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PubMed1996

Phylogenetic analysis of Streptomyces spp. causing potato scab based on 16S rRNA sequences.

The complete 16S rRNA sequences of 12 strains of Streptomyces spp., including potato scab pathogens, were determined. Among the strains of Streptomyces scabies that were isolated from diverse geographical areas and differed in melanoid pigment production, either no difference or one difference in sequence was observed. The sequence of S. scabies was most similar to the sequences of Streptomyces diastatochromogenes, Streptomyces bottropensis, and Streptomyces neyagawaensis, which belong to the Diastatochromogenes group. The levels of similarity of the 16S rRNA sequences of Streptomyces acidiscabies and S. scabies were almost the same as the levels of similarity between S. acidiscabies and other Streptomyces strains. Streptomyces sp. strain 91-Sy-13, which was isolated in Japan from potato scab and belongs to a distinct species on the basis of phenotypic characteristics and DNA relatedness, exhibited lower levels of 16S rRNA sequence similarity with other potato scab pathogens, as well as other Streptomyces species. The phylogenetic tree constructed on the basis of 16S rRNA sequence data showed that the Streptomyces spp. that cause potato scab composed unique branches. The results of our phylogenetic analysis based on complete 16S rRNA sequences confirmed the lack of close relationships among Streptomyces spp. that cause potato scab. Our findings suggest that potato scab is caused by phylogenetically diverse Streptomyces species and that the pathogenicities of these organisms developed independently.

Base Sequence↗
PubMed1995

Evidence for the placement of the gram-negative Catonella morbi (Moore and Moore) and Johnsonella ignava (Moore and Moore) within the Clostridium subphylum of the gram-positive bacteria on the basis of 16S rRNA sequences.

Comparative 16S rRNA analysis was used to determine the phylogenetic positions of Catonella morbi and Johnsonella ignava, which are members of two monospecific genera of gram-negative anaerobic bacilli isolated from human gingival crevices. Both of these genera were found to belong to cluster XIVa (M. D. Collins, P. A. Lawson, A. Willems, J. J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J. A. E. Farrow, Int. J. Syst. Bacteriol. 44:812-826, 1994) of the Clostridium subphylum of gram-positive bacteria. Within this cluster, which contains several Clostridium, Coprococcus, Eubacterium, and Ruminococcus species, C. morbi and J. ignava formed two distinct lines that were separate from all other taxa. Our findings support the separate generic status of the genera Catonella and Johnsonella and show that these genera do not belong to the family Bacteroidaceae but instead belong to the gram-positive Clostridium subphylum.

Base Sequence↗
PubMed2004

Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing.

The diversity of Archaea in anaerobic digesters was characterized by strand conformation polymorphism (SSCP) analysis and the sequencing of 16S rDNA genes. The 44 digesters sampled, located in eight different countries, treated effluents from agriculture, the food processing and petro-chemical industries, pulp and paper plant, breweries, slaughterhouses and municipal waste. All the existing processes were represented among the samples (fixed-film, fluidized bed, stirred-tank, UASB, sequential batch reactor, lagoon). Single strand conformation polymorphism analysis targeting the V3 region of 16S rDNA revealed between four to six distinct archaeal peaks per digester. The diversity of dominant Archaea in the 44 digesters was estimated as 23 different 16S rDNA sequences. Cloning of archaeal 16S rRNA genes from 11 distinct total genomic DNA, screening of clones by SSCP and the sequencing of 170 of them made it possible to characterize these SSCP peaks. All the sequences retrieved were members of the Euryarchaeaota subdomain. Furthermore, most of the sequences retrieved were very close to already known and cultivated strains or to environmental clones. The most frequent archaeal sequences were close to Methanosaeta concilii and to a 16S rDNA clone vadinDC06 located in the Methanobacterium clade (84% and 73% of digesters respectively). The other sequences were members of the Methanobacteriales and the Methanomicrobiales families. Only one sequence was far from any sequence of the database and it could be grouped with several sequences of environmental clones. Each digester harboured between two to nine archaeal sequences with only one of them corresponding to a putative acetate-utilizing species. Furthermore, the process in the digesters appeared to play a part in the distribution of archaeal diversity.

