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The 16S ribosomal RNA gene [or 16S ribosomal DNA (rDNA)] is a commonly used marker for bacterial identification due to its universal distribution among all bacterial species and a slow rate of sequence evolution. To reduce the dimensionality of large sequence datasets generated by high-throughput sequencing of 16S rDNAs, the reads are clustered into operational taxonomic units (OTUs) (Ye, 2011) that roughly represent taxa at phylogenetic levels defined by a user-defined sequence similarity cutoff. The abundance of each OTU is defined as the number of sequences in the OTU. Representative sequences from each OTU are chosen and used to assign taxonomy to the OTUs and to construct phylogenetic trees.
(Tanaseichuk et al., 2014) Phylogeny-based classification of microbial communities. Bioinformatics.