| Extended Bibliography: |
Show bibliography
| Ref #: |
46426 |
| Author(s): |
Conrads,G.;Claros,M.C.;Citron,D.M.;Tyrrell,K.L.;Merriam,V.;Goldstein,E.J. |
| Journal: |
Int J Syst Evol Microbiol |
| Title: |
16S-23S rDNA internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Fusobacterium |
| Volume: |
52 |
| Page(s): |
493-9 |
| Year: |
2002 |
| Keyword(s): |
GENBANK/AF342829
GENBANK/AF342830
GENBANK/AF342831
GENBANK/AF342832
GENBANK/AF342833
GENBANK/AF342834
GENBANK/AF342835
GENBANK/AF342836
GENBANK/AF342837
GENBANK/AF342838
GENBANK/AF342839
GENBANK/AF342840
GENBANK/AF342841
GENBANK/AF342842
GENBANK/AF342843
GENBANK/AF342844
GENBANK/AF342845
GENBANK/AF342846
GENBANK/AF342847
GENBANK/AF342848
GENBANK/AF342849
GENBANK/AF342850
GENBANK/AF342851
GENBANK/AF342852
GENBANK/AF342853
GENBANK/AF342854
GENBANK/AF342855
GENBANK/AF342856
GENBANK/AF342857
GENBANK/AF342858
GENBANK/AF342859
GENBANK/AF342860
GENBANK/AF342861
Base Sequence
DNA Primers
DNA, Ribosomal Spacer/*genetics
Fusobacterium/*classification/genetics
Molecular Sequence Data
Phylogeny
RNA, Ribosomal, 16S/chemistry
RNA, Ribosomal, 23S/chemistry
Species Specificity
|
| Remarks: |
The 16S-23S rDNA internal transcribed spacer (ITS) regions of all currently defined Fusobacterium species and related taxa such as Leptotrichia buccalis, Sebaldella termitidis and Streptobacillus moniliformans, were analysed to examine inter- and intraspecies as well as subspecies relationships. For the ITS-amplification, a new eubacterial universal primer pair was designed and used. The majority of the Fusobacterium strains, along with L. buccalis showed one major, and two to three weaker, distinct bands (short and long versions) with lengths of 800-830 bp and 1000-1100 bp. Nevertheless, six other patterns were also found within the genus Fusobacterium, demonstrating its heterogeneity. The ITS region was sequenced and found to consist both of conserved motifs, which functioned as a framework for alignment, and of variable sites, which provided high phylogenetic resolution. Analyses of the ITS-DNA sequences and ITS relative length (short version) allowed species and subspecies differentiation in most cases. The results confirmed the strikingly distant relationship between Fusobacterium prausnitzii and the genus Fusobacterium. Fusobacterium nucleatum subspecies, along with Fusobacterium naviforme, Fusobacterium simiae and Fusobacterium periodonticum, formed a cluster with an inherently high potential for diversification. Other clusters were formed by Fusobacterium necrophorum subspecies with Fusobacterium gonidaformans and by Fusobacterium varium with Fusobacterium mortiferum and Fusobacterium ulcerans. Fusobacterium russii as well as Fusobacterium perfoetens formed separate branches. Fusobacterium necrophorum subspp. necrophorum and funduliforme on the one hand, and Fusobacterium varium and Fusobacterium mortiferum on the other, were found to be very similar, even at the high-resolution ITS level. |
| URL: |
11931161 |
|
| Ref #: |
50644 |
| Author(s): |
Brune,A.;Evers,S.;Kaim,G.;Ludwig,W.;Schink,B. |
| Journal: |
Int J Syst Evol Microbiol |
| Title: |
Ilyobacter insuetus sp. nov., a fermentative bacterium specialized in the degradation of hydroaromatic compounds |
| Volume: |
52 |
| Page(s): |
429-32 |
| Year: |
2002 |
| Keyword(s): |
GENBANK/AJ307976
GENBANK/AJ307980
Biodegradation, Environmental
DNA, Bacterial/chemistry
DNA, Ribosomal/chemistry
Fermentation
Gram-Negative Aerobic Rods and Cocci/*classification/genetics/metabolism
Molecular Sequence Data
Phylogeny
Quinic Acid/metabolism
RNA, Ribosomal, 16S/chemistry
RNA, Ribosomal, 23S/chemistry
Sequence Analysis, DNA
Shikimic Acid/metabolism
|
| Remarks: |
