Identification of acetic acid bacteria isolated from Indonesian sources,especially of isolates classified in the genus Gluconobacter

Sixty-four strains of acetic acid bacteria were isolated from Indonesian sources such as fruits, flowers, and fermented foods by the enrichment culture at pH 3.5. Forty-five strains were routinely identified as Acetobacter strains because of their oxidation of acetate and lactate to carbon dioxide and water and their Q-9 isoprenolog, corresponding to 70% of all the 64 acetic acid bacteria isolated. Eight isolates were identified as Gluconacetobacter strains because of their oxidation of acetate and lactate and their Q-10 isoprenolog, occupying 13% of all the isolates. The remaining 11 isolates, accommodated in the genus Gluconobacter because of no oxidation of acetate and lactate and because of their Q-10 isoprenolog, accounted for 17% of all the isolates. They were divided into two groups based on DNA base compositions. One comprised the seven isolates, which had high G1C contents of DNA ranging from 60.3 to 63.5 mol% and of which DNAs hybridized with that of the type strain of Gluconobacter oxydans at values of 64-94% of DNA relatedness. The other comprised the remaining four isolates, which had low G+C contents of DNA ranging from 57.5 to 57.7 mol% and of which DNAs hybridized with that of the type strain of Gluconobacter frateurii at values of 63-77% of DNA relatedness. The high values of DNA relatedness, 84 to 96%, were obtained between the type strains of Gluconobacter cerinus and Gluconobacter asaii.     

Genetic relatedness among mycoplasmas as determined by nucleic acid homology

Reich, Paul R. (National Institutes of Health, Bethesda, Md.), Norman L. Somerson, James A. Rose, and Sherman M. Weissman. Genetic relatedness among mycoplasmas as determined by nucleic acid homology. J. Bacteriol. 91:153-160. 1966.-A sensitive membrane filter method to detect nucleic acid homology was used to determine genetic relatedness among mycoplasma isolates. Deoxyribonucleic acid (DNA) was isolated from mycoplasmas and used as a primer for synthesis of tritium-labeled, complementary ribonucleic acid (RNA) by the enzyme RNA polymerase. DNA from each mycoplasma isolate tested was reacted separately with complementary RNA synthesized with homologous or heterologous DNA as primer. The quantity of DNA-RNA hybrids formed was assayed by the nitrocellulose membrane filter method. The amount of radioactivity bound to the membrane filter was used to measure the degree of homology between the nucleic acids. The three mycoplasma isolates from human oral cavities (DC 63, V2785, Botteicher) and the prototype strain PG21 placed in the Mycoplasma hominis type 1 group by gel diffusion and complement-fixation testing were investigated with this technique. Analysis of the data confirmed their immunological grouping with the M. hominis type 1 and their distinction from other human mycoplasmas. In contrast to the data from immunological studies, none of the four isolates tested appeared to be identical to any other. Preliminary experiments with DNA from four other mycoplasma isolates from tissue cultures inoculated with human material revealed them to be closely related, and possibly identical. The advantages of this nucleic acid homology technique for the study of relatedness among mycoplasmas are described.     

DNA restriction patterns and DNA-DNA solution hybridization studies of Frankia isolates from Myrica pennsylvanica (bayberry).

Sixteen Frankia strains were isolated from Myrica pennsylvanica (bayberry) root nodules collected at diverse sites in New Jersey. Restriction pattern analysis of total genomic DNA was used to group the isolates into gel groups, and the genetic relatedness among the isolates was evaluated by DNA-DNA solution hybridization studies. Restriction pattern analysis provided a distinctive reproducible fingerprint for each isolate. Isolates fell into nine separate groups (strain types). More than one strain type was isolated from most sites. Isolates from two different gel groups were found in 3 of 10 nodules examined. Of the 16 isolates, 10 contained extrachromosomal DNA. Six different extrachromosomal DNA banding patterns were found. Genomically similar isolates carried related, but different, banding patterns. DNA hybridization studies indicated that isolates from a single plant species can be minimally related as determined by total genome homology. Homology ranged from 12 to 99%. Highly divergent strains were isolated from the same plant and found to cohabit the same nodule. Thus, this study demonstrated that Frankia strains which infect the same host plant are not only phenotypically different but also genetically diverse.     

