Methodology overview. After collecting the bacterial sample, DNA is extracted followed by amplification of 16S rDNA using universal primers. These fragments are then sequenced with high-throughput Pyrosequencing. Each read is queried against a database of known 16S rDNA sequence (mostly obtained from the Ribosomal Database Project) using the program BLAT and assigned to the most specific and confident node in the phylogeny. Accumulating all the reads in this fashion yields a weighted phylogenetic tree characterizing the bacterial content of the sample.