Acetates↗
PubMed1992

Phylogeny of 54 representative strains of species in the family Pasteurellaceae as determined by comparison of 16S rRNA sequences.

Virtually complete 16S rRNA sequences were determined for 54 representative strains of species in the family Pasteurellaceae. Of these strains, 15 were Pasteurella, 16 were Actinobacillus, and 23 were Haemophilus. A phylogenetic tree was constructed based on sequence similarity, using the Neighbor-Joining method. Fifty-three of the strains fell within four large clusters. The first cluster included the type strains of Haemophilus influenzae, H. aegyptius, H. aphrophilus, H. haemolyticus, H. paraphrophilus, H. segnis, and Actinobacillus actinomycetemcomitans. This cluster also contained A. actinomycetemcomitans FDC Y4, ATCC 29522, ATCC 29523, and ATCC 29524 and H. aphrophilus NCTC 7901. The second cluster included the type strains of A. seminis and Pasteurella aerogenes and H. somnus OVCG 43826. The third cluster was composed of the type strains of Pasteurella multocida, P. anatis, P. avium, P. canis, P. dagmatis, P. gallinarum, P. langaa, P. stomatis, P. volantium, H. haemoglobinophilus, H. parasuis, H. paracuniculus, H. paragallinarum, and A. capsulatus. This cluster also contained Pasteurella species A CCUG 18782, Pasteurella species B CCUG 19974, Haemophilus taxon C CAPM 5111, H. parasuis type 5 Nagasaki, P. volantium (H. parainfluenzae) NCTC 4101, and P. trehalosi NCTC 10624. The fourth cluster included the type strains of Actinobacillus lignieresii, A. equuli, A. pleuropneumoniae, A. suis, A. ureae, H. parahaemolyticus, H. parainfluenzae, H. paraphrohaemolyticus, H. ducreyi, and P. haemolytica. This cluster also contained Actinobacillus species strain CCUG 19799 (Bisgaard taxon 11), A. suis ATCC 15557, H. ducreyi ATCC 27722 and HD 35000, Haemophilus minor group strain 202, and H. parainfluenzae ATCC 29242. The type strain of P. pneumotropica branched alone to form a fifth group. The branching of the Pasteurellaceae family tree was quite complex. The four major clusters contained multiple subclusters. The clusters contained both rapidly and slowly evolving strains (indicated by differing numbers of base changes incorporated into the 16S rRNA sequence relative to outgroup organisms). While the results presented a clear picture of the phylogenetic relationships, the complexity of the branching will make division of the family into genera a difficult and somewhat subjective task. We do not suggest any taxonomic changes at this time.

Base Sequence↗
PubMed1998

Recovery of a Nitrosomonas-like 16S rDNA sequence group from freshwater habitats.

In order to study the diversity of ammonia-oxidising bacteria in freshwater habitats, including sediments, a molecular approach focused on the sequencing of 16S rDNA was adopted. 16S rDNA sequences showing affinity with the beta-subgroup of ammonia-oxidising bacteria were recovered by specific PCR of directly isolated DNA from freshwater samples, and samples from brackish water and Glyceria maxima rhizosphere were included in the analysis for comparison. The ammonia oxidiser-like sequences recovered from several locations, which exhibit differences in the composition of their total microbial communities as indicated by denaturing gradient gel electrophoresis, formed a strong monophyletic cluster including Nitrosomonas ureae. This is the first report presenting sequences from an apparently dominant group of Nitrosomonas-like organisms among the beta-subdivision of ammonia-oxidising bacteria in freshwater environments. This group of sequences extends the known diversity within the beta-subgroup of ammonia-oxidisers. The new sequences related to Nitrosomonas ureae do not match with some published primers and probes designed for the detection of Nitrosomonas species, which may explain why these sequences have not previously been detected in freshwater habitats. The sequence diversity detected within this group of sequences was minimal across the environments examined, and no patterns of distribution were indicated with respect to environmental factors such as sediment depth or location.

