- Volume 53, Issue 3, 2003
Volume 53, Issue 3, 2003
- Evolution, Phylogeny And Biodiversity
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Phylogenetic relationships between Bacillus species and related genera inferred from comparison of 3′ end 16S rDNA and 5′ end 16S–23S ITS nucleotide sequences
More LessThe 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.
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DNA–DNA hybridization study of Burkholderia species using genomic DNA macro-array analysis coupled to reverse genome probing
The present study was aimed at simplifying procedures to delineate species and identify isolates based on DNA–DNA reassociation. DNA macro-arrays harbouring genomic DNA of reference strains of several Burkholderia species were produced. Labelled genomic DNA, hybridized to such an array, allowed multiple relative pairwise comparisons. Based on the relative DNA–DNA relatedness values, a complete data matrix was constructed and the ability of the method to discriminate strains belonging to different species was assessed. This simple approach led successfully to the discrimination of Burkholderia mallei from Burkholderia pseudomallei, but also discriminated Burkholderia cepacia genomovars I and III, Burkholderia multivorans, Burkholderia pyrrocinia, Burkholderia stabilis and Burkholderia vietnamiensis. Present data showed a sufficient degree of congruence with previous DNA–DNA reassociation techniques. As part of a polyphasic taxonomic scheme, this straightforward approach is proposed to improve species definition, especially for application in the rapid screening necessary for large numbers of clinical or environmental isolates.
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Missing links in the divergence of Chlamydophila abortus from Chlamydophila psittaci
Pathological and serological evidence and DNA–DNA reassociation data indicate that Chlamydophila psittaci and Chlamydophila abortus are separate species. C. psittaci causes avian systemic disease and C. abortus causes abortion. Both previously belonged to Chlamydia psittaci are associated with zoonotic and enzootic outbreaks. Genetic studies suggest that they are closely related and because of the recent availability of diverse C. psittaci strains and comparative data for several genes, it was possible to explore this relationship. The parrot C. psittaci strain 84/2334 was found to have DNA sequences that were identical to an extrachromosomal plasmid in duck C. psittaci strain N352, to rnpB in strain R54 from a brown skua and to the rrn intergenic spacer in parakeet strain Prk/Daruma (from Germany, Antarctica and Japan, respectively). Analysis of ompA and the rrn spacer revealed progressive diversification of the strains, with 84/2334 resembling what might have been a recent ancestor of C. abortus. Another C. psittaci strain (VS225) showed evidence of having undergone convergent evolution towards the C. abortus-like genotype, whereas strain R54 diverged independently. For the first time, these studies link C. abortus in an evolutionary context to the C. psittaci lineage. It has been concluded that C. abortus diverged from C. psittaci, and so strain R54 was designated a C. psittaci strain. It is recommended that characterization of C. psittaci and C. abortus strains should utilize more than a single method and more than a single gene.
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Phylogenetic analysis of members of the genus Aeromonas based on gyrB gene sequences
More LessThe phylogenetic relationships of all known species of the genus Aeromonas were investigated by using the sequence of gyrB, a gene that encodes the B-subunit of DNA gyrase. Nucleotide sequences of gyrB were determined from 53 Aeromonas strains, including some new isolates, which were also characterized by analysis of the 16S rDNA variable regions. The results support the recognition of the family Aeromonadaceae, as distinct from Plesiomonas shigelloides and other enteric bacteria. This phylogenetic marker revealed strain groupings that are consistent with the taxonomic organization of all Aeromonas species described to date. In particular, gyrB results agreed with 16S rDNA analysis; moreover, the former showed a higher capacity to differentiate between species. The present analysis was useful for the elucidation of reported discrepancies between different DNA–DNA hybridization sets. Additionally, due to the sequence diversity found at the intraspecies level, gyrB is proposed as a useful target for simultaneous identification of species and strains. In conclusion, the gyrB gene has proved to be an excellent molecular chronometer for phylogenetic studies of the genus Aeromonas.
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- International Committee On Systematics Of Prokaryotes
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- Minutes
- Opinions
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Valid publication of the genus name Thermodesulfobacterium and the species names Thermodesulfobacterium commune (Zeikus et al. 1983) and Thermodesulfobacterium thermophilum (ex Desulfovibrio thermophilus Rozanova and Khudyakova 1974). Opinion 71
More LessThe Judicial Commission of the International Committee on Systematics of Prokaryotes decided that the date of valid publication of the genus name Thermodesulfobacterium and of the species names Thermodesulfobacterium commune and Thermodesulfobacterium thermophilum is 1995. Thermodesulfobacterium mobile Rozanova and Pivovarova 1988 is an illegitimate, later synonym of Thermodesulfobacterium thermophilum.
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Strain DSM 6035 is the type strain of Lactobacillus panis (Wiese et al. 1996). Opinion 72
More LessThe Judicial Commission of the International Committee on Systematics of Prokaryotes decided that strain DSM 6035 is the type strain of Lactobacillus panis with the consequence that the name Lactobacillus panis has been validly published.
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Paenibacillus durus (Collins et al. 1994, formerly Clostridium durum Smith and Cato 1974) has priority over Paenibacillus azotofixans (Seldin et al. 1984). Opinion 73
More LessThe Judicial Commission of the International Committee on Systematics of Prokaryotes decided that the name Paenibacillus durus has priority over Paenibacillus azotofixans, and that the latter is a later synonym of the former. The type strain is therefore strain ATCC 27763 (=DSM 1735).
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Strain NCIMB 13488 may serve as the type strain of Halorubrum trapanicum. Opinion 74
More LessThe Judicial Commission of the International Committee on Systematics of Prokaryotes decided that strain NCIMB 13488 may serve as the type strain of Halorubrum trapanicum.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)