Related Experiment Video
Updated: Sep 23, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification
Chun-Chieh Liao1, Po-Ying Fu2, Chih-Wei Huang1
1Institute of Information Science, Academia Sinica, 115 Taipei, Taiwan.
Motivation:
Taxonomic classification of 16S ribosomal RNA gene amplicon is an efficient and economic approach in microbiome analysis. 16S rRNA sequence databases like SILVA, RDP, EzBioCloud and HOMD used in downstream bioinformatic pipelines have limitations on either the sequence redundancy or the delay on new sequence recruitment. To improve the 16S rRNA gene-based taxonomic classification, we merged these widely used databases and a collection of novel sequences systemically into an integrated resource.
Results:
MetaSquare version 1.0 is an integrated 16S rRNA sequence database. It is composed of more than 6 million sequences and improves taxonomic classification resolution on both long-read and short-read methods.
Availability And Implementation:
Accessible at https://hub.docker.com/r/lsbnb/metasquare_db and https://github.com/lsbnb/MetaSquare.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
Related Concept Videos
Modern Molecular Taxonomy
Applications of Molecular Taxonomy
Microbial Classification System

