Journal Article10.1099/IJS.0.038075-0
Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species.
Ok-Sun Kim,Yong-Joon Cho,Kihyun Lee,Seok Hwan Yoon,Mincheol Kim,Hyunsoo Na,Sang-Cheol Park,Yoon-Seong Jeon,Jae-Hak Lee,Hana Yi,Sungho Won,Jongsik Chun +11 more
5.2K
TL;DR: It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates.
read more
Abstract: Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Biological control of winter wheat pathogens with the use of antagonistic Sphingomonas bacteria under greenhouse conditions
Urszula Wachowska,Witold Irzykowski,Małgorzata Jędryczka,Anna Daria Stasiulewicz-Paluch,Katarzyna Głowacka +4 more
TL;DR: The applied Sphingomonas cell suspension reduced the severity of flag leaf infection caused by pathogenic biotroph Blumeria graminis f.
50
Antioxidative Potential of a Streptomyces sp. MUM292 Isolated from Mangrove Soil
TL;DR: It is demonstrated that Streptomyces MUM292 can be a potential antioxidant resource for food and pharmaceutical industries.
Degradation of polypropylene–poly-L-lactide blend by bacteria isolated from compost
TL;DR: In this paper, five isolates (P3, P6, P8, P10, and P13) were selected based on their degradation abilities, i.e., polypropylene degrading bacteria (P1 to P16) were isolated from compost using enrichment technique.
50
Massilia eurypsychrophila sp. nov. a facultatively psychrophilic bacteria isolated from ice core.
Liang Shen,Yongqin Liu,Zhengquan Gu,Baiqing Xu,Ninglian Wang,Nianzhi Jiao,Hong-Can Liu,Yu-Guang Zhou +7 more
TL;DR: From the genotypic and phenotypic data, it is evident that strain B528-3(T) represents a novel species of the genus Massilia, for which the name Massilia eurypsychrophila sp.
50
The role of abiotic environmental conditions and herbivory in shaping bacterial community composition in floral nectar
TL;DR: Similar bacterial communities found in the nectar and on the surface of the bugs that were documented visiting the flowers imply that floral nectar bacteria dispersal is shaped not only by air borne bacteria and nectar consumers, but also by visiting vectors like the mirid bugs.
References
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
TL;DR: Version 4 of MEGA software expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses.
30.9K
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
Evolutionary trees from DNA sequences: A maximum likelihood approach
TL;DR: A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available that allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests.
14.5K