Analysis of run-to-run variation of bar-coded pyrosequencing for evaluating bacterial community shifts and individual taxa dynamics

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Ge, Yuan ^a   Schimel, Joshua P ^a   Holden, Patricia A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DNA BARCODING; DNA EXTRACTION; GENETIC VARIABILITY; MICROBIAL COMMUNITY; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; POPULATION DYNAMICS; PRINCIPAL COORDINATES ANALYSIS; PYROSEQUENCING; REPRODUCIBILITY; ANALYSIS OF VARIANCE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; GENETICS; HIGH THROUGHPUT SEQUENCING; METAGENOME; MICROBIOLOGY; PROCEDURES; STANDARDS;

ANALYSIS OF VARIANCE; BACTERIA; BIODIVERSITY; DNA BARCODING, TAXONOMIC; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOME; REPRODUCIBILITY OF RESULTS; SOIL MICROBIOLOGY;

EID: 84902603092     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0099414     Document Type: Article

References (25)

1. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380. (Pubitemid 41613494)
2. Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation sequencing technologies for environmental DNA research. Mol Ecol 21: 1794-1805.
3. Lundin D, Severin I, Logue JB, Östman Ö, Andersson AF, et al. (2012) Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity? Environ Microbiol Rep 4: 367-372.
4. Pilloni G, Granitsiotis MS, Engel M, Lueders T (2012) Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes. PLoS ONE 7: e40467.
5. Harris JK, Sahl JW, Castoe TA, Wagner BD, Pollock DD, et al. (2010) Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing. Appl Environ Microbiol 76: 3863-3868.
6. Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N, et al. (2010) Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods 7: 813-819.
7. Prosser JI (2010) Replicate or lie. Environ Microbiol 12: 1806-1810.
8. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5: 235-237. (Pubitemid 351325646)
9. Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, et al. (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 35: e130.
10. Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75: 5111-5120.
11. Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, et al. (2012) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6: 1007-1017.
12. Berg J, Brandt KK, Al-Soud WA, Holm PE, Hansen LH, et al. (2012) Selection for Cu-tolerant bacterial communities with altered composition, but unaltered richness, via long-term Cu exposure. Appl Environ Microbiol 78: 7438-7446.
13. Deng Y, He Z, Xu M, Qin Y, Van Nostrand JD, et al. (2012) Elevated carbon dioxide alters the structure of soil microbial communities. Appl Environ Microbiol 78: 2991-2995.
14. Yergeau E, Bokhorst S, Kang S, Zhou J, Greer CW, et al. (2012) Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments. ISME J 6: 692-702.
15. Sheik CS, Beasley WH, Elshahed MS, Zhou X, Luo Y, et al. (2011) Effect of warming and drought on grassland microbial communities. ISME J 5: 1692-1700.
16. Delmont TO, Simonet P, Vogel TM (2012) Describing microbial communities and performing global comparisons in the 'omic era. ISME J 6: 1625-1628.
17. Zhou J, Wu L, Deng Y, Zhi X, Jiang Y-H, et al. (2011) Reproducibility and quantitation of amplicon sequencing-based detection. ISME J 5: 1303-1313.
18. 2 and ZnO nanoparticles on soil bacterial communities. Environ Sci Technol 45: 1659-1664.
19. 2 and ZnO nanoparticles. Appl Environ Microbiol 78: 6749-6758.
20. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
21. Quince C, Lanzen A, Davenport R, Turnbaugh P (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12: 38.
22. Schloss PD, Gevers D, Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6: e27310.
23. White JR, Nagarajan N, Pop M (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352.
24. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
25. Zhou J, Jiang Y-H, Deng Y, Shi Z, Zhou BY, et al. (2013) Random sampling process leads to overestimation of b-diversity of microbial communities. mBio 4: e00324-00313.