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PubMed1995

Phylogeny of Serpulina based on sequence analyses of the 16S rRNA gene and comparison with a scheme involving biochemical classification.

Twenty-one putative Serpulina strains, representing six proposed biochemical groups, were selected for phylogenetic studies based on 16S rRNA sequencing. The biochemical groups were distinguished by the degree of beta-haemolysis, indole production, hippurate hydrolysis and alpha-galactosidase-, and beta-glucosidase activity. The 16S rRNA sequences of the U2 to U5 region, including three evolutionarily variable regions, from representatives of each biochemical group were determined by automated solid phase DNA sequencing after in vitro amplification by the polymerase chain reaction (PCR). The sequences generated were 532 nucleotides in length. Sequence alignments showed that all the strains were closely related, with six informative positions in the region sequenced. A dendrogram was constructed from these data and compared with the tentative biochemical classification. The results support the proposed biochemical classification and indicate that at least five genetic variants of the genus Serpulina can be identified.

Animals↗
PubMed2006

Simplified phenotypic scheme evaluated by 16S rRNA sequencing for differentiation between Yersinia enterocolitica and Y. enterocolitica-like species.

Many clinical laboratories are familiar with a sizeable group of "unserotypeable Yersinia enterocolitica" strains. Due to identification problems, this group may hide Y. bercovieri, Y. mollaretii, and Y. rohdei strains. We present a simple scheme to distinguish between pathogenic Y. enterocolitica and potentially nonpathogenic Y. enterocolitica-like strains.

Bacterial Typing Techniques↗
PubMed2006

Physiological, biochemical, and genetic characterization of an alicyclic amine-degrading Mycobacterium sp. strain THO100 isolated from a morpholine-containing culture of activated sewage sludge.

Mycobacterium sp. strain THO100 was isolated from a morpholine-containing culture of activated sewage sludge. This strain was able to utilize pyrrolidine, morpholine, piperidine, piperazine, and 1,2,3,6-tetrahydropyridine as the sole sources of carbon, nitrogen, and energy. The degradation pathway of pyrrolidine as the best substrate for cellular growth was proposed based on the assays of substrate-induced cytochrome P450 and constitutive enzyme activities toward 4-aminobutyric acid (GABA) and succinic semialdehyde (SSA). Its 16S ribosomal RNA gene sequence (16S rDNA) was identical to that of Mycobacterium tokaiense ATCC 27282(T). The morABC genes responsible for alicyclic amine degradation were nearly identical among different species of Mycobacteria. Remarkably, repetitive sequences at the intergenic spacer (IGS) region between morC and orf1' were detected by comparison of the nearly identical mor gene cluster regions. Considering the strain activity for alicyclic amine degradation, the deleted 65-bp DNA segment did not significantly alter the open reading frames, and the expression and functions of the P450(mor) system remained unaltered. In addition, we found a spontaneous deletion of P450(mor) from another strain HE5 containing the archetypal mor gene cluster, which indicated a possible occurrence of DNA recombination to rearrange the DNA.

Amines↗
PubMed2002

Partial 16S rRNA gene sequence diversity and numerical taxonomy of slow growing pigeonpea (Cajanus cajan L Millsp) nodulating rhizobia.

An investigation was carried out to determine the diversity of 30 isolates of slow growing pigeonpea nodulating rhizobia based on variations in partial sequences of the 16S rRNA gene and numerical analysis of 80 phenotypic traits. Phylogenetic analysis using molecular sequences of 23 isolates showed that ARPE1 separated from the other isolates at an average distance of >14% divergence level. The other isolates were all within 5% divergence from each other but separated into four main groups, with group 1 containing 16 of the 23 isolates. Comparisons to sequences of reference strains revealed that the group 1 isolates were phylogenetically closely related to the slow growing soybean nodulating rhizobia belonging to Bradyrhizobium elkanii, although only three of these isolates were able to nodulate soybean. Numerical analysis of phenotypic data of 19 isolates showed that 14 isolates clustered together in one branch of the phenogram, which included the group 1, group 2 and group 4 isolates from the phylogenetic analysis. The group 3 isolates were highly variable in the phenogram with similarity levels lower than 50% among these isolates.

