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Updated: Mar 8, 2026
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome
Chao Xie1,2, Chin Lui Wesley Goi3, Daniel H Huson4,5
1Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 117456, Singapore. xiechaos@gmail.com.
Background:
Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis.
Results:
Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion.
Conclusions:
RiboTagger permits fast recovery of SSU-RNA sequences from shotgun nucleic acid surveys of complex microbial communities. The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs.
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