The mesophilic, anaerobic bacterium strain VenChi2T was isolated with quinic acid (1,3,4,5-tetrahydroxy-cyclohexane-1-carboxylic acid) as the sole source of carbon and energy. Of more than 30 substrates tested, only quinic acid and shikimic acid (3,4,5-trihydroxy-1-cyclohexene-1-carboxylic acid) were utilized, yielding acetate, propionate, butyrate, H2 and CO2 as fermentation products. Sugars, alcohols, (di-)carboxylic acids, amino acids and aromatic compounds were not fermented and no external electron acceptors were used. Strain VenChi2T is a gram-negative, strictly anaerobic, coccoid rod; it does not employ the classical hydroaromatic pathway of aerobic bacteria for the degradation of hydroaromatic compounds (no aromatic intermediates involved). Comparative 16S and 23S rDNA sequence analyses placed strain VenChi2T in the fusobacteria phylum, with the closest relatives among species of the genera Ilyobacter and Propionigenium. The results indicate that, disregarding the taxonomically misplaced Ilyobacter delafieldii, which is a member of the clostridia, the validly described Ilyobacter and Propionigenium species are phylogenetically intermixed. Based on its phenotypic properties, strain VenChi2T (= DSM 6831T = ATCC BAA-291T) is assigned to the genus Ilyobacter as the type strain of a novel species, Ilyobacter insuetus sp. nov. |
| URL: |
11931152 |
|
| Ref #: |
25413 |
| Author(s): |
Paster,B.J.;Boches,S.K.;Galvin,J.L.;Ericson,R.E.;Lau,C.N.;Levanos,V.A.;Sahasrabudhe,A.;Dewhirst,F.E. |
| Journal: |
J Bacteriol |
| Title: |
Bacterial diversity in human subgingival plaque |
| Volume: |
183 |
| Page(s): |
3770-83 |
| Year: |
2001 |
| Keyword(s): |
Bacteria/*classification/genetics/isolation & purification
DNA, Bacterial/analysis
DNA, Ribosomal/analysis
Dental Plaque/*microbiology
Gingiva/*microbiology
Humans
Periodontal Diseases/*microbiology
Phylogeny
Polymerase Chain Reaction
RNA, Ribosomal, 16S/analysis
Sequence Analysis, DNA
|
| Remarks: |
The purpose of this study was to determine the bacterial diversity in the human subgingival plaque by using culture-independent molecular methods as part of an ongoing effort to obtain full 16S rRNA sequences for all cultivable and not-yet-cultivated species of human oral bacteria. Subgingival plaque was analyzed from healthy subjects and subjects with refractory periodontitis, adult periodontitis, human immunodeficiency virus periodontitis, and acute necrotizing ulcerative gingivitis. 16S ribosomal DNA (rDNA) bacterial genes from DNA isolated from subgingival plaque samples were PCR amplified with all-bacterial or selective primers and cloned into Escherichia coli. The sequences of cloned 16S rDNA inserts were used to determine species identity or closest relatives by comparison with sequences of known species. A total of 2,522 clones were analyzed. Nearly complete sequences of approximately 1,500 bases were obtained for putative new species. About 60% of the clones fell into 132 known species, 70 of which were identified from multiple subjects. About 40% of the clones were novel phylotypes. Of the 215 novel phylotypes, 75 were identified from multiple subjects. Known putative periodontal pathogens such as Porphyromonas gingivalis, Bacteroides forsythus, and Treponema denticola were identified from multiple subjects, but typically as a minor component of the plaque as seen in cultivable studies. Several phylotypes fell into two recently described phyla previously associated with extreme natural environments, for which there are no cultivable species. A number of species or phylotypes were found only in subjects with disease, and a few were found only in healthy subjects. The organisms identified only from diseased sites deserve further study as potential pathogens. Based on the sequence data in this study, the predominant subgingival microbial community consisted of 347 species or phylotypes that fall into 9 bacterial phyla. Based on the 347 species seen in our sample of 2,522 clones, we estimate that there are 68 additional unseen species, for a total estimate of 415 species in the subgingival plaque. When organisms found on other oral surfaces such as the cheek, tongue, and teeth are added to this number, the best estimate of the total species diversity in the oral cavity is approximately 500 species, as previously proposed. |
| URL: |
11371542 |
|
| Ref #: |
12738 |
| Author(s): |
Paster,B.J.;Boches,S.K.;Galvin,J.L.;Ericson,R.E.;Lau,C.N.;Levanos,V.A.;Sahasrabudhe,A.;Dewhirst,F.E. |
| Journal: |
J Bacteriol |
| Title: |
Bacterial diversity in human subgingival plaque |
| Volume: |
183 |
| Page(s): |
3770-83 |
| Year: |
2001 |
| Keyword(s): |
Bacteria/*classification/genetics/isolation & purification
DNA, Bacterial/analysis
DNA, Ribosomal/analysis
Dental Plaque/*microbiology
Gingiva/*microbiology
Human
Periodontal Diseases/*microbiology
Phylogeny
Polymerase Chain Reaction
RNA, Ribosomal, 16S/analysis
Sequence Analysis, DNA
Support, U.S. Gov't, P.H.S.
