Deoxyribonucleic Acid Relatedness Research Articles

Enterobacter gergoviae sp. nov.: a New Species of Enterobacteriaceae Found in Clinical Specimens and the Environment

The name Enterobacter gergoviae sp. nov. is proposed for a group of organisms isolated from various clinical sources in France, Africa, and the United States and from environmental sources. E. gergoviae deoxyribonucleic acid contains 60% guanine plus cytosine. Deoxyribonucleic acid relatedness studies showed E. gergoviae strains to be very highly related, as is characteristic of strains of a single species. The biochemical profiles of E. gergoviae strains were extremely similar. Phenotypically, E. gergoviae belongs to the family Enterobacteriaceae and is most similar to Enterobacter aerogenes. E. gergoviae is distinguishable from E. aerogenes by its positive urea reaction and negative reactions for KCN, sorbitol, mucate, and gelatinase. Strain CIP 76.01 (= ATCC 33028 = CDC 604-77) is the type strain of this new species.

Deoxyribonucleic acid relatedness among species of slowly-growing mycobacteria.

DNA-DNA hybridization is a reliable method for determining the phylogenetic relationship between bacterial strains The hybridization kinetics for DNA from different slowly-growing mycobacteria were measured optically in a spectrophotometer. The results indicate that M. tuberculosis and M. bovis belong to one species. M. avium and M. intracellulare are two species, but some serotypes, now designated M. intracellulare, actually belong to M. avium.

Deoxyribonucleic Acid Relatedness of Strains of Yellow-Pigmented, Group D Streptococci

Deoxyribonucleic acid (DNA) homology was used to examine genetic relatedness among 25 yellow-pigmented strains of group D streptococci and to clarify the possible genetic relatedness of these strains to Streptococcus faecium and Streptococcus faecalis. In all cases, the DNA of the yellow-pigmented strains hybridized with the DNA of S. faecium and S. faecalis at a level of less than 25%. Based on median thermal dissociation temperatures (Tm's) and hybridization tests, the yellow-pigmented strains were divided into two groups (I and II). DNAs of strains in group I had relatively low Tm’s and did not exhibit significant homology with DNA of the herein designated type strain (ATCC 25788) of S. faecium subsp. casseliflavus. The DNAs of group II strains, on the other hand, exhibited high Tm’s and had a high degree of homology with the DNA of the type strain of the above-mentioned subspecies. Three physiological traits were found to be peculiar to group II organisms: ability to grow in the presence of 6.5% sodium chloride, inability to ferment sorbitol, and inability to decarboxylate tyrosine. It is proposed that the group II strains constitute a separate and distinct species. Because the strains presently placed in this species include the type strain of S. faecium subsp. casseliflavus Mundt and Graham, the name of this species, according to the rules of the Bacteriological Code, is Streptococcus casseliflavus (Mundt and Graham) comb. nov.

Classification of the Legionnaires' Disease Bacterium: Legionella pneumophila, genus novum, species nova, of the Family Legionellaceae, familia nova

Deoxyribonucleic acid (DNA) relatedness was used to classify strains of the Legionnaires' disease (LD) bacterium. These DNA comparisons showed that all strains of the LD bacterium were members of the same species. Included were strains isolated from the environment and strains with three different O-antigens. The DNA from the LD bacterium was not significantly related to DNA from any other group of bacteria that was tested. Biochemical data, growth characteristics, and guanine-plus-cytosine ratios were used to rule out the possibility that the LD bacterium was significantly related to members of genera whose DNA was not tested. In view of these data we propose that the LD bacterium be named Legionella pneumophila species nova, the type species of Legionella, genus novum. The type strain of L. pneumophila is Philadelphia 1.

Deoxyribonucleic Acid Relatedness Between Serratia plymuthica and Other Serratia Species, with a Description of Serratia odorifera sp. nov. (Type Strain: ICPB 3995)

Seven new isolates of Serratia plymuthica (including two from a human source) and 24 isolates resembling unclustered Serratia strain 38 (Grimont et al., J. Gen. Microbiol 98:39-66, 1977) are described. Deoxyribonucleic acid relatedness studies, obtained with labeled reference deoxyribonucleic acid from S. plymuthica 392 confirm that S. plymuthica is a discrete species. Mean percent relatedness of S. plymuthica isolates to strain 392 was 88 ± 13.6 (standard deviation), whereas the mean percent relatedness of S. liquefaciens isolates (the closest species) to strain 392 was 52 ± 12.4. Strain 38 and twenty-four “38-like“ isolates constitute a new deoxyribonucleic acid hybridization group that is 28 to 43% related to Serratia species and to the “Citrobacter-like” group of Leclerc and Buttiaux, and 15 to 22% related to other known species of Enterobacteriaceae. This 38-like group constitutes a new species that is named Serratia odorifera sp. nov. (type strain, ICPB 3995). Two biotypes (1 and 2) are described. Strains of this species will grow on caprylate-thallous agar (selective for Serratia spp.), and they have a characteristic odor. Most strains of S. odorifera were recovered from clinical specimens.