DNA restriction patterns and DNA-DNA solution hybridization studies of Frankia isolates from Myrica pennsylvanica (bayberry)

Sixteen Frankia strains were isolated from Myrica pennsylvanica (bayberry) root nodules collected at diverse sites in New Jersey. Restriction pattern analysis of total genomic DNA was used to group the isolates into gel groups, and the genetic relatedness among the isolates was evaluated by DNA-DNA solution hybridization studies. Restriction pattern analysis provided a distinctive reproducible fingerprint for each isolate. Isolates fell into nine separate groups (strain types). More than one strain type was isolated from most sites. Isolates from two different gel groups were found in 3 of 10 nodules examined. Of the 16 isolates, 10 contained extrachromosomal DNA. Six different extrachromosomal DNA banding patterns were found. Genomically similar isolates carried related, but different, banding patterns. DNA hybridization studies indicated that isolates from a single plant species can be minimally related as determined by total genome homology. Homology ranged from 12 to 99%. Highly divergent strains were isolated from the same plant and found to cohabit the same nodule. Thus, this study demonstrated that Frankia strains which infect the same host plant are not only phenotypically different but also genetically diverse.     

New restriction fragment length polymorphism (RFLP) markers for Aspergillus fumigatus

In this study, we isolated and tested restriction fragment length polymorphism (RFLP) markers for Aspergillus fumigatus based on PCR products amplified by the random amplified polymorphic DNA (RAPD) primer R108. Four DNA fragments, Afd, Af5, Af4, and Af4A, were amplified. Fragments Afd and Af5 were 85% and 88% identical at the DNA level to part of the Afut1 retrotransposon from A. fumigatus. Fragment Af4A is a duplication of fragment Af4 and both showed similarity at the amino acid level with endonucleases from other fungal retrotransposons. We used both RAPD with primer R108 and RFLP assays with Afut1, Afd, and Af4A, to determine the genetic relatedness of clinical isolates of A. fumigatus isolated sequentially from four patients colonized with A. fumigatus. The combination of these different methods suggested that the isolates infecting the four patients were not identical.     

Genetic Differentiation by Nucleic Acid Homology II. Genotypic Variations Within Two Mycoplasma Species

Somerson, Norman L. (National Institutes of Health, Bethesda, Md.), Paul R. Reich, Barbara E. Walls, Robert M. Chanock, and Sherman M. Weissman. Genetic differentiation by nucleic acid homology. II. Genotypic variations within two Mycoplasma species. J. Bacteriol. 92:311-317. 1966.-A deoxyribonucleic-ribonucleic acid (DNA-RNA) homology technique was used to determine genetic relatedness among the nucleic acids of eight mycoplasmas which were serologically classified as Mycoplasma hominis type 1. The DNA preparations from these organisms were each found to be distinct. No subgrouping of the M. hominis type 1 strains could be demonstrated. In contrast, when the nucleic acids from six serologically related mycoplasmas which were isolated from tissue cultures were studied, the DNA from these species could not be distinguished. The DNA buoyant densities of the tissue culture isolates were similar. These isolates were closely related genetically to a porcine mycoplasma, M. hyorhinis.     

Occurrence and clonal relatedness of sec/tst-gene positive Staphylococcus aureus isolates of quartermilk samples of cows suffering from mastitis

AIMS: To investigate the prevalence of sec/tst-gene positive Staphylococcus aureus in bovine mastitis and to get information about the clonal relatedness of these clinical isolates. METHODS AND RESULTS: A total of 533 Staph. aureus strains isolated from bovine mastitic quartermilk samples at 493 randomized dairy farms in Hessia, Germany, from January 1997 until June 1998 were examined for enterotoxin C (sec) gene and toxic shock syndrome toxin (tst) gene by multiplex polymerase chain reaction. Fifty-three (9.3%) of the strains were sec/tst-gene positive. Phenotypic TSST-1 production was found in all positive strains by reversed passive latex agglutination test. With DNA macrorestriction analysis, sec/tst-gene positive strains were divided into five different macrorestriction types. Type I (10 isolates) and III (40 isolates) were found to be the predominant types in terms of frequency of isolation in the investigated area. These DNA macrorestriction types differed in only two bands in the 500 and 270 bp region. CONCLUSIONS: Closely related Staph. aureus strains seem to be responsible for an unusual large proportion of bovine mastitis cases in geographically widely distinct locations. SIGNIFICANCE AND IMPACT OF THE STUDY: This is one of the first reports about the relatedness of sec/tst-gene positive Staph. aureus clinical isolates from bovine mastitis.     

Delineation of Borrelia burgdorferi sensu stricto, Borrelia garinii sp. nov., and group VS461 associated with Lyme borreliosis.

