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Updated: Sep 15, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper
Ben J Woodcroft1, Samuel T N Aroney2, Rossen Zhao2
1Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia. b.woodcroft@qut.edu.au.
Abstract:
Determining the taxonomy and relative abundance of microorganisms in metagenomic data remains technically challenging. Here we present 'SingleM', which estimates community composition using conserved regions within universal marker genes. By accurately incorporating species lacking genomic representation, we show that unknown species dominate in most environmental microbial communities. Our website 'Sandpiper' collates microbial community profiles from 248,559 publicly available metagenomes.
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