Deoxyribonucleic Acid Relatedness of Proteus and Providencia Species

Deoxyribonucleic acid reassociation was used to determine relatedness among protei and providenciae and between these organisms and other members of the family Enterobacteriaceae. The results indicate the following. (i)Proteus mirabilis, Prot. morganii, and Providencia stuartii are homogeneous species. (ii) Prot. vulgaris, Prot. rettgeri, and Prov. alcalifaciens each contain more than one deoxyribonucleic acid relatedness group. (iii) A group of urea-positive strains previously called Prot. rettgeri biogroup 5 are, in fact, members of Prov. stuartii. (iv)Prot. myxofaciens is a valid species. (v) Protei are only distantly related to all other Enterobacteriaceae. Taxonomic revisions consistent with these observations are discussed. These include a proposal to place the currently recognized species of Proteus into one of three genera: The genus Proteus, containing Prot. mirabilis Hauser, Prot. vulgaris Hauser, and Prot. myxofaciens Cosenza and Podgwaite; a separate genus Morganella Fulton, for Prot. morganii (Winslow et al.) Yale; and the genus Providencia containing Prov. alcalifaciens (De Salles Gomes) Ewing, Prov. stuartii (Buttiaux et al.) Ewing, and Prov. rettgeri comb, nov.

Classification of the Legionnaires' disease bacterium: An interim report

Deoxyribonucleic acid (DNA) from strains of the Legionnaires' disease bacterium (LDB) was characterized in order to aid in the proper classification of this organism. The genome size of LDB DNA was estimated at 2.5×109 daltons by reassociation kinetics; a guanine-plus-cytosine content of LDB of 39% was established by optical thermal denaturation and buoyant density ultracentrifugation measurements. DNA relatedness studies on 12 strains of the LDB indicated that they were all members of the same species. DNA relatedness studies have thus far failed to show that the LDB is significantly related to any other organism, including all members of Enterobacteriaceae,Pasteurella multocida, Francisella tularensis, Rochalimaea quintana, Vibrio species,Staphylococcus epidermidis, andFlavobacterium meningosepticum.

Yersinia ruckeri sp. nov., the Redmouth (RM) Bacterium

Cultures of the redmouth (RM) bacterium, one of the etiological agents of redmouth disease in rainbow trout (Salmo gairdneri) and certain other fishes, were characterized by means of their biochemical reactions, by deoxyribonucleic acid (DNA) hybridization, and by determination of guanine-plus-cytosine (G+C) ratios in DNA. The DNA relatedness studies confirmed the fact that the RM bacteria are members of the family Enterobacteriaceae and that they comprise a single species that is not closely related to any other species of Enterobacteriaceae. They are about 30% related to species of both Serratia and Yersinia. A comparison of the biochemical reactions of RM bacteria and serratiae indicated that there are many differences between these organisms and that biochemically the RM bacteria are most closely related to yersiniae. The G+C ratios of RM bacteria were approximated to be between 47.5 and 48.5%. These values are similar to those of yersiniae but markedly different from those of serratiae. On the basis of their biochemical reactions and their G+C ratios, the RM bacteria are considered to be a new species of Yersinia, for which the name Yersinia ruckeri is proposed. Strain 2396-61 (= ATCC 29473) is designated the type strain of the species.

Deoxyribonucleic Acid Relatedness Among Erwiniae and Other Enterobacteria: II. Corn Stalk Rot Bacterium and Pectobacterium chrysanthemi

Relatedness of pectobacteria pathogenic to corn, grass, and sugar cane, and of isolates of Pectobacterium chrysanthemi pathogenic for chrysanthemum, dahlia, and dieffenbachia was determined by deoxyribonucleic acid (DNA) reassociation. Heterologous DNA preparations were allowed to reassociate. Thermal elution chromatography was used to separate reassociated nucleotide sequences from unreacted sequences and to determine the thermal stability of related sequences. DNA relatedness data indicate that corn stalk rot bacteria and strains pathogenic on grass are highly interrelated. Furthermore, strains of both types are distinct from Pectobacterium carotovorum and are most closely related to P. chrysanthemi. P. chrysanthemi strains fall into two relatedness groups, one of which contains isolates from chrysanthemum and guayule and the other isolates from dahlia or dieffenbachia. A sugar cane pathogen is 65% related to both the corn stalk rot bacteria and to strains of P. chrysanthemi. It is suggested that all of these organisms be considered as P. chrysanthemi and that the corn stalk rot and grass isolates be designated P. chrysanthemi pathovar zeae.

