Reclassification of Bacteroides levii (Holdeman, Cato, and Moore) in the Genus Porphyromonas, as Porphyromonas levii comb. nov.

Shah, Haroun N.; Collins, Matthew D.; Olsen, Ingar; Paster, Bruce J.; Dewhirst, Floyd E.

doi:10.1099/00207713-45-3-586

Cited by 26 publications

(12 citation statements)

References 37 publications

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“…More detailed analyses were then restricted to species representative of the five clusters previously described in this phylum (18). The genera Prevotella, Bacteroides, and Porphyromonas formed three distinct robust monophyletic units, a result in agreement with those of all previous studies (7,15,18,19,(31)(32)(33)(34)38). The genus Porphyromonas appeared as a sister group to the other two genera.…”

Section: Resultssupporting

confidence: 71%

A recent fixation of cfiA genes in a monophyletic cluster of Bacteroides fragilis is correlated with the presence of multiple insertion elements

et al. 1996

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Small-subunit ribosomal DNA sequences of 16 strains of Bacteroides fragilis were determined and compared with previously published sequences. Three phylogenetic methods (the neighbor-joining, maximum-likelihood, and maximum-parsimony methods) as well as a bootstrap analysis were used to assess the robustness of each topology. All phylogenetic analyses demonstrated that the B. fragilis strains were clearly divided into two robust monophyletic units which corresponded to the cfiA-negative and cfiA-positive groups. Strains of two previously identified DNA homology groups separated similarly into these two monophyletic units. According to the intensity of the hybridization signal with a cfiA probe, the cfiA-positive cluster could be further divided into two groups. This difference might reflect the existence of two, probably closely related cfiA-type genes. In the strongly hybridizing cfiA-positive strains, the gene is capable of conferring high-level resistance to the carbapenems and to most ␤-lactamase inhibitors as well, while in the weakly hybridizing cfiA-positive strains, only the latter type of resistance is known to occur. The presence of the cfiA-type genes within a monophyletic cluster of B. fragilis that apparently represents only a minority of the species B. fragilis is suggestive of a recent acquisition. The fact that this cluster is also the predominant pool of all known B. fragilis insertion elements, which have been found to play an important role in the expression of carbapenem resistance, raises the possibility that both genetic determinants, i.e., the resistance gene(s) and insertion elements, may have coevolved.Bacteroides fragilis, the anaerobic bacterial species most frequently isolated from human infections (3, 4), shows little phenotypic variability but can nevertheless be assigned to different genotypic groups (11,22). DNA homology studies led to the distinction of two homology groups, called I and II (11). DNA relatedness between B. fragilis ATCC 25285 T , representative of homology group I, and strains of homology group II ranged from 64 to 72%, while intragroup relatedness ranged from 80 to 90% (11). About 80% of B. fragilis strains isolated in clinical studies can be assigned to homology group I (11). Although strains from homology groups I and II are phenotypically indistinguishable (12), strains of homology group II lack susceptibility to the synergistic effect of such ␤-lactamase inhibitors as clavulanic acid, sulbactam, and tazobactam (2, 40), which are potent inhibitors of the vast majority of the ␤-lactamases produced by clinical isolates of B. fragilis (3,4,10,20,40). These are active-site serine enzymes, loosely related to those of Ambler's class A (1, 17, 28). Probing with cfiA gene sequences led to the distinction within B. fragilis of the cfiAnegative and cfiA-positive groups, representing ca. 3 and 97%, respectively, of the clinical B. fragilis isolates (22, 23). The cfiA gene, which has been searched for only in B. fragilis, encodes a metallo-␤-lactamase (5, 21, 25, 37), i.e...

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Section: Resultssupporting

confidence: 71%

A recent fixation of cfiA genes in a monophyletic cluster of Bacteroides fragilis is correlated with the presence of multiple insertion elements

et al. 1996

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“…The description is as given by Shah et al (1995) with the following restriction. The genomic G+C content of the type strain is 45.7%.…”

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of Bacteroidetes

et al. 2016

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The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

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“…The 16S rRNA sequence similarity and DN〈-DNA hybridization results were consistent with the PLLO belonging to the Porphyromonas genus, which was also supported by the biochemical data. Our biochemical characterization of PLLO showed that it was phenotypically similar to P. levii (19). The PLLO produced pigmented colonies on blood agar and were sensitive to the special-potency vancomycin disk and produced complex metabolic end product profiles that included acetic, propionic, isobutyric, butyric, and isovaleric acids; the major cellular fatty acid was iso-C 15:0 , similar to the Porphyromonas genus (10,19).…”

Section: P Levii Was Originally Included In the Genusmentioning

confidence: 92%

“…Bacteroides, but biochemical and 16S rRNA sequence studies indicated that it belongs in the genus Porphyromonas (19). A 98% 16S rRNA sequence similarity is generally accepted as an indication of the same species (20), and in DN〈-DNA hybridization studies, a threshold of 70% or greater similarity indicates relationship at the species level (22).…”

Section: P Levii Was Originally Included In the Genusmentioning

confidence: 99%

See 1 more Smart Citation

Porphyromonas somerae sp. nov., a Pathogen Isolated from Humans and Distinct from Porphyromonas levii

Summanen¹,

Durmaz

Väisänen

et al. 2005

J Clin Microbiol

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Porphyromonas levii is an anaerobic, pigmented gram-negative bacillus originally isolated from bovine rumen. We describe 58 human clinical strains of P. levii-like organisms, isolated from various human clinical specimens that are phenotypically similar to the type strain of P. levii, a rumen isolate (ATCC 29147). Our biochemical, comparative 16S rRNA sequence analyses, and DN〈-DNA relatedness studies indicate that the human P. levii-like organisms are similar to each other but genetically different from the P. levii type strain isolated from bovine rumen. We therefore propose the name Porphyromonas somerae to encompass the human P. levii-like organisms. P. somerae was predominantly isolated from patients with chronic skin and soft tissue or bone infections, especially in the lower extremities.

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Reclassification of Bacteroides levii (Holdeman, Cato, and Moore) in the Genus Porphyromonas, as Porphyromonas levii comb. nov.

Cited by 26 publications

References 37 publications

A recent fixation of cfiA genes in a monophyletic cluster of Bacteroides fragilis is correlated with the presence of multiple insertion elements

A recent fixation of cfiA genes in a monophyletic cluster of Bacteroides fragilis is correlated with the presence of multiple insertion elements

Genome-Based Taxonomic Classification of Bacteroidetes

Porphyromonas somerae sp. nov., a Pathogen Isolated from Humans and Distinct from Porphyromonas levii

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