We studied 48 Borrelia isolates that were associated with Lyme borreliosis or were isolated from ticks and identified three DNA relatedness groups by using the S1 nuclease method. The three DNA groups (genospecies) were associated with specific rRNA gene restriction patterns, protein electrophoresis patterns, and patterns of reactivity with murine monoclonal antibodies. Genospecies I corresponded to Borrelia burgdorferi sensu stricto since it contained the type strain of this species (strain ATCC 35210); this genospecies included 28 isolates from Europe and the United States. Genospecies II was named Borrelia garinii sp. nov. and included 13 isolates from Europe and Japan. Genospecies III (group VS461) included seven isolates from Europe and Japan.     

Characterization and Relatedness of Marine Vibrios Pathogenic to Fish: Deoxyribonucleic Acid Homology and Base Composition

Deoxyribonucleic acid (DNA) isolated from several pathogenic marine vibrios was utilized in studies of base composition and nucleotide sequence relationships. Patterns of relatedness inferred from DNA criteria were found to correlate closely with those inferred from morphological, physiological, and serological analysis of the same organisms. The utility of the phenotypic and genotypic approaches to the determination of relatedness is discussed.     

Deoxyribonucleic Acid Base Sequence Homologies of Some Budding and Prosthecate Bacteria

The genetic relatedness of a number of budding and prosthecate bacteria was determined by deoxyribonucleic acid (DNA) homology experiments of the direct binding type. Strains of Hyphomicrobium sp. isolated from aquatic habitats were found to have relatedness values ranging from 9 to 70% with strain "EA-617," a subculture of the Hyphomicrobium isolated by Mevius from river water. Strains obtained from soil enrichments had lower values with EA-617, ranging from 3 to 5%. Very little or no homology was detected between the amino acid-utilizing strain Hyphomicrobium neptunium and other Hyphomicrobium strains, although significant homology was observed with the two Hyphomonas strains examined. No homology could be detected between prosthecate bacteria of the genera Rhodomicrobium, Prosthecomicrobium, Ancalomicrobium, or Caulobacter, and Hyphomicrobium strain EA-617 or H. neptunium LE-670. The grouping of Hyphomicrobium strains by their relatedness values agrees well with a grouping according to the base composition of their DNA species. It is concluded that bacteria possessing cellular extensions represent a widely diverse group of organisms.     

Molecular characterization of Irish E. coli O157:H7 isolates of human, bovine, ovine and porcine origin

Aims:  To determine the degree of relatedness between isolates of Escherichia coli O157:H7 of human, bovine, ovine and porcine origin.
Methods and Results:  Escherichia coli O157:H7 isolates were compared using (i) PFGE Xba I patterns, (ii) PCR profiles of virulence genes and (iii) the DNA sequences of genes reported to play a role in pathogenicity. The 77 E. coli O157:H7 isolates demonstrated 49 different PFGE patterns of which, eight were common to multiple isolates, and the remaining 41 were distinct. Isolates of different origin did not correlate, except for one cluster consisting of two human and two beef isolates. The majority of animal isolates had the same PCR profiles of virulence genes as those isolated from clinical patients. Single nucleotide polymorphisms (SNPs) were identified in the sequence of a 255-bp region of the vtx2 subunit A gene.
Conclusions:  Six SNPs were detected in the vtx2 A gene, defining four different haplotypes. One nonsynonymous substitution encoded for an amino acid change from glutamic to aspartic acid.
Significance and Impact of the Study:  Results indicate that although E. coli O157:H7 isolates of differing origin were distinct by PFGE, the DNA sequences of the main virulence genes associated with human clinical illness were conserved.     

Cytological and Deoxyribonucleic Acid-Deoxyribonucleic Acid Hybridization Studies on Lactobacillus Isolates from San Francisco Sourdough

Molecular taxonomic and electron microscopy studies were performed on four bacterial isolates obtained from different sources of San Francisco sourdough (SD). These bacteria were first isolated by Kline and Sugihara who tentatively described them as a previously unreported species of heterofermentative Lactobacillus; they suggested the name Lactobacillus sanfrancisco. The guanine plus cytosine base composition (%GC) of the deoxyribonucleic acid (DNA) ranged from 38 to 40%. The possible genetic relatedness of these SD isolates to five known species of Lactobacillus with comparable GC contents was assessed in the present work by means of DNA-DNA hybridization competition experiments. Little or no DNA homology was observed between the SD bacteria and the known species. The SD bacteria exhibited a high degree of homology (>88%) among themselves, suggesting that the four isolates were identical taxonomically. Also, the electron photomicrographs revealed structures similar to those of gram-positive bacilli. Accordingly, since these SD isolates have the characteristic phenotypic and morphological properties of the genus Lactobacillus and are not related genetically to any known species, the tentative characterization by the above workers of these isolates as a new species is substantiated.     

