This stage will consist of phylogenetic characterisation of microbial populations by targeting sequences of their ribosomal-RNA operon (for example: 16S-rRNA gene for bacteria, and either 18S-rRNA or intergenic spacer region for eukaryotes), most commonly used in microbe identification The analysis will involve DNA extraction, purification, and gene-target polymerase chain reaction (PCR). Communities will be screened by denaturant gradient gel electrophoresis (DGGE) and the composition will ultimately be determined by high-throughput sequencing technology.

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Image: courtesy of Charles Knapp