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Updated: May 29, 2026
06:34
Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Identification and classification of the genus Bacteroides by multilocus sequence analysis.
Mitsuo Sakamoto1, Moriya Ohkuma1
1Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan.
Microbiology (Reading, England)
|September 28, 2011
Summary
Multilocus sequence analysis using housekeeping genes provides robust phylogenetic insights into Bacteroides species identification. This method offers superior discrimination compared to 16S rRNA gene sequencing for classifying these bacteria.
Area of Science:
- Microbiology
- Genetics
- Bioinformatics
Background:
- The genus Bacteroides is crucial in gut microbial ecosystems.
- Accurate species identification and classification are vital for understanding their roles.
Purpose of the Study:
- To evaluate the efficacy of Multilocus Sequence Analysis (MLSA) for Bacteroides species discrimination.
- To compare the phylogenetic resolution offered by different housekeeping genes and 16S rRNA.
Main Methods:
- Amplification and sequencing of internal gene fragments (dnaJ, gyrB, hsp60, recA, rpoB, 16S rRNA) from 38 Bacteroides strains.
- Phylogenetic analyses using Neighbour-Joining (NJ), Maximum-Likelihood (ML), and Maximum-Parsimony (MP) methods.
- Concatenation of sequences for robust phylogenetic reconstruction.
Main Results:
- MLSA of housekeeping genes demonstrated higher discriminatory power than 16S rRNA gene sequencing.
- The gyrB and dnaJ genes were found to be the most informative among the analyzed housekeeping genes.
- Concatenated sequence analysis (4816 bp) resolved robust phylogenetic relationships, revealing ten distinct clades.
- A species definition was proposed based on ≥97.5% gene sequence similarity across five protein-coding genes and 16S rRNA.
Conclusions:
- MLSA of housekeeping genes is a reliable and effective method for the identification and classification of Bacteroides species.
- This approach provides a more resolved phylogenetic framework for the genus Bacteroides.
- The proposed similarity threshold aids in defining species within the genus.
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