Species Status of Hanseniaspora guilliermondii Pijper

Selected yeasts presently classified as Hanseniaspora valbyensis Kloecker 1912 were examined for their physiological and morphological properties and their deoxyribonucleic acid (DNA) relatedness. The strain designated H. guilliermondii Pijper 1928 is herein recognized as a species separate from H. valbyensis. H. guilliermondii is distinguished from H. valbyensis by insignificant DNA reassociations, assimilation of 2-keto-gluconate, growth at 37°C, and formation of four ascospores per ascus.

Phenotypic Description, Numerical Analysis, and Proposal for an Improved Taxonomy and Nomenclature of the Genus Zymomonas Kluyver and van Niel 1936

One hundred thirty-eight phenotypic features were determined in 38 Zymomonas strains from diverse origin (Zairese fermenting palm saps, Mexican pulque, British spoiled beer, and sick cider). The similarity between all the strains was very high: 27 features were present, and 74 features were absent in all of them; 37 features were variable. By numerical analysis all strains formed one cluster above the simple matching coefficient of 0.88. There were no significant differences between motile and nonmotile strains or between sucrose-fermenting and non-sucrose-fermenting strains. A strain from sick cider in Bristol, United Kingdom, was a border case in its phenotypic features, deoxyribonucleic acid relatedness, and protein electropherograms. We propose: (i) to discontinue the use of the species name of Zymomonas anaerobia and its subspecies Z. anaerobia subsp. anaerobia and Z. anaerobia subsp. immobilis, and to include all of the strains in this species in Zymomonas mobilis; (ii) to consider Zymomonas congolensis as a nomen nudum and as a synonym of Z. mobilis. We concluded the following from our data: That Z. mobilis is the only species in the genus Zymomonas so far; that all the strains of our Zymomonas collection except one belong in Z. mobilis subsp. mobilis, the type strain of which is ATCC 10988; and that the cider sickness organisms belong in Z. mobilis subsp. pomaceae (Millis) comb. nov., with type strain T. H. Delft (= strain I [Barker] = ATCC 29192).

Characterization of Yersinia enterocolitica and Yersinia pseudotuberculosis by Deoxyribonucleic Acid Hybridization and by Biochemical Reactions

Strains of Yersinia enterocolitica and Yersinia pseudotuberculosis were characterized by deoxyribonucleic acid (DNA) hybridization, and the extent of DNA relatedness between the strains was assessed by hydroxyapatite chromatography. DNAs from 24 strains of Y. pseudotuberculosis were highly related, but Y. pseudotuberculosis was only 40 to 60% related to Y. enterocolitica. Y. enterocolitica strains formed three DNA relatedness groups, and the data strongly suggest a fourth relatedness group. Each relatedness group can be defined biochemically. One DNA relatedness group corresponds to typical Y. enterocolitica; the second is rhamnose positive; the third is rhamnose positive, melibiose positive, a-methyl glucoside positive, and raffinose positive. The suggested fourth hybridization group is sucrose negative. Although all of these DNA relatedness groups should remain in the genus Yersinia, only the first group is Y. enterocolitica. All of the yersiniae tested are distantly, but significantly, related to other members of Enterobacteriaceae. Yersiniae were more related to members of Enterobacteriaceae than to Pasteurella multocida.

DNA relatedness among species of Enterobacter and Serratia.

Species of Enterobacter and Serratia were examined for deoxyribonucleic acid relatedness to Klebsielleae, to atypical erwiniae, and to other members of Enterobacteriaceae. Deoxyribonucleic acid hybridization and then hydroxyapatite chromatography was the technique used to assess relatedness. Strains of Enterobacter cloacae formed two separate hybridization groups that correlate with the presence or absence of yellow pigment. Pigmented E. cloacae were 75-100% related, but they were only 40-50% related to unpigmented strains. Conversely, unpigmented strains were 70% or more related but were only 40-50% related to the pigmented strains. Both pigmented and unpigmented E. cloacae were 40-45% related to Enterobacter aerogenes and klebsiellae, and 20-30% related to Serratia species and Enterobacter hafniae. Atypical erwiniae were highly related to E. cloacae. Serratia marcescens strains formed one closely related group. Serratia liquefaciens strains formed a single, more disperse, relatedness group, as did isolates of Serratia rubidaea. These species were related throughout a substantial portion of their genomes. A group of lysine-positive "Citrobacter-like" strains were 40-50% related to Serratia species. Only four E. hafniae strains were tested. Two of these were highly related, while the other two were only 50% related to the reference strain. Enterobacter hafniae was only 15-20% related to other Enterobacteriaceae.

