| Extended Bibliography: |
Show bibliography
| Ref #: |
15329 |
| Author(s): |
Rainey,F.A.;Lang,E.;Stackebrandt,E. |
| Journal: |
FEMS Microbiol Lett |
| Title: |
The phylogenetic structure of the genus Acinetobacter |
| Volume: |
124 |
| Page(s): |
349-53 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/X81657
GENBANK/X81658
GENBANK/X81659
GENBANK/X81660
GENBANK/X81661
GENBANK/X81662
GENBANK/X81663
GENBANK/X81664
GENBANK/X81665
GENBANK/X81666
GENBANK/X81667
GENBANK/X81668
Acinetobacter/*classification/genetics
DNA, Ribosomal/*genetics
Molecular Sequence Data
Phylogeny
Sequence Analysis, DNA
|
| Remarks: |
16S rDNA sequence analysis was performed on the type strains of all validly described Acinetobacter species and five unnamed Acinetobacter strains. The phylogenetic analyses confirm that Acinetobacter is a coherent genus within the gamma subclass of Proteobacteria and that the species are phylogenetically well defined. A. calcoaceticus, A. lwoffii, A. johnsonii and A. haemolyticus form one cluster of closely related species, the pair A. junii and A. baumannii forms a second cluster. A. radioresistens stands phylogenetically isolated. The study reveals that three undescribed strains can be assigned to individually described species, while strains DSM 30009 and DSM 590 may represent two novel Acinetobacter species. |
| URL: |
7851741 |
|
| Ref #: |
15318 |
| Author(s): |
Yamamoto,S.;Harayama,S. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Phylogenetic analysis of Acinetobacter strains based on the nucleotide sequences of gyrB genes and on the amino acid sequences of their products |
| Volume: |
46 |
| Page(s): |
506-11 |
| Year: |
1996 |
| Keyword(s): |
GENBANK/D73412
GENBANK/D73413
GENBANK/D73414
GENBANK/D73415
GENBANK/D73416
GENBANK/D73417
GENBANK/D73418
GENBANK/D73419
GENBANK/D73420
GENBANK/D73421
GENBANK/D73422
GENBANK/D73423
GENBANK/D73424
GENBANK/D73425
GENBANK/D73426
GENBANK/D73427
GENBANK/D73428
GENBANK/D73429
GENBANK/D73430
GENBANK/D73431
GENBANK/D73432
GENBANK/D73433
GENBANK/D73434
GENBANK/D73435
GENBANK/D73436
GENBANK/D73437
GENBANK/D73438
GENBANK/D73439
GENBANK/D73440
GENBANK/D73441
Acinetobacter/classification/*genetics
Amino Acid Sequence
Bacterial Proteins/genetics
DNA Gyrase
DNA Topoisomerases, Type II/*genetics
Genes, Bacterial
Molecular Sequence Data
Phylogeny
|
| Remarks: |
Partial nucleotide sequences of the gyrB genes (DNA gyrase B subunit genes) of 15 Acinetobacter strains, including the type and reference strains of genomic species 1 to 12 (A. calcoaceticus [genomic species 1], A. baumannii [genomic species 2], Acinetobacter genomic species 3, A. haemolyticus [genomic species 4], A. junii [genomic species 5], Acinetobacter genomic species 6, A. johnsonii [genomic species 7], A. lwoffii [genomic species 8], Acinetobacter genomic species 9, Acinetobacter genomic species 10, Acinetobacter genomic species 11, and A. radioresistens [genomic species 12]), were determined by sequencing the PCR-amplified fragments of gyrB. The gyrB sequence homology among these Acinetobacter strains ranged from 69.6 to 99.7%. A phylogenetic analysis, using the gyrB sequences, indicates that genomic species 1, 2, and 3 formed one cluster (87.3 to 90.3% identity), while genomic species 8 and 9 formed another cluster (99.7% identity). These results are consistent with those of DNA-DNA hybridization and of biochemical systematics. On the other hand, the topology of the published phylogenetic tree based on the 16S rRNA sequences of the Acinetobacter strains was quite different from that of the gyrB-based tree. The numbers of substitution in the 16S rRNA gene sequences were not high enough to construct a reliable phylogenetic tree. The gyrB-based analysis indicates that the genus Acinetobacter is highly diverse and that a reclassification of this genus would be required. |