Base Sequence↗
PubMed2002

16S rDNA sequence analysis of environmental Bdellovibrio-and-like organisms (BALO) reveals extensive diversity.

Bdellovibrio-and-like organisms (BALO) are Gram-negative, predatory bacteria that inhabit terrestrial, freshwater and salt-water environments. Historically, these organisms have been classified together despite documented genetic differences between isolates. The genetic diversity of these microbes was assessed by sequencing the 16S rRNA gene. Primers that selectively amplify predator 16S rDNA, and not contaminating prey DNA, were utilized to study 17 freshwater and terrestrial and nine salt-water BALO isolates. When the 16S rDNA sequences were compared with representatives of other bacterial classes, 25 of the 26 BALO isolates clustered into two groups. One group, supported 100% by bootstrap analysis, included all of the Bdellovibrio bacteriovorus isolates. Each member of this group was isolated from either a freshwater or terrestrial source. The genetic distance between these isolates was less than 12%. The other group, supported 94% by bootstrap analysis, includes Bacteriovorax starrii, Bacteriovorax stolpii and the salt-water isolates. The salt-water isolates form a subgroup (83% by bootstrap) and differ within the subgroup by less than 110%. This observation implies that the salt-water isolates arose from Bacteriovorax progenitors. The difference between isolates in different clades is over 17%, a quantity similar to differences between bacterial species in different classes. However, both the Bdellovibrio and Bacteriovorax clades were closest to other representatives of the delta-Proteobacteria using maximum-likelihood. One freshwater isolate, James Island, was distinct from all other BALO (> 19%), but differed from Pseudomonas putida, a member of the gamma-Proteobacteria, by only 3%. Thus, by 16S rDNA sequence analysis, the BALO appear to have multiple origins, contrary to the unified taxonomic grouping based on morphology and natural history. These observations are consistent with the need to review and revise the taxonomy of these organisms.

Base Sequence↗
PubMed1997

[Sequencing the 16S rDNA of representative strain of new rhizobial group and determining of its phylogenetic relationship].

The full-length 16S rDNA sequence of representative strain SH2672 were sequenced by the dideoxy-mediated chain-termination method. This sequence was compared with that of type strains of all known rhizobia and related bacteria. An unrooted phylogenetic tree was produced. In this tree, strain SH2672, Mesorhizobium loti, M. huakuii, M. tianshanense, M. mediterraneum, and M. ciceri constituted a branch. Within this branch, the similarity values of 16S rDNA sequences between strain SH2672 and M. loti, M. huakuii, M. tianshanense, M. mediterraneum and M. ciceri were 96.3%, 96.4%, 97.2%, 95.1% and 95.6% respectively. All similarity values was more than 95%, this indicated that these species should belong to the same genus. The values of DNA-DNA homology between type strains of these species were less than 70%, which showed that strain SH2672 (representative strain of new group) represented a new rhizobial species.

Base Sequence↗
PubMed2006

Homogeneity of the 16S rDNA sequence among geographically disparate isolates of Taylorella equigenitalis.

BACKGROUND: At present, six accessible sequences of 16S rDNA from Taylorella equigenitalis (T. equigenitalis) are available, whose sequence differences occur at a few nucleotide positions. Thus it is important to determine these sequences from additional strains in other countries, if possible, in order to clarify any anomalies regarding 16S rDNA sequence heterogeneity. Here, we clone and sequence the approximate full-length 16S rDNA from additional strains of T. equigenitalis isolated in Japan, Australia and France and compare these sequences to the existing published sequences. RESULTS: Clarification of any anomalies regarding 16S rDNA sequence heterogeneity of T. equigenitalis was carried out. When cloning, sequencing and comparison of the approximate full-length 16S rDNA from 17 strains of T. equigenitalis isolated in Japan, Australia and France, nucleotide sequence differences were demonstrated at the six loci in the 1,469 nucleotide sequence. Moreover, 12 polymorphic sites occurred among 23 sequences of the 16S rDNA, including the six reference sequences. CONCLUSION: High sequence similarity (99.5% or more) was observed throughout, except from nucleotide positions 138 to 501 where substitutions and deletions were noted.