|
| Remarks: |
The purpose of this study was to determine the bacterial diversity in the human subgingival plaque by using culture-independent molecular methods as part of an ongoing effort to obtain full 16S rRNA sequences for all cultivable and not-yet-cultivated species of human oral bacteria. Subgingival plaque was analyzed from healthy subjects and subjects with refractory periodontitis, adult periodontitis, human immunodeficiency virus periodontitis, and acute necrotizing ulcerative gingivitis. 16S ribosomal DNA (rDNA) bacterial genes from DNA isolated from subgingival plaque samples were PCR amplified with all-bacterial or selective primers and cloned into Escherichia coli. The sequences of cloned 16S rDNA inserts were used to determine species identity or closest relatives by comparison with sequences of known species. A total of 2,522 clones were analyzed. Nearly complete sequences of approximately 1,500 bases were obtained for putative new species. About 60% of the clones fell into 132 known species, 70 of which were identified from multiple subjects. About 40% of the clones were novel phylotypes. Of the 215 novel phylotypes, 75 were identified from multiple subjects. Known putative periodontal pathogens such as Porphyromonas gingivalis, Bacteroides forsythus, and Treponema denticola were identified from multiple subjects, but typically as a minor component of the plaque as seen in cultivable studies. Several phylotypes fell into two recently described phyla previously associated with extreme natural environments, for which there are no cultivable species. A number of species or phylotypes were found only in subjects with disease, and a few were found only in healthy subjects. The organisms identified only from diseased sites deserve further study as potential pathogens. Based on the sequence data in this study, the predominant subgingival microbial community consisted of 347 species or phylotypes that fall into 9 bacterial phyla. Based on the 347 species seen in our sample of 2,522 clones, we estimate that there are 68 additional unseen species, for a total estimate of 415 species in the subgingival plaque. When organisms found on other oral surfaces such as the cheek, tongue, and teeth are added to this number, the best estimate of the total species diversity in the oral cavity is approximately 500 species, as previously proposed. |
| URL: |
21264390 |
|
| Ref #: |
12703 |
| Author(s): |
Conrads,G.;Claros,M.C.;Citron,D.M.;Tyrrell,K.L.;Merriam,V.;Goldstein,E.J. |
| Journal: |
Int J Syst Evol Microbiol |
| Title: |
16S-23S rDNA internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Fusobacterium |
| Volume: |
52 |
| Page(s): |
493-9 |
| Year: |
2002 |
| Keyword(s): |
GENBANK/AF342829
GENBANK/AF342830
GENBANK/AF342831
GENBANK/AF342832
GENBANK/AF342833
GENBANK/AF342834
GENBANK/AF342835
GENBANK/AF342836
GENBANK/AF342837
GENBANK/AF342838
GENBANK/AF342839
GENBANK/AF342840
GENBANK/AF342841
GENBANK/AF342842
GENBANK/AF342843
GENBANK/AF342844
GENBANK/AF342845
GENBANK/AF342846
GENBANK/AF342847
GENBANK/AF342848
GENBANK/AF342849
GENBANK/AF342850
GENBANK/AF342851
GENBANK/AF342852
GENBANK/AF342853
GENBANK/AF342854
GENBANK/AF342855
GENBANK/AF342856
GENBANK/AF342857
GENBANK/AF342858
GENBANK/AF342859
GENBANK/AF342860
GENBANK/AF342861
Base Sequence
DNA Primers
DNA, Ribosomal Spacer/*genetics
Fusobacterium/*classification/genetics
Molecular Sequence Data
Phylogeny
RNA, Ribosomal, 16S/chemistry
RNA, Ribosomal, 23S/chemistry
Species Specificity
Support, Non-U.S. Gov't
|
| Remarks: |
The 16S-23S rDNA internal transcribed spacer (ITS) regions of all currently defined Fusobacterium species and related taxa such as Leptotrichia buccalis, Sebaldella termitidis and Streptobacillus moniliformans, were analysed to examine inter- and intraspecies as well as subspecies relationships. For the ITS-amplification, a new eubacterial universal primer pair was designed and used. The majority of the Fusobacterium strains, along with L. buccalis showed one major, and two to three weaker, distinct bands (short and long versions) with lengths of 800-830 bp and 1000-1100 bp. Nevertheless, six other patterns were also found within the genus Fusobacterium, demonstrating its heterogeneity. The ITS region was sequenced and found to consist both