| URL: |
8934907 |
|
| Ref #: |
15405 |
| Author(s): |
Yamamoto,S.;Bouvet,P.J.;Harayama,S. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization |
| Volume: |
49 Pt 1 |
| Page(s): |
87-95 |
| Year: |
1999 |
| Keyword(s): |
GENBANK/AB008684
GENBANK/AB008685
GENBANK/AB008686
GENBANK/AB008687
GENBANK/AB008688
GENBANK/AB008689
GENBANK/AB008690
GENBANK/AB008691
GENBANK/AB008692
GENBANK/AB008693
GENBANK/AB008694
GENBANK/AB008695
GENBANK/AB008696
GENBANK/AB008697
GENBANK/AB008698
GENBANK/AB008699
GENBANK/AB008700
GENBANK/AB008701
GENBANK/AB008702
GENBANK/AB008703
GENBANK/AB008704
GENBANK/AB008705
GENBANK/AB008706
GENBANK/AB008707
GENBANK/AB008708
GENBANK/AB008709
GENBANK/AB008710
GENBANK/AB008711
GENBANK/AB008712
GENBANK/AB008713
Acinetobacter/*classification/genetics
Base Sequence
DNA Gyrase
DNA Topoisomerases, Type II/*genetics
DNA, Bacterial/*analysis
Molecular Sequence Data
*Nucleic Acid Hybridization
Phylogeny
RNA, Ribosomal, 16S/chemistry
|
| Remarks: |
The phylogenetic relationships of 49 Acinetobacter strains, 46 of which have previously been classified into 18 genomic species by DNA-DNA hybridization studies, were investigated using the nucleotide sequence of gyrB, the structural gene for the DNA gyrase B subunit. The phylogenetic tree showed linkages between genomic species 1 (Acinetobacter calcoaceticus), 2 (Acinetobacter baumannii), 3 and TU13; genomic species 6, BJ15, BJ16 and BJ17; genomic species 5, BJ13 (synonym of TU14) and BJ14; genomic species 7 (Acinetobacter johnsonii), 10 and 11; and genomic species 8 and 9. The phylogenetic grouping of Acinetobacter strains based on gyrB genes was almost congruent with that based on DNA-DNA hybridization studies. Consequently, gyrB sequence comparison can be used to resolve the taxonomic positions of bacterial strains at the level of genomic species. However, minor discrepancies existed in the grouping of strains of genomic species 8, 9 and BJ17. The phylogenetic tree for these strains was reconstructed from the sequence of rpoD, the structural gene for the RNA polymerase sigma 70 factor. The latter tree was 100% congruent with the grouping based on DNA-DNA hybridization. The reliability of DNA-DNA hybridization may be superior to that of sequence comparison of a single protein-encoding gene in resolving closely related organisms since the former method measures the homologies between the nucleotide sequences of total genomic DNAs. Three strains that have not been characterized previously by DNA-DNA hybridization seem to belong to two new genomic species, one including strain ATCC 33308 and the other including strains ATCC 31012 and MBIC 1332. |
| URL: |
10028249 |
|
| Ref #: |
95501 |
| Author(s): |
Jaspers,E.;Nauhaus,K.;Cypionka,H.;Overmann,J. |
| Journal: |
FEMS Microbiol Ecol |
| Title: |
Multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton |
| Volume: |
36 |
| Page(s): |
153-164 |
| Year: |
2001 |
| Remarks: |
