Phylum-Specific Primer Design and Implication in Quantification of the Microbial Community Structure in GuJingGong Pit Mud

Abstract:

In recent years, despite the significant improvement of sequencing technologies such as the pyrosequencing, rapid evaluation of microbial community structures remains very difficult because of the abundance and complexity of organisms in almost all natural microbial communities. In this paper, a group of phylum-specific primers were elaborately designed based on a single nucleotide discrimination technology to quantify the main microbial community structure from GuJingGong pit mud samples using the real-time quantitative PCR (qPCR). Specific PCR (polymerase chain reaction) primers targeting a particular group would provide promising sensitivity and more in-depth assessment of microbial communities.

• Periodical: Advanced Materials Research (Volume 1051)
• Pages: 311-316
• DOI: https://doi.org/10.4028/www.scientific.net/AMR.1051.311
• Online since: October 2014
• Authors: Xi Mei Luo, Zhi Lei Gao, Hui Min Zhang, An Jun Li, Hong Kui He, Chang Lu Guo, Zhi Zhou Zhang*
• Keywords: Microbial Community, Phylum-Specific, Primer, QPCR, Quantification

References

[1] Blackwood CB, Oaks A, Buyer JS. Phylum- and class-specific PCR primers for general microbial community analysis. Appl. Environ. Microbiol. 71(2005): 6193-8.

DOI: 10.1128/aem.71.10.6193-6198.2005

[2] Shin SG, Lee C, et al. Use of order-specific primers to investigate the methanogenic diversity in acetate enrichment system. J. Ind. Microbiol. Biotechnol. 35(2008): 1345-52.

DOI: 10.1007/s10295-008-0417-7

[3] Bacchetti De Gregoris T, Aldred N, et al. Improvement of phylum- and class-specific primers for real-time PCR quantification of bacterial taxa. J. Microbiol. Methods. 86(2011): 351-6.

DOI: 10.1016/j.mimet.2011.06.010

[4] Huimin Zhang, Changlu Guo, et al. qPCR Quantification Strategy of Minor Species in A Complex Microbial Community Using Species-specific Primers. J. Pure Appl. Microbiol. 7(2013): 601-610.

[5] Hui-min Zhang, Ying Shu, et al. Analysis on bacterial communities in GuJingGong Daqu through culture-free approach. Modern Food Technol. 30(2014): 44-49.

[6] Zhang Hui-min, Wang Jie, et al. Preliminary analysis on eukaryotic bacterial communities in GuJingGong Daqu through culture-free approaches. Food Industry. 35(2014): 158-162.

[7] Zhang Hui-min, Li Tian-Chan, et al. Preliminary analysis on bacterial communities in GuJingGong pit mud through culture-free approach. Food Industry Technol. 2014, in press.

[8] Bui M, Liu Z. Simple allele-discriminating PCR for cost-effective and rapid genotyping and mapping. Plant Methods. 8(2009): 5: 1-8.

DOI: 10.1186/1746-4811-5-1

[9] Ward DM, Weller R, Bateson MM. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature. 345(1990): 63-65.

DOI: 10.1038/345063a0

[10] Chen, Xihan, Yonghui Zeng, and Nianzhi Jiao. Development and evaluation of specific 16S rDNA primers for marine Cytophaga–Flavobacteria cluster. Mol. Ecol. Notes. 6(2006): 1278-1281.

DOI: 10.1111/j.1471-8286.2006.01514.x

[11] Stach JE, Maldonado LA, et al. New primers for the class Actinobacteria: application to marine and terrestrial environments. Environ. Microbiol. 5(2003): 828-41.

DOI: 10.1046/j.1462-2920.2003.00483.x

[12] Case RJ, Boucher Y, et al. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl. Environ. Microbiol. 73(2007): 278-88.

DOI: 10.1128/aem.01177-06

[13] Kim S, Misra A. SNP genotyping: technologies and biomedical applications. Annu. Rev. Biomed. Eng. 9(2007): 289-320.

DOI: 10.1146/annurev.bioeng.9.060906.152037

[14] Mühling M, Woolven-Allen J, Murrell JC, Joint I. Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities. ISME J. 2(2008): 379-92.

DOI: 10.1038/ismej.2007.97

[15] Heuer H, Krsek M, et al. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63(1997): 3233-41.

DOI: 10.1128/aem.63.8.3233-3241.1997

[16] Marchesi JR, Sato T, et al. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl. Environ. Microbiol. 64(1998): 795-9.

DOI: 10.1128/aem.64.2.795-799.1998

[17] Myakishev MV, Khripin Y, et al. High-throughput SNP genotyping by allele-specific PCR with universal energy-transfer-labeled primers. Genome Res. 11(2001): 163-9.

DOI: 10.1101/gr.157901