Characterization of Hemophilic and Related Bacteria by Their Respiratory Quinones and Cytochromes

Nineteen strains of gram-negative organisms representing 10 Haemophilus species, Eikenella corrodens, and the so-called Haemophilus vaginalis were investigated for cytochromes and respiratory quinones. Phenotypical variation of cytochrome and quinone contents was checked using cells grown with oxygen and fumarate as alternative electron acceptors. The cytochromes were detected by difference spectra of briefly sonicated cells at room temperature, and the quinones were determined in lipid extracts by difference spectrophotometry and partly by thin-layer chromatography. In contrast to other conventional groups of chemo-organotrophic, gram-negative bacteria that have been found to be highly homogeneous with respect to the respiratory chain components, the organisms investigated here may be divided into three categories by their respiratory quinones, namely (i) bacteria containing desmethylmenaquinone as sole respiratory quinoneH. influenzae, H. aegyptius, H. paraphrophilus, H. parahaemolyticus, H. parainfluenzae (in part), (ii) bacteria containing both ubiquinone and desmethylmenaquinone-H. haemoglobinophilus, H. parasuis, H. paragallinarum, H. parainfluenzae (in part), and (iii) bacteria containing only ubiquinone-H. piscium, so-called H. vaginalis, and E. corrodens. The data presented may contribute to further characterization, independent of growth factor requirements, of the taxonomic entities investigated. In the absence of information on deoxyribonucleic acid relatedness between the organisms under study, a provisional reclassification of Haemophilus and related taxa on the basis of respiratory quinones is discussed.

Deoxyribonucleic Acid Relatedness Among Erwiniae and Other Enterobacteriaceae: the Gall, Wilt, and Dry-Necrosis Organisms (Genus Erwinia Winslow et al., sensu stricto)

Species representing the genus Erwinia (sensu stricto, the gall-, wilt-, and dry-necrosis-producing phytopathogens) were examined for relatedness to each other, to pectobacteria, and to other members of the family Enterobacteriaceae. The technique employed to show relatedness was deoxyribonucleic acid (DNA) hybridization and hydroxyapatite chromatography. The results indicate that all erwiniae are significantly related to Pectobacterium and to other enterobacteria. DNA relatedness reveals six species of Erwinia: E. amylovora, E. nigrifluens, E. quercina, E. rubrifaciens, E. salicis, and E. tracheiphila. E. nigrifluens, E. rubrifaciens, and E. salicis show close intrageneric relatedness, whereas the other species exhibit as much relatedness to members of other genera as to the other Erwinia species. The data support the two-genus concept of Erwinia and Pectobacterium.

Bifidobacterium animalis (Mitsuoka) comb. nov. and the "minimum" and "subtile" Groups of New Bifidobacteria Found in Sewage

Twenty-two strains of bifidobacteria from the feces of chickens, rats, and rabbits, and from sewage, formed a single deoxyribonucleic acid (DNA) homology group displaying complete homology with Bifidobacterium longum subsp. animalis Mitsuoka biotype a strain R 101-8 (=ATCC 25527). The DNA relatedness of this group of strains to the known species of the genus Bifidobacterium ranged from 5 to 40%. Therefore, we propose that B. longum Reuter subsp. animalis Mitsuoka biotype a should be elevated to species rank as Bifidobacterium animalis (Mitsuoka) comb. nov. The type strain is ATCC 25527. Also, a small number of strains isolated from sewage are suggested as probably being distinctive bifidobacteria and are placed in two new groups designated “minimum” and “subtile” The reference strains for these groups are F392 (=ATCC 27538) and F395 (=ATCC 27537), respectively.

Deoxyribonucleic Acid Reassociation in the Taxonomy of Enteric Bacteria

A brief summary of the deoxyribonucleic acid (DNA) relatedness of members of the family Enterobacteriaceae is presented. The application and utility of DNA relatedness to bacterial taxonomy are discussed in order to stimulate greater awareness and use of this technique. Applications include: (i) the recognition of new taxa; (ii) the identification of grossly atypical strains in a taxon; (iii) the classification of poorly studied groups of organisms; and (iv) changes in existing classifications. Also discussed are the identification and differentiation of bacteria in the clinical laboratory. Guidelines for the molecular definition of species are presented.

Polynucleotide sequence relatedness among three groups of pathogenic Escherichia coli strains.

Escherichia coli strains that cause dysentery-like disease, parenteral infection, and infantile diarrhea form specific groups based on mobility of O and K antigens in immunoelectrophoresis. Members from each of these groups were assayed for gross nucleotide sequence relatedness. The method used was interspecific deoxyribonucleic acid (DNA) reassociation reactions carried out free in solution. Reassociated DNA was separated from unreacted DNA by passage through hydroxyapatite. DNA relatedness between these groups was approximately 80%. The groups containing those strains causing parenteral infection and those responsible for dysentery-like disease showed preferentially high intragroup DNA relatedness. The group containing strains responsible for infantile diarrhea did not show preferentially high intragroup DNA relatedness with the reference strain employed. These strains, however, did exhibit preferentially high DNA relatedness to a second reference strain.