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- TBC: A Clustering Algorithm Based on Prokaryotic Taxonomy
- Jae-Hak Lee , Hana Yi , Yoon-Seong Jeon , Sungho Won , Jongsik Chun
- J. Microbiol. 2012;50(2):181-185. Published online April 27, 2012
- DOI: https://doi.org/10.1007/s12275-012-1214-6
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- 20 Crossref
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Abstract
- High-throughput DNA sequencing technologies have revolutionized the study of microbial ecology. Massive sequencing of PCR amplicons of the 16S rRNA gene has been widely used to understand the microbial community structure of a variety of environmental samples. The resulting sequencing reads are clustered into operational taxonomic units that are then used to calculate various statistical indices that represent the degree of species diversity in a given sample. Several algorithms have been developed to perform this task, but they tend to produce different outcomes. Herein, we propose a novel sequence clustering algorithm, namely Taxonomy-Based Clustering (TBC). This algorithm incorporates the basic concept of prokaryotic taxonomy in which only comparisons to the type strain are made and used to form species while omitting full-scale multiple sequence alignment. The clustering quality of the proposed method was compared with those of MOTHUR, BLASTClust, ESPRITTree, CD-HIT, and UCLUST. A comprehensive comparison using three different experimental datasets produced by pyrosequencing demonstrated that the clustering obtained using TBC is comparable to those obtained using MOTHUR and ESPRIT-Tree and is computationally efficient. The program was written in JAVA and is available from http://sw. ezbiocloud.net/tbc.
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Citations
Citations to this article as recorded by
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Journal of Microbiology.2012; 50(6): 1081. CrossRef
- Application of Machine Learning to Solid Particle Erosion of APS-TBC and EB-PVD TBC at Elevated Temperatures
Journal Article
- Mobilization Functions of the Bacteriocinogenic Plasmid pRJ6 of Staphylococcus aureus
- Marcus Livio Varella Coelho , Hilana Ceotto , Danielle Jannuzzi Madureira , Ingolf F. Nes , Maria do Carmo de Freire Bastos
- J. Microbiol. 2009;47(3):327-336. Published online June 26, 2009
- DOI: https://doi.org/10.1007/s12275-009-0044-7
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- 13 Scopus
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Abstract
- Plasmid pRJ6 is the first known bacteriocinogenic mobilizable (Mob) plasmid of Staphylococcus aureus. Its Mob region is composed of four mob genes (mobCDAB) arranged as an operon, a genetic organization uncommon among S. aureus Mob plasmids. oriTpRJ6 was detected in a region of 431 bp, positioned immediately upstream of mobC. This region, when cloned into pCN37, was able to confer mobilization to the recombinant plasmid only in the presence of pRJ6. The entire Mob region, including oriTpRJ6, is much more similar to Mob regions from several coagulase-negative staphylococci plasmids, although some remarkable similarities with S. aureus Mob plasmids can also be noted. These similarities include the presence within oriTpRJ6 of the three mcb (MobC binding sites), firstly described in pC221 and pC223, an identical nick site also found in these same plasmids, and a nearly identical srapC223 site (sequence recognized by MobA). pRJ6 was successfully transferred to S. epidermidis by conjugation in the presence of the conjugative plasmid pGO1. Altogether these findings suggest that pRJ6 might have been originally a coagulase-negative staphylococci plasmid that had been transferred successfully to S. aureus.
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