Animals↗
PubMed2002

Phylogenetic structure of the genera Flexibacter, Flexithrix, and Microscilla deduced from 16S rRNA sequence analysis.

The 16S rDNA sequences of 40 strains of 17 species in the genus Flexibacter, 5 strains of 4 species in the genus Microscilla, and 1 strain of Flexithrix dorotheae, including all type strains of approved and validated species in these genera, were determined to reveal their phylogenetic relationships. The 16S rRNA sequence analysis demonstrated the extreme heterogeneity of the genera Flexibacter and Microscilla. The strains examined diverged into 24 distinct lines of descent (1 group included both flexibacteria and flexithrix, and 1 group included both flexibacteria and microscilla) that were remote from each other at the genus level or higher. Flexibacter strains were scattered across the cytophaga-flavobacteria-bacteroides phylum and divided into 20 phylogenetic groups, and the genus Microscilla was separated into 5 groups. Flexibacter flexilis, the type species of the genus Flexibacter, and Microscilla marina, the type species of the genus Microscilla, were isolated from other organisms in their respective genera. This means that each genus should be restricted to only the type species. Flexithrix dorotheae, the type species of the genus Flexithrix, clustered with Flexibacter aggregans. The heterogeneity was found not only within genera but also within species. Flexibacter aggregans, Flexibacter aurantiacus, Flexibacter flexilis, Flexibacter roseolus, Flexibacter tractuosus, and "Microscilla sericea" each contained phylogenetically distant strains. The taxonomic concept of the genera Flexibacter, Flexithrix, and Microscilla should be reorganized in accordance with the natural relationships revealed in this study.

Bacteroides↗
PubMed1989

Identification of Vibrio anguillarum in fish by using partial 16S rRNA sequences and a specific 16S rRNA oligonucleotide probe.

16S rRNA from seven different Vibrio anguillarum strains was partially sequenced and compared. From this sequence information we could design a 25-base-long oligonucleotide and use it as a specific probe for identification of V. anguillarum. This was determined by RNA-DNA colony hybridization and slot-blot hybridization. Strong, specific hybridization to the probe was observed for all V. anguillarum strains tested. Furthermore, no cross-hybridization could be seen against five other bacterial species. The detection limit was 5 x 10(3) bacteria per ml. It was even possible to detect V. anguillarum, by slot-blot hybridization, directly in a homogenized kidney from a fish that had died of vibriosis. The partial sequence information revealed small but significant differences between strains of the same species. These sequence differences are sufficiently significant to allow serotyping on the RNA level. Comparing strains of different serotypes revealed a 10-base and an 11-base difference in V. anguillarum serotypes O8 and O9, respectively, in a 122-base partial sequence.

Animals↗
PubMed1993

Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer.

The 16S rRNA gene sequences of 19 strains covering 97% of the molecules were determined for the members of the family Rhizobiaceae and related bacteria by PCR and DNA sequencer. The three biovars of Agrobacterium were located separately, whereas Agrobacterium rubi clustered with A. tumefaciens. Phylogenetic locations for the species of the genera Rhizobium, Sinorhizobium, Agrobacterium, Phylobacterium, Mycoplana (M. dimorpha), Ochrobactrum, Brucella and Rochalimaea (a rickettsia) were intermingled with each other with the similarity values higher than 92%. The family Rhizobiaceae should be redefined including the above-mentioned genera despite the ability for plant association and nitrogen fixation. Bradyrhizobium japonicum and Mycoplana bullata were far remote from the other species and should be excluded from this family.

