Metatranscriptomics is a method used to comprehensively capture bacterial activity within microbiota at the transcription level. It has become an alternative to the 16S rDNA sequencing, which uses only the 16S rRNA gene for predicting bacterial composition. By conducting metatranscriptomics, investigators can obtain substantial information about what types of genes are transcribed at the time of sampling and which bacterial taxa are responsible for their transcription. Here, I describe a protocol for metatranscriptomics for oral microbiota by using high-throughput sequencing technology. A remarkable feature of this protocol is that it uses the level of rRNA expression as the internal control for measuring transcriptional activity of each bacterial taxon. The normalized mRNA level is given by the mRNA/rRNA ratio, which indicates the extent of transcriptional activity.
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