Genetic interrelationships of saccharolytic Clostridium botulinum types B, E and F and related clostridia as revealed by small-subunit rRNA gene sequences

Hutson, R

doi:10.1016/0378-1097(93)90495-n

Cited by 76 publications

(95 citation statements)

References 19 publications

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“…Genomic DNA was DSM 5388T DSM 8431 DSM 2767T DSM 3847T DSM 5503T DSM 3222T DSM 1801T DSM 1682T DSM 6736T NCIMB 10651T DSM 6877 BN11 NCTC 279T X77842 X76163 X76161 X77843 X77844 X76748 X76742 X77846 X76749 X7785 1 X77847 X77836 X76750 X77837 X77848 X76744 X76740 X77834 X76162 X77845 X76 164 X76746 X77840 X77838 X77839 X7784 1 X76745 X77850 X76747 X7. extracted from cells in the mid-logarithmic growth phase and was purified by the method of Lawson et al (26). 16s rRNA gene fragments were generated by PCR as previously described (19). Amplified products were purified by using a Magic DNA Clean-up System (Promega) and were sequenced directly by using c~-~'S-labeled dATP and a Sequenase version 2.0 sequencing kit (United States Biochemicals) (19).…”

Section: Methodsmentioning

confidence: 99%

“…16s rRNA gene fragments were generated by PCR as previously described (19). Amplified products were purified by using a Magic DNA Clean-up System (Promega) and were sequenced directly by using c~-~'S-labeled dATP and a Sequenase version 2.0 sequencing kit (United States Biochemicals) (19).…”

Section: Methodsmentioning

confidence: 99%

“…If phylogenetic data are to be used as the basis for future taxonomic restructuring of the genus Clostridium, it is imperative that as many species as possible be sequenced and that the branching patterns of trees be resolved with confidence, In recent years there has been considerable progress toward this end, with complete (or nearly complete) 16s rRNA sequences available for more than 80 clostridial species (5,19,20,27,29,30,34,35,37,38,50). In this paper we describe the 16s rRNA gene sequences of an additional 34 clostridial strains and the results of a comparative sequence analysis and thereby provide an almost complete picture of the genealogical interrelationships in the genus.…”

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confidence: 99%

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The Phylogeny of the Genus Clostridium: Proposal of Five New Genera and Eleven New Species Combinations

Collins¹,

Lawson²,

Willems³

et al. 1994

International Journal of Systematic Bacteriology

1,629

1,344

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The 16s rRNA gene sequences of 34 named and unnamed clostridial strains were determined by PCR direct sequencing and were compared with more than 80 previously determined clostridial sequences and the previously published sequences of representative species of other low-G+C-content gram-positive genera, thereby providing an almost complete picture of the genealogical interrelationships of the clostridia. The results of our phylogenetic analysis corroborate and extend previous findings in showing that the genus Clostridium is extremely heterogeneous, with many species phylogenetically intermixed with other sporeforming and non-spore-forming genera. The genus Clostridium is clearly in need of major revision, and the rRNA structures defined in this and previous studies may provide a sound basis for future taxonomic restructuring. The problems and different possibilities for restructuring are discussed in light of the phenotypic and phylogenetic data, and a possible hierarchical structure for the clostridia and their close relatives is presented. On the basis of phenotypic criteria and the results of phylogenetic analyses the following five new genera and 11 new combinations are proposed: Caloramator gen. nov., with Caloramator fervidus comb. nov.; Filifactor gen. nov., with Filifactor villosus comb. nov.; Moorella gen. nov., with Moorella thermoacetica comb. nov. and Moorella thermoautotrophica comb. nov.; Oxobacter gen. nov., with Oxobacter pfennigii comb. nov.; Oxalophagus gen. nov., with Oxalophagus oxalicus comb. nov.; Eubacterium barkeri comb. nov.; Paenibacillus durum comb. nov.; Thermoanaerobacter kivui comb. nov.; Thermoanaerobacter thermocopriae comb. nov.; and Thermoanerobacterium thermosaccharolyticum comb. nov. ~ ~~Great advances, have been made over the past decade in unravelling the phylogenetic complexities within the grampositive endospore-forming bacteria. For example, 16s rRNA oligonucleotide cataloging and, more recently, almost complete rRNA (or gene) sequencing have shown that the aerobic endospore-forming bacilli are phylogenetically very heterogeneous, consisting of at least six highly divergent lines (1,11,51). As a result of these studies, taxonomic reorganization of the genus Bacillus was initiated with the introduction of the genus Alicyclobacillus for some acidophilic species (51) and the genus Paenibacillus (2) for Bacillus polymyxa and its close relatives (rRNA group 3 [l]). Although the remainder of the genus is still in need of taxonomic revision, the phylogenetic groups established by rRNA analysis are already forming the foundation for a new molecular data-based taxonomy for this group of organisms. Knowledge of the natural interrelationships within the anaerobic genus Clostridium is more fragmented than knowledge of the interrelationships among the aerobic bacilli. The earliest, and until recently the most comprehensive, phylogenetic study of the genus Clostridium was published by Johnson and Francis (22), who demonstrated that there is considerable diversity within the genus by u...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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The Phylogeny of the Genus Clostridium: Proposal of Five New Genera and Eleven New Species Combinations

Collins¹,

Lawson²,

Willems³

et al. 1994

International Journal of Systematic Bacteriology

1,629

1,344

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“…Lyophilized cells were resuspended in 500 pl of TES buffer (0.05 M Tris-HC1, 0.005 M EDTA, 0.05 M NaCl, pH 8.0), and genomic DNA was extracted directly from this cell suspension by the method of Lawson et al (10). The 16s rRNA genes were amplified as described previously (9) and purified by using a Prep-A-Gene kit (Bio-Rad, Hercules, Calif.) according to the manufacturer's instructions. The 16s rDNA fragments were sequenced by using a Taq DyeDeoxy Terminator Cycle Sequencing Kit (Applied Biosystems Inc., Foster City, Calif.) and an automated sequencer (Applied Biosystems Inc.; model 373A).…”