Base Sequence↗
PubMed1999

Phylogenetic relationships between toxic and non-toxic strains of the genus Microcystis based on 16S to 23S internal transcribed spacer sequence.

16S to 23S ribosomal DNA internal transcribed spacer sequences of 47 strains of the genus Microcystis were determined. Derived maximum likelihood and DNA distance trees indicated that Microcystis can be divided into three clusters. The first cluster included toxic and non-toxic strains, the second only toxic ones, and the third only non-toxic ones. The tree topologies were not necessarily correlated with morphospecies distinction or phycobilin pigment composition, and one genotype may have more than one morphotype. Phylogenetic analysis based on intergenic spacer sequences was thought to be effective for understanding relationships among closely related species and strains.

Base Sequence↗
PubMed2000

Phylogenetic investigations of the stephanoberyciformes and beryciformes, particularly whalefishes (Euteleostei: Cetomimidae), based on partial 12S rDNA and 16S rDNA sequences.

DNA data were collected from a number of acanthomorph fishes for 12S rDNA (30 sequences) and 16S rDNA (39 sequences) to investigate the phylogenetic relationships of genera within Cetomimidae (whalefishes) and of this family within the Stephanoberyciformes/Beryciformes assemblage. The Cetomimidae are apparently monophyletic. Within the family, species of Gyrinomimus and Cetomimus form a clade but the former genus is paraphyletic with respect to the latter. Cetostoma is sister to Ditropichthys rather than to Gyrinomimus plus Cetomimus as suggested by morphological analyses. Rondeletiidae + Cetomimidae + Barbourisiidae are shown, as expected from morphological analyses, as a monophyletic group in the 12S rDNA analyses, but not in the 16S rDNA or combined analyses, although the shortest trees showing the group require only one extra step in each case. These three families plus Melamphaidae (our sample of Stephanoberyciformes) are not shown as a group in any analysis, with Melamphaidae being sister to Berycidae in the 16S and combined analyses, but dispersed in the 12S analyses. Maximum-parsimony trees without imposed constraints are notably shorter than trees constrained to show ordinal groupings or either of the two main current hypotheses of Stephanoberyciformes/Beryciformes relationships. The length difference is highly significant for most comparisons using either 12S or 16S rDNA sets or their combination, and significant or nearly so for all comparisons. In particular, the Beryciformes is unlikely to be monophyletic. The Holocentridae are included, with high bootstrap and Bremer support, in a clade of non-beryciforms comprising the Gempylidae, Zeidae, and Atheriniformes (the only higher acanthomorphs sampled) and not with other Beryciform families. In these data, the Berycidae are the sister to the Melamphaidae, a stephanoberyciform family.

Animals↗
PubMed2006

Two cases of sucrose-fermenting Vibrio vulnificus infection in which 16S rDNA sequencing was useful for diagnosis.

Vibrio vulnificus is a Gram-negative bacterium which is associated with severe infections in humans. We experienced two cases of sucrose-fermenting V. vulnificus infection. The causative agents in both cases were unidentifiable by conventional identification systems because of their unique characteristics, and sequencing of 16S rDNA was found to be useful for diagnosis.

Aged↗
PubMed2002

Differentiation between Mycobacterium farcinogenes and Mycobacterium senegalense strains based on 16S-23S ribosomal DNA internal transcribed spacer sequences.

16S ribosomal DNA (rDNA) and 16S-23S internal transcribed spacer rDNA sequence analyses were performed on Mycobacterium farcinogenes and M. senegalense strains and 26 strains of other rapidly growing mycobacteria to investigate the phylogenetic structure of bovine farcy mycobacteria within the M. fortuitum complex. M. farcinogenes and M. senegalense were indistinguishable in their 5"-end 16S rDNA but showed both considerable interspecies spacer sequence divergence and a high level of intraspecies sequence stability. A rapid detection assay using PCR and hybridization with species-specific probes was developed. The assay was specific among 46 species other than M. farcinogenes and M. senegalense and correctly identified all M. farcinogenes and M. senegalense strains. PCR- and 16S-23S rDNA sequence-based detection will be a valuable approach for diagnosis of the causal agents of African bovine farcy in cattle.

