Extended Bibliography: |
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Ref #: |
22093 |
Author(s): |
Xu,D.;Cote,J.C. |
Journal: |
Int J Syst Evol Microbiol |
Title: |
Phylogenetic relationships between Bacillus species and related genera inferred from comparison of 3' end 16S rDNA and 5' end 16S-23S ITS nucleotide sequences |
Volume: |
53 |
Page(s): |
695-704 |
Year: |
2003 |
Keyword(s): |
GENBANK/AF478062
GENBANK/AF478063
GENBANK/AF478064
GENBANK/AF478065
GENBANK/AF478066
GENBANK/AF478067
GENBANK/AF478068
GENBANK/AF478069
GENBANK/AF478070
GENBANK/AF478071
GENBANK/AF478072
GENBANK/AF478073
GENBANK/AF478074
GENBANK/AF478075
GENBANK/AF478076
GENBANK/AF478077
GENBANK/AF478078
GENBANK/AF478079
GENBANK/AF478080
GENBANK/AF478081
GENBANK/AF478082
GENBANK/AF478083
GENBANK/AF478084
GENBANK/AF478085
GENBANK/AF478086
GENBANK/AF478087
GENBANK/AF478088
GENBANK/AF478089
GENBANK/AF478090
GENBANK/AF478091
GENBANK/AF478092
GENBANK/AF478093
GENBANK/AF478094
GENBANK/AF478095
GENBANK/AF478096
GENBANK/AF478097
GENBANK/AF478098
GENBANK/AF478099
GENBANK/AF478100
GENBANK/AF478101
GENBANK/AF478102
GENBANK/AF478103
GENBANK/AF478104
GENBANK/AF478105
GENBANK/AF478106
GENBANK/AF478107
GENBANK/AF478108
GENBANK/AF478109
GENBANK/AF478110
GENBANK/AF478111
3' Untranslated Regions/*genetics
5' Untranslated Regions/*genetics
Bacillus/*classification/genetics
DNA, Ribosomal/analysis
DNA, Ribosomal Spacer/*analysis
Genes, rRNA
Molecular Sequence Data
*Phylogeny
RNA, Ribosomal, 16S/*genetics
RNA, Ribosomal, 23S/genetics
*Sequence Analysis, DNA
Species Specificity
|
Remarks: |
The nucleotide sequences of the 3' end of the 16S rDNA and the 16S-23S internal transcribed spacer (ITS) of 40 Bacillaceae species were determined. These included 21 Bacillus, 9 Paenibacillus, 6 Brevibacillus, 2 Geobacillus, 1 Marinibacillus and 1 Virgibacillus species. Comparative sequence analysis of a 220 bp region covering a highly conserved 150 bp sequence located at the 3' end of the 16S rRNA coding region and a conserved 70 bp sequence located at the 5' end of the 16S-23S ITS of the 40 species and six sequences available in GenBank were used to infer the phylogenetic relationships between all 46 taxa. When a maximal distance (D(max), where D refers to the number of nucleotide substitutions per site) of 0.31 was introduced as a threshold to determine groupings, 10 phylogenetically distinct clusters were revealed. Twenty-six Bacillus species were separated in seven groups (I, II, III, IV, V, VI and X), but Bacillus circulans remained ungrouped. All six Brevibacillus species under study were in Group VII. The nine Paenibacillus species fell into two distinct groups (VIII and IX). Species with D(max) values within 0.05 were considered to be very closely related. These were Bacillus psychrophilus and Bacillus psychrosaccharolyticus in Group II; 'Bacillus maroccanus' and Bacillus simplex in Group II; Bacillus amyloliquefaciens, Bacillus atrophaeus, Bacillus mojavensis and Bacillus subtilis in Group VI; Bacillus fusiformis and Bacillus sphaericus in Group VI; Brevibacillus brevis and Brevibacillus formosus in Group VII; Paenibacillus gordonae and Paenibacillus validus in Group VIII; and Bacillus anthracis, Bacillus cereus, Bacillus mycoides and Bacillus thuringiensis in Group X. The phylogenetic classification presented here is, in general, in agreement with current classifications based on phenotypic and molecular data. Our findings suggest, however, that in some cases, further divisions or, conversely, further groupings might be warranted. Should current classifications be re-examined in the light of our results, D(max) values of 0.31 and 0.05, as exemplified here, may prove useful threshold values for the grouping of Bacillaceae into taxa akin to genera and species, respectively. These D(max) thresholds may also reveal, in a different way, bacterial species for which further characterization might be warranted for proper classification and/or reassignment. |
