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SSU metagenomics

See also
OTU clustering
  What is an OTU?
Finding species in SSU reads
  SSU reference databases

Metagenomics using SSU rRNA
Next-generation sequencing allows high-throughput acquisition of nucleotide sequences for genes or regions for which universal PCR primers are available, i.e. primers that match a large majority of the species of interest. In microbial ecology, small subunit ribosomal RNA (SSU rRNA) genes are typically used: 16S for prokaryotes, ITS for fungi and 18S for eukaryotes. A typical SSU metagenomics experiment generates thousands (pyrosequencing) to millions (Illumina) of reads.