Animals↗
PubMed2000

Phylogenetic analysis of the genus Thermoactinomyces based on 16S rDNA sequences.

The almost complete 16S rDNA sequences of the type strains of eight validly described species and two invalid species of the genus Thermoactinomyces were determined and phylogenetically analysed. The validly described Thermoactinomyces species formed phylogenetic lineages related to the family Bacillaceae, as shown previously. However, the available strains of 'Thermoactinomyces glaucus' and 'Thermoactinomyces monosporus' exhibited their closest phylogenetic affinities not to the genus Thermoactinomyces but to the genus Saccharomonospora. Some Thermoactinomyces species were shown to be closely related from 16S rDNA sequence analysis. Particularly, Thermoactinomyces vulgaris KCTC 9076T and Thermoactinomyces candidus KCTC 9557T had the same 16S rDNA sequences and Thermoactinomyces thalpophilus KCTC 9789T and Thermoactinomyces sacchari KCTC 9790T showed 16S rDNA similarity value of almost 100%. From phylogenetic analysis based on 16S rDNA sequences, it is suggested that the genus Thermoactinomyces should be taxonomically re-evaluated using other useful taxonomic markers.

DNA, Bacterial↗
PubMed1990

Transfer of Kingella indologenes (Snell and Lapage 1976) to the genus Suttonella gen. nov. as Suttonella indologenes comb. nov.; transfer of Bacteroides nodosus (Beveridge 1941) to the genus Dichelobacter gen. nov. as Dichelobacter nodosus comb. nov.; and assignment of the genera Cardiobacterium, Dichelobacter, and Suttonella to Cardiobacteriaceae fam. nov. in the gamma division of Proteobacteria on the basis of 16S rRNA sequence comparisons.

The 16S rRNA sequences of Kingella indologenes, Cardiobacterium hominis, and Bacteroides nodosus were determined by direct RNA sequencing, using a modified Sanger method. Sequence comparisons indicated that these three species represent a novel family in the gamma division of Proteobacteria. On the basis of these data, K. indologenes and B. nodosus cannot retain their current generic status as they are not closely related to other members of their assigned genera. Therefore, we propose transfer of K. indologenes to the new genus Suttonella as Suttonella indologenes and transfer of B. nodosus to the new genus Dichelobacter as Dichelobacter nodosus and assign the genera Cardiobacterium, Suttonella, and Dichelobacter to a new family, Cardiobacteriaceae, in the gamma division of Proteobacteria.

Bacteroides↗
PubMed1990

The phylogeny of Aerococcus and Pediococcus as determined by 16S rRNA sequence analysis: description of Tetragenococcus gen. nov.

The phylogenetic interrelationships of the genera Pediococcus and Aerococcus were investigated using reverse transcriptase sequencing of 16S rRNA. The genus Pediococcus was found to be phylogenetically heterogeneous. The four species P. acidilactici, P. damnosus, P. parvulus and P. pentosaceus formed a phylogenetically distinct group. Within this pediococcal cluster, P. acidilactici was closely related to P. pentosaceus whereas P. damnosus showed a specific relationship with P. parvulus. The species P. dextrinicus, although showing significant sequence relatedness with these pediococcal species, was peripheral to the genus. Pediococcus halophilus exhibited low sequence homology with all of the species examined and formed a distinct line of descent. Pediococcus halophilus exhibited a closer affinity with enterococci and carnobacteria than with the other lactic acid bacteria. Pediococcus urinae-equi was phylogenetically very closely related to Aerococcus viridans. The 16S rRNA sequences of the type strains of these species differed by only two nucleotides (99.9% sequence homology) and clearly demonstrate that P. urinae-equi is a member of the genus Aerococcus.

Base Sequence↗