The diversity of cultured planktonic bacteria was analyzed. Bacterial strains were isolated from a eutrophic lake (Zwischenahner Meer, Niedersachsen, Germany) at three different sampling dates (October 1997, April and May 1998). Phylogenetic diversity was assessed by polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and sequencing of 16S rRNA gene fragments. Enterobacterial repetitive intergenic consensus (ERIC)-PCR revealed a high genomic diversity within the strain collections, which exceeded the diversity of the 16S rRNA gene sequences considerably. The composition of each of the three strain collections was unique since strains isolated at different dates always exhibited different ERIC-PCR fingerprints. Growth tests with 59 different carbon substrates demonstrated that even strains with identical ERIC-PCR fingerprints, isolated on one sampling date, differed in their physiology. The culturable fraction investigated in the present study constituted a relatively small fraction (</=15%) of the whole bacterioplankton assemblage. Nevertheless, the high physiological diversity in this fraction already indicates that a multitude of different ecological niches must exist in the planktonic environment. The majority of strains isolated in April prior to the decay of the phytoplankton bloom were members of the Cytophaga-Flavobacterium group. One month later, not a single strain of this group could be isolated. When a group-specific PCR-DGGE technique was employed, rapid shifts in the diversity of non-cultured Cytophaga-Flavobacteria also became evident. Based on the rapid shifts in the composition of cultivated as well as some non-cultivated bacteria, the ecological niches in the planktonic habitat must undergo rapid temporal changes. |
| URL: |
11451519 |
|
| Ref #: |
15314 |
| Author(s): |
Ibrahim,A.;Gerner-Smidt,P.;Liesack,W. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Phylogenetic relationship of the twenty-one DNA groups of the genus Acinetobacter as revealed by 16S ribosomal DNA sequence analysis |
| Volume: |
47 |
| Page(s): |
837-41 |
| Year: |
1997 |
| Keyword(s): |
GENBANK/Z93434
GENBANK/Z93435
GENBANK/Z93436
GENBANK/Z93437
GENBANK/Z93438
GENBANK/Z93439
GENBANK/Z93440
GENBANK/Z93441
GENBANK/Z93442
GENBANK/Z93443
GENBANK/Z93444
GENBANK/Z93445
GENBANK/Z93446
GENBANK/Z93447
GENBANK/Z93448
GENBANK/Z93449
GENBANK/Z93450
GENBANK/Z93451
GENBANK/Z93452
GENBANK/Z93453
GENBANK/Z93454
Acinetobacter/*classification/*genetics
DNA Primers
DNA, Bacterial/analysis
DNA, Ribosomal/*analysis
Molecular Sequence Data
Nucleic Acid Hybridization
*Phylogeny
Polymerase Chain Reaction
Sequence Analysis, DNA
|
| Remarks: |
The inter- and intrageneric relationships of members of the genus Acinetobacter were investigated by performing a comparative sequence analysis of PCR-amplified 16S ribosomal DNAs (rDNAs) from 21 strains representing all of the DNA groups that have been described. Phylogenetic treeing confirmed that Acinetobacter spp. form a coherent cluster within the gamma subdivision of the class Proteobacteria that includes strains with overall levels of 16S rDNA sequence similarity of more than 94%. The analysis of intrageneric relationships suggested that the majority of the strains cluster in five clearly distinguishable clusters, and this conclusion was supported by the results obtained with the different methods used for phylogenetic analysis (i.e., the maximum-likelihood, parsimony, and distance matrix methods). The first cluster contains the representatives of DNA groups 2 (Acinetobacter baumannii) and TU13, whereas the second cluster comprises representatives of DNA groups 3, "Close To TU13," and "between 1 and 3." The representatives of closely related Acinetobacter DNA groups 8 (Acinetobacter twoffii) and 9 belong to the third cluster, which includes the representative of DNA group 6 as well. The fourth cluster is formed by DNA groups BJ15, BJ16, and BJ17, and the fifth cluster comprises DNA groups 1 (Acinetobacter calcoaceticus), BJ14, 