Abstract
Metagenomics approach involves direct genetic analysis of environmental samples, evading the tedious culturing process. Polymerase chain reaction is one invaluable tool used for such analyses. Here, we describe one protocol for metagenomic DNA isolation that gives inhibitor-free DNA suitable for PCR and other genetic manipulations. Subsequently, the chapter describes the use of PCR as an indicator of quality of DNA and to amplify a marker of phylogeny. Further, the application of PCR for detection of specific genes and screening of metagenomic libraries is outlined.
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References
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685
Miller DN (2001) Evaluation of gel filtration resins for the removal of PCR-inhibitory substances from soil and sediments. J Microbiol Methods 44:49–58
Tina KJ, Bindiya ES, Raghul Subin S, Bhat SG (2014) Appraisal of extraction protocols for metagenomic DNA from fish gut microbiota. IJAIR 3:7–13
Devi SG, Fathima AA, Radha S, Arunraj R, Curtis WR, Ramya M (2015) A rapid and economical method for efficient DNA extraction from diverse soils suitable for metagenomic applications. PLoS One 10:e0132441
Gutiérrez-Lucas LR, Montor-Antonio JJ, Cortés-López NG, del Moral S (2014) Strategiesfor the extraction, purification and amplification of metagenomic DNA from soil growing sugarcane. Adv Biol Chem 4:281–289
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
Hamady M, Knight R (2009) Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res 19:1141–1152
Kotik M (2009) Novel genes retrieved from environmental DNA by polymerase chain reaction: current genome-walking techniques for future metagenome applications. J Biotechnol 144:75–82
Itoh N, Isotani K, Makino Y, Kato M, Kitayama K, Ishimota T (2014) PCR-based amplification and heterologous expression of pseudomonas alcohol dehydrogenase genes from the soil metagenome for biocatalysis. Enzyme MicrobTechnol 55:140–150
Shivaji S, Bhanu NV, Aggarwal RK (2000) Identification of Yersinia pestis as the causative organism of plague in India as determined by 16S rDNA sequencing and RAPD-based genomic fingerprinting. FEMS Microbiol Lett 189:247–252
Yaacob MA, Hasan WA, Ali MS, Rahman RN, Salleh AB, Basri M, Leow TC (2014) Characterisation and molecular dynamic simulations of J15 asparaginase from Photobacterium sp. strain J15. Acta Biochim Pol 61:745–752
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
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Johny, T.K., Bhat, S.G. (2017). PCR in Metagenomics. In: Domingues, L. (eds) PCR. Methods in Molecular Biology, vol 1620. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-7060-5_17
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DOI: https://doi.org/10.1007/978-1-4939-7060-5_17
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