The electrophoretic movement of soluble proteins and the production of unusual amino acids in Rhizobium isolates as taxonomic criteria

Summary This paper shows that a characteristic and distinctive set of proteins can be recognised in the Rhizobium cultures isolated from the various host species examined, and allow the isolates to be placed into groups. The acid-producing isolates of Lotus form a homogeneous group, but the non-acid producers examined form a separate but rather heterogeneous group. The clover acid producers form another homogeneous group. There is a good correlation between groupings based on amino acid patterns and those based on protein patterns. These approaches, however, give little information on the relatedness of one group to another, a conclusion also valid for other bacteria, algae and fungi. The technique therefore cannot be used as major criteria in classification, but can be a useful aid in rhizobial taxonomy.     

A survey on distribution and toxigenicity of <Emphasis Type="Italic">Aspergillus flavus</Emphasis> from indoor and outdoor hospital environments

In the present study, genetic diversity and mycotoxin profiles of Aspergillus flavus isolated from air (indoors and outdoors), levels (surfaces), and soils of five hospitals in Southwest Iran were examined. From a total of 146 Aspergillus colonies, 63 isolates were finally identified as A. flavus by a combination of colony morphology, microscopic criteria, and mycotoxin profiles. No Aspergillus parasiticus was isolated from examined samples. Chromatographic analyses of A. flavus isolates cultured on yeast extract–sucrose broth by tip culture method showed that approximately 10% and 45% of the isolates were able to produce aflatoxin B₁ (AFB₁) and cyclopiazonic acid (CPA), respectively. Around 40% of the isolates produced sclerotia on Czapek–Dox agar. The isolates were classified into four chemotypes based on the ability to produce AF and CPA that majority of them (55.5%) belonged to chemotype IV comprising non-mycotoxigenic isolates. Random amplified polymorphic DNA (RAPD) profiles generated by a combination of four selected primers were used to assess genetic relatedness of 16 selected toxigenic and non-toxigenic isolates. The resulting dendrogram demonstrated the formation of two separate clusters for the A. flavus comprised both mycotoxigenic and non-toxigenic isolates in a random distribution. The obtained results in this study showed that RAPD profiling is a promising and efficient tool to determine intra-specific genetic variation among A. flavus populations from hospital environments. A. flavus isolates, either toxigenic or non-toxigenic, should be considered as potential threats for hospitalized patients due to their obvious role in the etiology of nosocomial aspergillosis.     

Characterization of Bordetella pertussis strains of recent isolation.

During the clinical trial conducted in Italy to evaluate the efficacy of new acellular pertussis vaccines, the most favorable conditions for the recovery and characterization of Bordetella pertussis strains, isolated from children with cough, were adopted. The nasopharyngeal aspirates were collected and sent to the laboratory in refrigerated conditions within 24 hours. Charcoal agar selective and non selective plates were used, and most of the isolates were recovered after 3-4 days of incubation. Confirmation of all suspected colonies included the use of biochemical tests and specific agglutination reaction with B. pertussis antiserum. Serotyping of fimbriae, susceptibility to erythromycin and DNA fingerprinting by Pulsed Field Gel Electrophoresis (PFGE), were performed to characterize B. pertussis isolates and to determine relatedness among different strains. Serotype 1,3 was the most represented in the bacterial population examined. A predominant pulsetype (PTA) characterized most of the isolates accounting for 71.4% of the strains examined. Eight subclones (23.5%) and three unrelated pulsetypes were also found. No resistant strains to erythromycin were detected.     

Rapid identification of genetic variation and pathotype of Leptosphaeria maculans by random amplified polymorphic DNA assay.

Canadian isolates of Leptosphaeria maculans, the causal agent of blackleg of crucifers, were examined for genetic relatedness by the random amplified polymorphic DNA assay. DNA polymorphisms amplified with random decamer primers were used to distinguish three groups of isolates. Group 1 contained all isolates of the virulent pathotype, group 2 contained isolates of the avirulent pathotype from western Canada, and group 3 contained avirulent pathotype isolates from Ontario. These results agreed with other reports which showed many genetic differences between pathotypes and were consistent with the hypothesis that the virulent pathotype was recently introduced into Canada and has diverged relatively little. In contrast, the avirulent pathotype has probably been present in Canada for a longer time and has diverged with geographic isolation. In addition to establishing genetic relationships, DNA fingerprints generated by the random amplified polymorphic DNA assay have potential applications in pathotype identification and blackleg disease management.     