10, and 11. Within the fifth cluster the 16S rDNA sequences of DNA group 10 and 11 strains are nearly identical. The representatives of DNA groups 4 (Acinetobacter haemolyticus), 5 (Acinetobacter junii), 7 (Acinetobacter johnsonii), 12 (Acinetobacter radioresistens), TU14, and TU15 form individual branches that are not significantly affiliated with any of the five clusters identified. Apart from the clustering of the most closely related DNA groups, the general topology of the distance dendrogram revealed some discrepancy with previous DNA-DNA hybridization data, which may point to the inadequacy of comparative 16S rDNA sequence analysis for reflecting true evolutionary relationships of closely related bacterial taxa. Important, however, was the presence of unique sequence motifs in each of the 21 different DNA groups studied, which may be useful for rapid differentiation of DNA groups of the genus Acinetobacter. |
| URL: |
9226915 |
|
| Ref #: |
15172 |
| Author(s): |
La Scola,B.;Gundi,V.A.;Khamis,A.;Raoult,D. |
| Journal: |
J Clin Microbiol |
| Title: |
Sequencing of the rpoB gene and flanking spacers for molecular identification of Acinetobacter species |
| Volume: |
44 |
| Page(s): |
827-32 |
| Year: |
2006 |
| Keyword(s): |
GENBANK/DQ207407
GENBANK/DQ207408
GENBANK/DQ207409
GENBANK/DQ207410
GENBANK/DQ207411
GENBANK/DQ207412
GENBANK/DQ207413
GENBANK/DQ207414
GENBANK/DQ207415
GENBANK/DQ207416
GENBANK/DQ207417
GENBANK/DQ207418
GENBANK/DQ207419
GENBANK/DQ207420
GENBANK/DQ207421
GENBANK/DQ207422
GENBANK/DQ207423
GENBANK/DQ207424
GENBANK/DQ207425
GENBANK/DQ207426
GENBANK/DQ207427
GENBANK/DQ207428
GENBANK/DQ207429
GENBANK/DQ207430
GENBANK/DQ207471
GENBANK/DQ207472
GENBANK/DQ207473
GENBANK/DQ207474
GENBANK/DQ207475
GENBANK/DQ207476
GENBANK/DQ207477
GENBANK/DQ207478
GENBANK/DQ207479
GENBANK/DQ207480
GENBANK/DQ207481
GENBANK/DQ207482
GENBANK/DQ207483
GENBANK/DQ207484
GENBANK/DQ207485
GENBANK/DQ207486
GENBANK/DQ207487
GENBANK/DQ207488
GENBANK/DQ207489
GENBANK/DQ207490
GENBANK/DQ207491
GENBANK/DQ207492
GENBANK/DQ207493
GENBANK/DQ207494
GENBANK/DQ207495
GENBANK/DQ207496
GENBANK/DQ207497
GENBANK/DQ207498
GENBANK/DQ207499
GENBANK/DQ207500
GENBANK/DQ207501
GENBANK/DQ207502
GENBANK/DQ207503
GENBANK/DQ207504
GENBANK/DQ207505
GENBANK/DQ207506
GENBANK/DQ207507
GENBANK/DQ207508
GENBANK/DQ207509
GENBANK/DQ207510
GENBANK/DQ207511
GENBANK/DQ207512
GENBANK/DQ207513
GENBANK/DQ207514
GENBANK/DQ207515
GENBANK/DQ207516
GENBANK/DQ207517
GENBANK/DQ231239
Acinetobacter/*classification/enzymology/*genetics/isolation &
purification
Animals
Base Sequence
DNA, Bacterial/genetics
DNA, Intergenic/genetics
DNA-Directed RNA Polymerases/*genetics
*Genes, Bacterial
Humans
Molecular Sequence Data
Phylogeny
Species Specificity
|
| Remarks: |
Acinetobacter species are defined on the basis of several phenotypic characters, results of DNA-DNA homology, and more recently, similarities or dissimilarities in 16S rRNA gene sequences. However, the 16S rRNA gene is not polymorphic enough to clearly distinguish all Acinetobacter species. We used an RNA polymerase beta-subunit gene (rpoB)-based identification scheme for the delineation of species within the genus Acinetobacter, and towards that end, we determined the complete rpoB gene and flanking spacer (rplL-rpoB and rpoB-rpoC) sequences of the 17 reference strains of Acinetobacter species and 7 unnamed genomospecies. By using complete gene sequences (4,089 bp), we clearly separated all species and grouped them into different clusters. A phylogenetic tree constructed using these sequences was supported by bootstrap values higher than