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

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.

SUBMITTER: Kachiprath B

PROVIDER: S-EPMC5752666 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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

Kachiprath Bhavya B Jayanath G G Solomon Solly S Sarasan Manomi M

3 Biotech 20180103 1

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 diff ...[more]

PMID: 29354355

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

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

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