URL: |
12807189 |
|
Ref #: |
24297 |
Author(s): |
Satomi,M.;La Duc,M.T.;Venkateswaran,K. |
Journal: |
Int J Syst Evol Microbiol |
Title: |
Bacillus safensis sp. nov., isolated from spacecraft and assembly-facility surfaces |
Volume: |
56 |
Page(s): |
1735-40 |
Year: |
2006 |
Keyword(s): |
Bacillus/*classification/genetics/isolation & purification
Bacterial Proteins/genetics
DNA Fingerprinting
DNA Gyrase/genetics
DNA, Bacterial/genetics
*Environmental Microbiology
Nucleic Acid Hybridization
Phylogeny
Polymerase Chain Reaction
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Repetitive Sequences, Nucleic Acid/genetics
Sequence Homology, Nucleic Acid
*Spacecraft
Species Specificity
|
Remarks: |
Thirteen strains of a novel spore-forming, Gram-positive, mesophilic heterotrophic bacterium were isolated from spacecraft surfaces (Mars Odyssey Orbiter) and assembly-facility surfaces at the Jet Propulsion Laboratory in California and the Kennedy Space Center in Florida. Phylogenetic analysis of 16S rRNA gene sequences has placed these novel isolates within the genus Bacillus, the greatest sequence similarity (99.9 %) being found with Bacillus pumilus. However, these isolates share a mere 91.2 % gyrB sequence similarity with Bacillus pumilus, rendering their 16S rRNA gene-derived relatedness suspect. Furthermore, DNA-DNA hybridization showed only 54-66 % DNA relatedness between the novel isolates and strains of B. pumilus. rep-PCR fingerprinting and previously reported matrix-assisted laser desorption/ionization time-of-flight mass spectrometry protein profiling clearly distinguished these isolates from B. pumilus. Phenotypic analyses also showed some differentiation between the two genotypic groups, although the fatty acid compositions were almost identical. The polyphasic taxonomic studies revealed distinct clustering of the tested strains into two distinct species. On the basis of phenotypic characteristics and the results of phylogenetic analyses of 16S rRNA and gyrB gene sequences, repetitive element primer-PCR fingerprinting and DNA-DNA hybridization, the 13 isolates represent a novel species of the genus Bacillus, for which the name Bacillus safensis sp. nov. is proposed. The type strain is FO-36b(T) (=ATCC BAA-1126(T)=NBRC 100820(T)). |
URL: |
16902000 |
|
Ref #: |
1300 |
Author(s): |
Skerman,V.B.D.;McGowan,V.;Sneath,P.H.A.(ed) |
Journal: |
Int. J. Syst. Bacteriol. |
Title: |
Approved Lists of Bacterial Names. |
Volume: |
30 |
Page(s): |
225-420 |
Year: |
1980 |
|
Ref #: |
3768 |
Author(s): |
Fahmy,F.;Flossdorf,J.;Claus,D. |
Journal: |
System. Appl. Microbiol. |
Title: |
The DNA base composition of the type strains of the genus Bacillus. |
Volume: |
6 |
Page(s): |
60-65 |
Year: |
1985 |
|
Ref #: |
4714 |
Author(s): |
Seki,T.;Chung,C.-K.;Mikami,H.;Oshima,Y. |
Journal: |
Int. J. Syst. Bacteriol. |
Title: |
Deoxyribonucleic acid homology and taxonomy of the genus Bacillus. |
Volume: |
28 |
Page(s): |
182-189 |
Year: |
1978 |
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