| Taxonomy Citation ID | Reference | ||||
|---|---|---|---|---|---|
| 47532 |
Aliyu H,
Lebre P,
Blom J,
Cowan D,
De Maayer P,
( 2016 ) Phylogenomic re-assessment of the thermophilic genus Geobacillus. PMID : 27726901 DOI : 10.1016/j.syapm.2016.09.004 Abstract >>
Geobacillus is a genus of Gram-positive, aerobic, spore-forming obligate thermophiles. The descriptions and subsequent affiliations of the species in the genus have mostly been based on polyphasic taxonomy rules that include traditional sequence-based methods such as DNA-DNA hybridization and comparison of 16S rRNA gene sequences. Currently, there are fifteen validly described species within the genus. The availability of whole genome sequences has provided an opportunity to validate and/or re-assess these conventional estimates of genome relatedness. We have applied whole genome approaches to estimate the phylogenetic relatedness among the sixty-three Geobacillus strains for which genome sequences are currently publicly available, including the type strains of eleven validly described species. The phylogenomic metrics AAI (Average Amino acid Identity), ANI (Average Nucleotide Identity) and dDDH (digital DNA-DNA hybridization) indicated that the current genus Geobacillus is comprised of sixteen distinct genomospecies, including several potentially novel species. Furthermore, a phylogeny constructed on the basis of the core genes identified from the whole genome analyses indicated that the genus clusters into two monophyletic clades that clearly differ in terms of nucleotide base composition. The G+C content ranges for clade I and II were 48.8-53.1% and 42.1-44.4%, respectively. We therefore suggest that the Geobacillus species currently residing within clade II be considered as a new genus.
|
12759 |
Euzéby JP,
Tindall BJ,
N/A N/A,
( 2004 ) Status of strains that contravene Rules 27(3) and 30 of the Bacteriological Code. Request for an opinion. PMID : 14742499 DOI : 10.1099/ijs.0.03022-0 Abstract >>
In the period from January 2001, at least 207 new names proposed in articles in the International Journal of Systematic and Evolutionary Microbiology or cited in Validation Lists are not in accordance with Rules 27(3) and 30 of the Bacteriological Code. The purpose of the present Request for an Opinion is to clarify the status of the names listed and to provide a solution whereby they may be considered to be validly published.
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| 21941 | De Vos, P., and Truper, H.G. "Judicial Commission of the International Committee on Systematic Bacteriology IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia." Int. J. Syst. Evol. Microbiol. (2000) 50:2239-2244. (Note: The name 'Geobacillus kaustophilus' may not be validly published due to the fact that the type strain was not deposited in culture collections in two different countries as required by the emended Bacteriological Code described by De Vos & Truper. Euzeby and Tindall propose a solution for the valid publication of this species.) | ||||
| 9054 | VALIDATION LIST No. 28. Int. J. Syst. Bacteriol. (1989) 39:93-94. | ||||
| 9055 | Prickett: N.Y. Agric. Exp. Stn. Tech. Bull. (1928) 147: 38. [No PubMed record available.] | 2469 |
Nazina TN,
Tourova TP,
Poltaraus AB,
Novikova EV,
Grigoryan AA,
Ivanova AE,
Lysenko AM,
Petrunyaka VV,
Osipov GA,
Belyaev SS,
Ivanov MV,
( 2001 ) Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th. PMID : 11321089 DOI : 10.1099/00207713-51-2-433 Abstract >>
Five hydrocarbon-oxidizing strains were isolated from formation waters of oilfields in Russia, Kazakhstan and China. These strains were moderately thermophilic, neutrophilic, motile, spore-forming rods, aerobic or facultatively anaerobic. The G+C content of their DNA ranged from 49.7 to 52.3 mol%. The major isoprenoid quinone was menaquinone-7; cellular fatty acid profiles consisted of significant amounts of iso-15:0, iso-16:0 and iso-17:0 fatty acids (61.7-86.8% of the total). Based on data from 16S rDNA analysis and DNA-DNA hybridization, the subsurface isolates could be divided into two groups, one of which consisted of strains UT and X and the other of which consisted of strains K, Sam and 34T. The new strains exhibited a close phylogenetic relationship to thermophilic bacilli of 'Group 5' of Ash et al. [Ash, C., Farrow, J. A. E., Wallbanks, S. & Collins, M. D. (1991). Lett Appl Microbiol 13, 202-206] and a set of corresponding signature positions of 16S rRNA. Comparative analysis of the 16S rDNA sequences and fatty acid compositions of the novel isolates and established species of thermophilic bacilli indicated that the subsurface strains represent two new species within a new genus, for which the names Geobacillus subterraneus gen. nov., sp. nov., and Geobacillus uzenensis sp. nov. are proposed. It is also proposed that Bacillus stearothermophilus, Bacillus thermoleovorans, Bacillus thermocatenulatus, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans be transferred to this new genus, with Geobacillus stearothermophilus (formerly Bacillus stearothermophilus) as the type species.
|
3602 |
Priest FG,
Goodfellow M,
Todd C,
( 1988 ) A numerical classification of the genus Bacillus. PMID : 3246588 DOI : 10.1099/00221287-134-7-1847 Abstract >>
Three hundred and sixty-eight strains of aerobic, endospore-forming bacteria which included type and reference cultures of Bacillus and environmental isolates were studied. Overall similarities of these strains for 118 unit characters were determined by the SSM, SJ and DP coefficients and clustering achieved using the UPGMA algorithm. Test error was within acceptable limits. Six cluster-groups were defined at 70% SSM, which corresponded to 69% SP and 48-57% SJ. Groupings obtained with the three coefficients were generally similar but there were some changes in the definition and membership of cluster-groups and clusters, particularly with the SJ coefficient. The Bacillus strains were distributed among 31 major (4 or more strains), 18 minor (2 or 3 strains) and 30 single-member clusters at the 83% SSM level. Most of these clusters can be regarded as taxospecies. The heterogeneity of several species, including Bacillus brevis, B. circulans, B. coagulans, B. megateriun, B. sphaericus and B. stearothermophilus, has been indicated and the species status of several taxa of hitherto uncertain validity confirmed. Thus on the basis of the numerical phenetic and appropriate (published) molecular genetic data, it is proposed that the following names be recognized; Bacillus flexus (Batchelor) nom. rev., Bacillus fusiformis (Smith et al.) comb. nov., Bacillus kaustophilus (Prickett) nom. rev., Bacillus psychrosaccharolyticus (Larkin & Stokes) nom. rev. and Bacillus simplex (Gottheil) nom. rev. Other phenetically well-defined taxospecies included 'B. aneurinolyticus', 'B. apiarius', 'B. cascainensis', 'B. thiaminolyticus' and three clusters of environmental isolates related to B. firmus and previously described as 'B. firmus-B. lentus intermediates'. Future developments in the light of the numerical phenetic data are discussed.
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| 47987 | Sunna, A., Tokaijian, S., Burghardt, J., Rainey, F., Antranikian, G., and Hashwa, F. "Identification of Bacillus kaustophilus, Bacillus thermocatenulatus and Bacillus strain HSR as members of Bacillus thermoleovorans." Syst. Appl. Microbiol. (1997) 20:232-227. [No PubMed record available.] |