those obtained with 16S rRNA or the gyrB or recA gene. Four pairs of primers enabled us to amplify and sequence two highly polymorphic partial sequences (350 and 450 bp) of the rpoB gene. These and flanking spacers were designed and tested for rapid identification of the 17 reference strains of Acinetobacter species and 7 unnamed genomospecies. Each of these four variable sequences enabled us to delineate most species. Sequences of at least two polymorphic sequences should be used to distinguish Acinetobacter grimontii, Acinetobacter junii, Acinetobacter baylyi, and genomic species 9 from one another. Finally, 21 clinical isolates of Acinetobacter baumannii were tested for intraspecies relationships and assigned correctly to the same species by comparing the partial sequences of the rpoB gene and its flanking spacers. |
| URL: |
16517861 |
|
| Ref #: |
11981 |
| Author(s): |
Rainey,F.A.;Lang,E.;Stackebrandt,E. |
| Journal: |
FEMS Microbiol Lett |
| Title: |
The phylogenetic structure of the genus Acinetobacter |
| Volume: |
124 |
| Page(s): |
349-53 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/X81657
GENBANK/X81658
GENBANK/X81659
GENBANK/X81660
GENBANK/X81661
GENBANK/X81662
GENBANK/X81663
GENBANK/X81664
GENBANK/X81665
GENBANK/X81666
GENBANK/X81667
GENBANK/X81668
Acinetobacter/*classification/genetics
DNA, Ribosomal/*genetics
Molecular Sequence Data
Phylogeny
Sequence Analysis, DNA
|
| Remarks: |
16S rDNA sequence analysis was performed on the type strains of all validly described Acinetobacter species and five unnamed Acinetobacter strains. The phylogenetic analyses confirm that Acinetobacter is a coherent genus within the gamma subclass of Proteobacteria and that the species are phylogenetically well defined. A. calcoaceticus, A. lwoffii, A. johnsonii and A. haemolyticus form one cluster of closely related species, the pair A. junii and A. baumannii forms a second cluster. A. radioresistens stands phylogenetically isolated. The study reveals that three undescribed strains can be assigned to individually described species, while strains DSM 30009 and DSM 590 may represent two novel Acinetobacter species. |
| URL: |
95154670 |
|
| Ref #: |
12052 |
| Author(s): |
La Scola,B.;Barrassi,L.;Raoult,D. |
| Journal: |
FEMS Microbiol Ecol |
| Title: |
Isolation of new fastidious alpha Proteobacteria and Afipia felis from hospital water supplies by direct plating and amoebal co-culture procedures |
| Volume: |
34 |
| Page(s): |
129-137 |
| Year: |
2000 |
| Remarks: |
As water is a source of nosocomial infections in hospitals, the presence of fastidious Gram-negative bacteria in water samples taken in a university hospital was investigated. Water samples were inoculated onto agar plates and into amoebal microplates for co-culture. Sixty-eight alpha proteobacteria isolates were obtained and characterized using phenotypic methods and 16S rRNA gene sequence comparison. The latter approach divided the strains into seven clusters. Of these, one corresponded to previously recognized Afipia felis and it is likely that six were closely related new species. As these bacteria are fastidious and can not be cultivated on standard microbiological media, their possible role in hospital-acquired human infections should be investigated. |
| URL: |
0 |
|
| Ref #: |
11979 |
| Author(s): |
Ibrahim,A.;Gerner-Smidt,P.;Liesack,W. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Phylogenetic relationship of the twenty-one DNA groups of the genus Acinetobacter as revealed by 16S ribosomal DNA sequence analysis |
| Volume: |
47 |
| Page(s): |
837-41 |
| Year: |
