Porphyromonas macacae comb. nov., a Consequence of Bacteroides macacae Being a Senior Synonym of Porphyromonas salivosa

Love, Daria N.

doi:10.1099/00207713-45-1-90

Cited by 32 publications

(14 citation statements)

References 11 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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“…Of the others, P. asaccharolytica is found at human nonoral sites (3); P. canis, P. cansulci, P. canoris, and P. cangingivalis are found in dogs (12,22); P. salivosa and P. circumdentaria are found in cats (21); P. macacae is from macaques (3); P. levii is found in cattle (14); and P. gulae is found in a range of animal species (7). Although P. salivosa and P. macacae were originally isolated from cats and macaques, respectively, they have been shown to be the same species; the name P. macacae has precedence (20).…”

Section: Discussionmentioning

confidence: 99%

Culture-Independent Identification of Periodontitis-Associated Porphyromonas and Tannerella Populations by Targeted Molecular Analysis

et al. 2004

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Periodontitis is the commonest bacterial disease of humans and is the major cause of adult tooth loss. About half of the oral microflora is unculturable; and 16S rRNA PCR, cloning, and sequencing techniques have demonstrated the high level of species richness of the oral microflora. In the present study, a PCR primer set specific for the genera Porphyromonas and Tannerella was designed and used to analyze the bacterial populations in subgingival plaque samples from inflamed shallow and deep sites in subjects with periodontitis and shallow sites in age-and sex-matched controls. A total of 308 clones were sequenced and found to belong to one of six Porphyromonas or Tannerella species or phylotypes, one of which, Porphyromonas P3, was novel. Tannerella forsythensis was found in significantly higher proportions in patients than in controls. Porphyromonas catoniae and Tannerella phylotype BU063 appeared to be associated with shallow sites. Targeted culture-independent molecular ecology studies have a valuable role to play in the identification of bacterial targets for further investigations of the pathogenesis of bacterial infections.

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“…For example, symbiotic populations of Rhizobiurn species require a symbiosis plasmid (49), while the nearby rhizosphere populations of the same bacterial spe-On: Sat, 12 May 2018 12:10:53 VOL. 47,1997 DNA SEQUENCE DATA AND BACTERIAL ECOLOGICAL DIVERSITYx cies are best adapted when they lack the plasmid (74). In such cases, a cell lineage can repeatedly adapt to one population's environment and then to another's by gaining or losing a plasmid.…”

Section: Discussionmentioning

confidence: 99%

Discovery and Classification of Ecological Diversity in the Bacterial World: The Role of DNA Sequence Data

Palys

Nakamura

Cohan

1997

International Journal of Systematic Bacteriology

346

312

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All living organisms fall into discrete clusters of closely related individuals on the basis of gene sequence similarity. Evolutionary genetic theory predicts that in the bacterial world, each sequence similarity cluster should correspond to an ecologically distinct population. Indeed, surveys of sequence diversity in proteincoding genes show that sequence clusters correspond to ecological populations. Future population surveys of protein-coding gene sequences can be expected to disclose many previously unknown ecological populations of bacteria. Sequence similarity clustering in protein-coding genes is recommended as a primary criterion for demarcating taxa.For two decades, systematists have applied whole-genome hybridization as a universal criterion for demarcating species of bacteria: systematists have widely recognized bacterial species as phenotypically distinct groups of strains with 70% or greater annealing of genomic fragments in DNA-DNA hybridization (36,85). This criterion has been widely used because it can be easily applied to any taxon, and most importantly, the groupings of bacteria based on DNA-DNA hybridization are often the same as those based on phenotypic characters and ecology (36).However, it is becoming increasingly evident that any particular cut-off value (such as 70%) is arbitrary and not guaranteed to yield groups of bacteria that correspond to real ecological units (82). Also, it is not clear what determines the fraction of genomic segments that anneal in hybridization experiments (82; but see reference 43): is it the fraction of genes that are shared or the sequence similarity at shared gene loci? Accordingly, no evolutionary genetic theory predicts why groups of strains with greater than 70% annealing should correspond to ecologically distinct populations.There is, however, another molecular approach that may provide a universal criterion for classifying bacterial diversity. This approach relies on the observation that all living organisms, both prokaryotic and eukaryotic, fall into clusters of closely related organisms based on the sequence similarity of shared genes (1, 15,48). That is, bacteria and other organisms fall into clearly distinct sequence clusters, where the average sequence divergence between strains of different clusters is far greater than the average divergence between strains of the same cluster. Recent theory has suggested that each sequence similarity cluster observed in the bacterial world might correspond to an ecologically distinct population (14, 15, 17, 18). If this conjecture is correct, then a classification system based on sequence clusters would have a theoretical grounding that is lacking in the genomic hybridization approach.In this study, we will demonstrate that the DNA sequences of protein-coding genes are more effective than DNA-DNA hybridization for classifying the ecological diversity of bacteria. We first extend the theoretical argument of Cohan (14) that

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Porphyromonas macacae comb. nov., a Consequence of Bacteroides macacae Being a Senior Synonym of Porphyromonas salivosa

Cited by 32 publications

References 11 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

Culture-Independent Identification of Periodontitis-Associated Porphyromonas and Tannerella Populations by Targeted Molecular Analysis

Discovery and Classification of Ecological Diversity in the Bacterial World: The Role of DNA Sequence Data

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