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CTAB influenced differential elution of metagenomic DNA from saltpan and marine sediments

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Abstract

A simple, reliable method for genomic DNA extraction from sediments with minimum contaminants was developed to address the risk of poor quality DNA in metagenomic studies. Nine DNA extraction methods using 20% cetyl-trimethyl-ammonium bromide (CTAB) were performed and compared to develop an extraction protocol that can offer humic acid-free metagenomic DNA from marine and saltpan sediments. Community DNA extraction was executed via., Zhou et al. modified protocol using 20% CTAB treatment at different steps to compare the efficacy of humic acid removal. Out of nine DNA extraction methods, method 6 significantly improved the quality of DNA with efficient removal of humic substances. 16S rRNA gene amplification and spectrophotometric analysis confirmed the efficiency of method 6 to remove DNA inhibitors from marine sediments as well as saltpan samples. Inhibitors extracted along with metagenomic DNA outcome increased DNA yield and PCR inhibition in method 1 and 3. However, repeated 20% CTAB wash in method 6 ensured 16S amplification and least yield and concentration. Current study explains a detailed protocol based on 20% CTAB wash for the extraction of humic acid-free DNA from diverse sediment samples.

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Acknowledgements

Authors are grateful to Dept. of Marine biology, Microbiology and Biochemistry and National Centre for Aquatic Animal Health (NCAAH), Cochin University of Science and Technology for providing necessary facilities for this study. Authors are also thankful to Dr. Rosamma Philip, Professor and Dr. Preetha K., Dept. of Marine biology, Microbiology and Biochemistry and Dr. Jayesh Puthumana, DBT-IYBA fellow, National Centre for Aquatic Animal Health (NCAAH) for their valuable guidance and scientific support.

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  1. Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Cochin, Kerala, 682016, India

    Bhavya Kachiprath, G. Jayanath, Solly Solomon & Manomi Sarasan

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  1. Bhavya Kachiprath
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  2. G. Jayanath
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  3. Solly Solomon
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Correspondence to Bhavya Kachiprath.

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Kachiprath, B., Jayanath, G., Solomon, S. et al. CTAB influenced differential elution of metagenomic DNA from saltpan and marine sediments. 3 Biotech 8, 44 (2018). https://doi.org/10.1007/s13205-017-1078-x

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