Computational protocol: Metagenomic analysis for the microbial consortium of anaerobic CO oxidizers

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Protocol publication

[…] Total genomic DNA was extracted from samples using the Power Water™ DNA isolation kit following the manufacturer’s instructions. A portion of the bacterial 16S rDNA gene with hypervariable V6 region was then used as a template to amplify by polymerase chain reaction (PCR) with a standard thermal cycler. Those PCR products were purified with a purification kit and the sequencing was performed with the Illumina Hiseq2000 platform after verification by the agarose gel electrophoresis. Non-chimeric sequence reads from the Illumina Hiseq2000 platform were analysed and finally clustered into OTUs with the software Mothur (version 1.27.0). The taxonomic analysis of OTUs were performed with the software BLAST (version 2.2.23) using the SILVA database to determine the phylogenetic affiliations of microbial community (http://www.vamps.mbl.edu/resources/databases.php). […]

Pipeline specifications

Software tools mothur, VAMPS
Applications Phylogenetics, Metagenomic sequencing analysis
Chemicals Carbon Monoxide, Methane