of conserved motifs, which functioned as a framework for alignment, and of variable sites, which provided high phylogenetic resolution. Analyses of the ITS-DNA sequences and ITS relative length (short version) allowed species and subspecies differentiation in most cases. The results confirmed the strikingly distant relationship between Fusobacterium prausnitzii and the genus Fusobacterium. Fusobacterium nucleatum subspecies, along with Fusobacterium naviforme, Fusobacterium simiae and Fusobacterium periodonticum, formed a cluster with an inherently high potential for diversification. Other clusters were formed by Fusobacterium necrophorum subspecies with Fusobacterium gonidaformans and by Fusobacterium varium with Fusobacterium mortiferum and Fusobacterium ulcerans. Fusobacterium russii as well as Fusobacterium perfoetens formed separate branches. Fusobacterium necrophorum subspp. necrophorum and funduliforme on the one hand, and Fusobacterium varium and Fusobacterium mortiferum on the other, were found to be very similar, even at the high-resolution ITS level. |
| URL: |
21928123 |
|
| Ref #: |
12904 |
| Author(s): |
Brune,A.;Evers,S.;Kaim,G.;Ludwig,W.;Schink,B. |
| Journal: |
Int J Syst Evol Microbiol |
| Title: |
Ilyobacter insuetus sp. nov., a fermentative bacterium specialized in the degradation of hydroaromatic compounds |
| Volume: |
52 |
| Page(s): |
429-32 |
| Year: |
2002 |
| Keyword(s): |
GENBANK/AJ307976
GENBANK/AJ307980
Biodegradation
DNA, Bacterial/chemistry
DNA, Ribosomal/chemistry
Fermentation
Gram-Negative Aerobic Rods and Cocci/*classification/genetics/metabolism
Molecular Sequence Data
Phylogeny
Quinic Acid/metabolism
RNA, Ribosomal, 16S/chemistry
RNA, Ribosomal, 23S/chemistry
Sequence Analysis, DNA
Shikimic Acid/metabolism
Support, Non-U.S. Gov't
|
| Remarks: |
The mesophilic, anaerobic bacterium strain VenChi2T was isolated with quinic acid (1,3,4,5-tetrahydroxy-cyclohexane-1-carboxylic acid) as the sole source of carbon and energy. Of more than 30 substrates tested, only quinic acid and shikimic acid (3,4,5-trihydroxy-1-cyclohexene-1-carboxylic acid) were utilized, yielding acetate, propionate, butyrate, H2 and CO2 as fermentation products. Sugars, alcohols, (di-)carboxylic acids, amino acids and aromatic compounds were not fermented and no external electron acceptors were used. Strain VenChi2T is a gram-negative, strictly anaerobic, coccoid rod; it does not employ the classical hydroaromatic pathway of aerobic bacteria for the degradation of hydroaromatic compounds (no aromatic intermediates involved). Comparative 16S and 23S rDNA sequence analyses placed strain VenChi2T in the fusobacteria phylum, with the closest relatives among species of the genera Ilyobacter and Propionigenium. The results indicate that, disregarding the taxonomically misplaced Ilyobacter delafieldii, which is a member of the clostridia, the validly described Ilyobacter and Propionigenium species are phylogenetically intermixed. Based on its phenotypic properties, strain VenChi2T (= DSM 6831T = ATCC BAA-291T) is assigned to the genus Ilyobacter as the type strain of a novel species, Ilyobacter insuetus sp. nov. |
| URL: |
21928114 |
|
| Ref #: |
1355 |
| Author(s): |
Kato,K.;Umemoto,T.;Sagawa,H.;Kotani,S. |
| Journal: |
Curr. Microbiol. |
| Title: |
Lanthionine as an essential constituent of cell wall peptidoglycan of Fusobacterium nucleatum. |
| Volume: |
3 |
| Page(s): |
147-152 |
| Year: |
1979 |
|
| Ref #: |
3893 |
| Author(s): |
Dzink,J.L.;Sheenan,M.T.;Socransky,S.S. |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
Proposal of three subspecies of Fusobacterium nucleatum Knorr 1922: Fusobacterium nucleatum subsp. nucleatum subsp. nov., comb. nov.; Fusobacterium nucleatum subsp. polymorphum subsp. nov., nom. rev., comb. nov.; and Fusobacterium nucleatum subsp. vincen |
| Volume: |
40 |
| Page(s): |
74-78 |
| Year: |
1990 |
|
| Ref #: |
6924 |
| Author(s): |
DeutschesInstitutfürNormungDIN.NormenausschußMedizin(NAMed) |
| Title: |
DIN 58959-7. Qualitätsmanagement in der medizinischen Mikrobiologie. Teil 7: Allgemeine Anforderungen an das Mitführen von Kontrollstämmen. Beiblatt 2: ATCC- und DSM-Nummern häufig verwendeter Kontrollstämme. |
| Year: |
1997 |
|
|
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