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confidence: 99%

Phylogenetic Placement of Dialister pneumosintes (formerly Bacteroides pneumosintes) within the Sporomusa Subbranch of the Clostridium Subphylum of the Gram-Positive Bacteria

Willems

Collins

1995

International Journal of Systematic Bacteriology

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The nucleotide sequence of the 16s rRNA gene of the type strain of Dialisfer pneumosinfes was determined. Phylogenetic analysis revealed that this species belongs to the Sporomusa branch of the Clostridum subphylum of the gram-positive bacteria and should therefore be excluded from the family Bacferoidaceae. Within this branch, which encompasses several other gram-negative taxa, such as Acidarninococcus, Pectinatus, Phascolarcobacferium, Quinella, Selenomonas, and Zymophilus, Dialisfer showed a specific, albeit distant, affinity with the genera Megasphaera and VeiUoneUa. Anaerorhabdus, Fibrobacter, Megamonas, Mitsuokella, Porphyromonas, Prevotella, Rikenella, Ruminobacter, Sebaldella, and Tissierella) (see reference 13 for a review). Shah and Collins in 1989 (14) proposed that the genus Bacteroides be restricted to the saccharolytic, nonpigmented species of the Bacteroides fiagilis group. B. pneumosintes differs markedly from this genus as defined by Shah and Collins (14), and its true taxonomic affiliations remained uncertain. On the basis of phenotypic criteria, Moore and Moore (11) have recently resurrected the genus Dialister, to accommodate B. pneumosintes. In this study, we have sequenced the 16s rRNA gene of the type strain of Dialister pneumosintes to determine its phylogenetic proximity to the genus Bacteroides and other members of the family Ba cteroidaceae.A freeze-dried culture of the type strain of D. pneumosintes (ATCC 33WST) was obtained from the American Type Culture Collection, Rockville, Md. Because of the phenotypic similarities of Veillonella and Dialister species (e.g., small cell size and non-spore-forming, nonmotile anaerobes), the 16s rRNA genes of three Veillonella species from the human oral cavity were also sequenced. Veillonella atypica (DSM 20739T), Veillonella dispar (DSM 20735*), and Veillonella pawula (DSM 200gT) were obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany. Lyophilized cells were resuspended in 500 pl of TES buffer (0.05 M Tris-HC1, 0.005 M EDTA, 0.05 M NaCl, pH 8.0), and genomic DNA was extracted directly from this cell suspension by the method of Lawson et al. (10). The 16s rRNA genes were amplified as described previously (9) and purified by using a Prep-A-Gene kit (Bio-Rad, Hercules, Calif.) according to the manufacturer's instructions. The 16s rDNA fragments were sequenced by using a Taq DyeDeoxy Terminator Cycle Sequencing Kit (Applied Biosystems Inc., Foster City, Calif.) and an automated sequencer (Applied Biosystems Inc.; model 373A). The new sequences were compared with sequences of reference organisms, which were obtained from the EMBL and GenBank data libraries. Once the closest known phylogenetic relatives had been established, sequences were aligned by using the PILEUP program (3), and the alignments were corrected manually. For comparative phylogenetic analyses approximately 100 bases at the 5' end of the rRNA sequence were excluded because of alignment uncertainties. Phylogenetic analyses were performe...

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“…A phylogenetic analysis was performed by comparative 16S rRNA gene sequence analysis. A large fragment of the 16S rRNA gene (corresponding to positions 30-1521 of the Escherichia coli 16S rRNA gene) was amplified by PCR using conserved primers close to the 3h-and 5h-ends of the gene, as described previously (Hutson et al, 1993). The PCR product was sequenced directly using a Taq DyeDeoxy terminator cycle sequencing kit (Applied Biosystems) and an automatic DNA sequencer (model 373A ; Applied Biosystems).…”

Section: Methodsmentioning

confidence: 99%

Aerococcus sanguicola sp. nov., isolated from a human clinical source.

Lawson¹,

Falsen²,

Truberg-Jensen³

et al. 2001

International Journal of Systematic and Evolutionary Microbiology

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Phenotypic and phylogenetic studies were performed on an unknown, Grampositive, catalase-negative coccus isolated from human blood. Comparative 16S rRNA gene sequencing demonstrated that the organism represents a new subline within the genus Aerococcus. The unknown bacterium was readily distinguished from the three currently recognized Aerococcus species, Aerococcus christensenii, Aerococcus urinae and Aerococcus viridans, by biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that this unknown bacterium from blood be classified as Aerococcus sanguicola sp. nov. The type strain of Aerococcus sanguicola is CCUG 43001 T (l CIP 106533 T ).

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Genetic interrelationships of saccharolytic Clostridium botulinum types B, E and F and related clostridia as revealed by small-subunit rRNA gene sequences

Cited by 76 publications

References 19 publications

The Phylogeny of the Genus Clostridium: Proposal of Five New Genera and Eleven New Species Combinations

The Phylogeny of the Genus Clostridium: Proposal of Five New Genera and Eleven New Species Combinations

Phylogenetic Placement of Dialister pneumosintes (formerly Bacteroides pneumosintes) within the Sporomusa Subbranch of the Clostridium Subphylum of the Gram-Positive Bacteria

Aerococcus sanguicola sp. nov., isolated from a human clinical source.

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