1997 |
| Keyword(s): |
GENBANK/Z93434
GENBANK/Z93435
GENBANK/Z93436
GENBANK/Z93437
GENBANK/Z93438
GENBANK/Z93439
GENBANK/Z93440
GENBANK/Z93441
GENBANK/Z93442
GENBANK/Z93443
GENBANK/Z93444
GENBANK/Z93445
GENBANK/Z93446
GENBANK/Z93447
GENBANK/Z93448
GENBANK/Z93449
GENBANK/Z93450
GENBANK/Z93451
GENBANK/Z93452
GENBANK/Z93453
GENBANK/Z93454
Acinetobacter/*classification/*genetics
DNA Primers
DNA, Bacterial/analysis
DNA, Ribosomal/*analysis
Molecular Sequence Data
Nucleic Acid Hybridization
*Phylogeny
Polymerase Chain Reaction
Sequence Analysis, DNA
|
| Remarks: |
The inter- and intrageneric relationships of members of the genus Acinetobacter were investigated by performing a comparative sequence analysis of PCR-amplified 16S ribosomal DNAs (rDNAs) from 21 strains representing all of the DNA groups that have been described. Phylogenetic treeing confirmed that Acinetobacter spp. form a coherent cluster within the gamma subdivision of the class Proteobacteria that includes strains with overall levels of 16S rDNA sequence similarity of more than 94%. The analysis of intrageneric relationships suggested that the majority of the strains cluster in five clearly distinguishable clusters, and this conclusion was supported by the results obtained with the different methods used for phylogenetic analysis (i.e., the maximum-likelihood, parsimony, and distance matrix methods). The first cluster contains the representatives of DNA groups 2 (Acinetobacter baumannii) and TU13, whereas the second cluster comprises representatives of DNA groups 3, "Close To TU13," and "between 1 and 3." The representatives of closely related Acinetobacter DNA groups 8 (Acinetobacter twoffii) and 9 belong to the third cluster, which includes the representative of DNA group 6 as well. The fourth cluster is formed by DNA groups BJ15, BJ16, and BJ17, and the fifth cluster comprises DNA groups 1 (Acinetobacter calcoaceticus), BJ14, 10, and 11. Within the fifth cluster the 16S rDNA sequences of DNA group 10 and 11 strains are nearly identical. The representatives of DNA groups 4 (Acinetobacter haemolyticus), 5 (Acinetobacter junii), 7 (Acinetobacter johnsonii), 12 (Acinetobacter radioresistens), TU14, and TU15 form individual branches that are not significantly affiliated with any of the five clusters identified. Apart from the clustering of the most closely related DNA groups, the general topology of the distance dendrogram revealed some discrepancy with previous DNA-DNA hybridization data, which may point to the inadequacy of comparative 16S rDNA sequence analysis for reflecting true evolutionary relationships of closely related bacterial taxa. Important, however, was the presence of unique sequence motifs in each of the 21 different DNA groups studied, which may be useful for rapid differentiation of DNA groups of the genus Acinetobacter. |
| URL: |
97370609 |
|
| Ref #: |
4025 |
| Author(s): |
Bouvet,P.J.M.;Grimont,P.A.D. |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
Taxonomy of the genus Acinetobacter with the recognition of Acinetobacter baumannii sp. nov., Acinetobacter haemolyticus sp. nov., Acinetobacter johnsonii sp. nov., and Acinetobacter junii sp. nov., and emended descriptions of Acinetobacter calcoaceticus |
| Volume: |
36 |
| Page(s): |
228-240 |
| Year: |
1986 |
|
| Ref #: |
6586 |
| Author(s): |
Rainey,F.A.;Lang,E.;Stackebrandt,E. |
| Journal: |
FEMS Microbiol. Lett. |
| Title: |
The phylogenetic structure of the genus Acinetobacter. |
| Volume: |
124 |
| Page(s): |
349-354 |
| Year: |
1994 |
|
|
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