Rapid identification of genetic variation and pathotype of Leptosphaeria maculans by random amplified polymorphic DNA assay.

Canadian isolates of Leptosphaeria maculans, the causal agent of blackleg of crucifers, were examined for genetic relatedness by the random amplified polymorphic DNA assay. DNA polymorphisms amplified with random decamer primers were used to distinguish three groups of isolates. Group 1 contained all isolates of the virulent pathotype, group 2 contained isolates of the avirulent pathotype from western Canada, and group 3 contained avirulent pathotype isolates from Ontario. These results agreed with other reports which showed many genetic differences between pathotypes and were consistent with the hypothesis that the virulent pathotype was recently introduced into Canada and has diverged relatively little. In contrast, the avirulent pathotype has probably been present in Canada for a longer time and has diverged with geographic isolation. In addition to establishing genetic relationships, DNA fingerprints generated by the random amplified polymorphic DNA assay have potential applications in pathotype identification and blackleg disease management.     

Conservation of transfer ribonucleic acid and 5S ribonucleic acid cistrons in Enterobacteriaceae.

The genes for tranfer ribonucleic acid (tDNA) and 5S ribonucleic acid (5SDNA) were isolated from the total deoxyribonucleic acid (DNA) of Escherichia coli. The relatedness of tDNA and 5S from E. coli and other species of Enterobacteriaceae was determined by reassociation of the isolated genes labeled with 32PO4 to unlabeled, unfractionated DNA. Double-stranded DNA was separated from unreacted DNA by hydroxyapatite chromatography. Thermal elution profiles were done to determine the amount of unpaired bases present in related DNA sequences. Relative to total DNA, both 5S DNA and tDNA were highly conserved throughout the Enterobacteriaceae, including the genera Yersinia and Proteus.     

Differentiation between human and ovine isolates of Bordetellaparapertussis using pulsed-field gel electrophoresis

Abstract The genetic relatedness of 18 human and 29 ovine isolates of Bordetella parapertussis was examined by macrorestriction digestion of DNA with the rarely cutting enzyme Xba I and resolution by pulsed-field gel electrophoresis. There was clear separation of human and ovine isolates and variation within host types. The human isolates were separated into three types as were the 24 Scottish ovine isolates. Species-specific bands were observed with the human isolates at 114, 134, 166, 213, 346 and 372 kb. No species-specific bands were found in the B. parapertussis ovine isolates. Isolates of B. parapertussis recovered from sheep in New Zealand gave a further two DNA banding patterns which were clearly different from the Scottish ovine and the human isolates. These results indicate that human and ovine isolates of B. parapertussis are genetically distinct and that variation exists within isolates from the same host species. Pulsed-field gel electrbphoresis therefore appears to be a powerful discriminatory tool for the classification of B. parapertussis .     

<i>Acetobacter okinawensis</i> sp. nov., <i>Acetobacter papayae</i> sp. nov., and <i>Acetobacter persicus</i> sp. nov.; novel acetic acid bacteria isolated from stems of sugarcane, fruits, and a flower in Japan

Eleven strains of acetic acid bacteria were isolated from stems of sugarcane, fruits, and a flower in Japan. The isolates were separated into three groups, Groups I, II, and III, in the genus Acetobacter according to phylogenetic analysis based on 16S rRNA sequences. The isolates had sequence similarities of 99.8-100% within the Group, 99.3-99.6% to those of the type strains of each related Acetobacter species, and less than 98.4% to those of the type strains of other Acetobacter species. Genomic DNA G+C contents of Groups I, II, and III were 59.2-59.4, 60.5-60.7, and 58.7-58.9 mol%, respectively. The isolates in the Group showed high values of DNA-DNA relatedness to each other, but low values less than 46% to the type strains of related Acetobacter species. A good correlation was found between the three Groups and groups based on DNA G+C contents and DNA-DNA relatedness. All the strains had Q-9 as the main component, and Q-8 and Q-10 as minor components. The isolates in the three Groups did not completely match with any Acetobacter species on catalase reaction, the production of ketogluconic acids from D-glucose, growth on ammoniac nitrogen with ethanol (Hoyer-Frateur medium and Frateur modified Hoyer medium), growth on 30% (w/v) D-glucose, growth in 10% (v/v) ethanol, or DNA G+C contents. On the basis of phylogenetic relationships in the genus Acetobacter and chemosystematic and phenotypic characteristics, the three Groups were regarded as novel species in the genus Acetobacter. Acetobacter okinawensis sp. nov. is proposed for Group I, Acetobacter papayae sp. nov. for Group II, and Acetobacter persicus sp. nov. for Group III.