeant, Martin J ^a   Constantinidou, Chrystala ^a   Cogan, Tristan ^b   Penn, Charles W ^a   Pallen, Mark J ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S; RNA 16S; DNA; PRIMER DNA;

AMPLICON; ARTICLE; BACTERIAL FLORA; BACTEROIDES; BIFIDOBACTERIUM; CAMPYLOBACTER; CECUM CONTENT; CHICKEN; COMMUNITY STRUCTURE; CONTROLLED STUDY; DNA EXTRACTION; ESCHERICHIA COLI; FECES ANALYSIS; FIRMICUTES; FREEZING; HIGH THROUGHPUT SEQUENCING; INTESTINE PARAMETERS; LACTOBACILLUS; NONHUMAN; PYROSEQUENCING; RNA EXTRACTION; SPECIES DIVERSITY; TEMPERATURE; THAWING; ANIMAL; CECUM; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; SEQUENCE ANALYSIS;

BACTERIA (MICROORGANISMS); BIFIDOBACTERIUM; OTUS;

ANIMALS; CECUM; CHICKENS; DNA; DNA PRIMERS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA; TEMPERATURE;

EID: 84861546470     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038094     Document Type: Article

References (22)

1. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG, (1990) Genetic Diversity in Sargasso Sea Bacterioplankton. Nature 345: 60-63.
2. Scupham AJ, Jones JA, Wesley IV, (2007) Comparison of DNA extraction methods for analysis of turkey cecal microbiota. Journal of Applied Microbiology 102: 401-409.
3. Salonen A, Nikkila J, Jalanka-Tuovinen J, Immonen O, Rajilic-Stojanovic M, et al. (2010) Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis. Journal of Microbiological Methods 81: 127-134.
4. Wu JY, Jiang XT, Jiang YX, Lu SY, Zou F, et al. (2010) Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method. BMC Microbiology 10: 7.10.1186/1471-2180-10-255.
5. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P, (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology 12: 118-123.
6. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, et al. (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Applied and Environmental Microbiology 74: 2461-2470.
7. Claesson MJ, Wang QO, O'Sullivan O, Greene-Diniz R, Cole JR, et al. (2010) Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Research 38;10,1093/nar/ gkq873.
8. Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, et al. (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. Isme Journal 4: 642-647.
9. Bru D, Martin-Laurent F, Philippot L, (2008) Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example. Applied and Environmental Microbiology 74: 1660-1663.
10. Sipos R, Szekely AJ, Palatinszky M, Revesz S, Marialigeti K, et al. (2007) Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. Fems Microbiology Ecology 60: 341-350.
11. Isenbarger TA, Finney M, Rios-Velazquez C, Handelsman J, Ruvkun G, (2008) Miniprimer PCR, a new lens for viewing the microbial world. Applied and Environmental Microbiology 74: 840-849.
12. Apajalahti J, (2005) Comparative gut microflora, metabolic challenges, and potential opportunities. Journal of Applied Poultry Research 14: 444-453.
13. Kabir SML, (2009) The Role of Probiotics in the Poultry Industry. International Journal of Molecular Sciences 10: 3531-3546.
14. Hajati H, Rezaei M, (2010) The Application of Prebiotics in Poultry Production. International Journal of Poultry Science 9: 298-304.
15. Torok VA, Allison GE, Percy NJ, Ophel-Keller K, Hughes RJ, (2011) Influence of antimicrobial feed additives on broiler commensal posthatch gut microbiota development and performance. Appl Environ Microbiol 77: 3380-3390.
16. Scupham AJ, Jones JA, Rettedal EA, Weber TE, (2010) Antibiotic Manipulation of Intestinal Microbiota To Identify Microbes Associated with Campylobacter jejuni Exclusion in Poultry. Applied and Environmental Microbiology 76: 8026-8032.
17. Watanabe K, Kodama Y, Harayama S, (2001) Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. J Microbiol Methods 44: 253-262.
18. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ, (2011) Removing NoiseFrom Pyrosequenced Amplicons. Bmc Bioinformatics 12 10.1186/1471-2105-12-38.
19. Edgar RC, (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
20. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797.
21. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Research 37: D141-D145.
22. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7: 335-336.