Bradyrhizobium↗
PubMed1997

Comparison of 16S ribosomal DNA sequences of all Xanthomonas species.

The phylogenetic relationships of all validly described species of the genus Xanthomonas and the type strain of Stenotrophomonas maltophilia were analyzed by sequencing and comparing 16S ribosomal DNAs (rDNAs). The two genera exhibited a mean sequence similarity value of 96.6%, corresponding to differences at 50 nucleotide positions on average. The species of the genus Xanthomonas exhibited relatively high levels of overall sequence similarity; the mean similarity value was 98.2%, which corresponds to an average of 14 mutual nucleotide differences. Within the genus Xanthomonas, a group containing Xanthomonas albilineans, Xanthomonas hyacinthi, Xanthomonas theicola, and Xanthomonas translucens clustered apart from the main Xanthomonas core, whereas Xanthomonas sacchari formed a third phylogenetic lineage. Due to the very restricted variability in 16S rDNA sequences within the genus Xanthomonas, rDNA signatures that have possible diagnostic value for differentiating the Xanthomonas species could not be determined with certainty. When sequence similarities were compared with DNA-DNA pairing data determined previously, there was only a limited correlation. This illustrates the different resolving powers of the techniques for determining phylogenetic hierarchies and for species delineation.

Base Sequence↗
PubMed1993

Phylogeny of twenty Thermus isolates constructed from 16S rRNA gene sequence data.

The sequences of the 16S rRNA genes of 20 Thermus isolates were determined to a high fidelity by using automated DNA sequencing and fluorescent-dye-labelled primers. The strains tested included members of the three validly named Thermus species and representatives of major taxonomic clusters defined previously for this genus. The parsimony method was used to reconstruct the phylogeny of the strains from the aligned sequences, and a bootstrap analysis revealed a number of well-supported clades. Our results are not consistent with groupings inferred from numerical taxonomy data but support the conjecture that the genus Thermus contains more species than the three currently recognized species.

Base Sequence↗
PubMed2006

[Study on Bartonella vinsonii berkhoffii isolated from blood of native dogs in China].

OBJECTIVE: To isolate and identify Bartonella strains from native dogs in Shandong province in China. METHODS: EDTA-anticoagulated blood samples were collected from 71 native dogs in Yanggu county of Shandong province in March 2005. All isolates were grown on brain heart infusion agar plates containing 5% defibrinated rabbit blood. The agar plates were incubated at 37 degrees C in a humidified with 5% CO2 environment for 4 weeks or longer. All Bartonella-like isolates were examined by routine Gram and Giménez staining and then followed by polymerase chain reaction (PCR) and PCR-RFLP analysis for identification and differentiation of the isolates. Sequencing 16S rRNA, citrate synthase (gltA) gene and 16S-23S rRNA ITS were carried out and sequential similarities were calculated using the DNASTAR5 software package. The phylogenetic tree was inferred from each bootstrap sample, using the neighbor-joining methods as executed in the MEGA 3.1 software. The translation from DNA to protein were determined by DNASIS 2.5. RESULTS: The two Bartonella-like organisms (strains Q52SHD and Q64SHD) were isolated from the blood of 71 dogs. Light microscopic examination of the Gram and Giménez-stained micro-organisms showed small, short and slightly curved pleomorphic gram-negative bacilli. Amplified products of the three pairs of Bartonella genus-specific primers carried the same size as the predicted of those Bartonella species. Data from PCR-RFLP analysis showed that the two strains that having the same profiles were all different from the B. henselae type strain-16S rRNA, gltA and 16S-23S rRNA ITS sequences from the two isolates were 100.0%, 99.7% and 97.2% homologous to B. vinsonii berkhoffii. CONCLUSIONS: Based on these findings, the two isolates Q52SHD and Q64SHD were demonstrated as B. vinsonii berkhoffii. To our knowledge, this was the first report on the presence of Bartonella infection in native dogs from China, which constituted a large reservoir of Bartonella species in this country.

Animals↗
PubMed2006

Variation in the nod gene RFLPs, nucleotide sequences of 16S rRNA genes, Nod factors, and nodulation abilities of Bradyrhizobium strains isolated from Thai Vigna plants.

The analysis of nod genes and 16S rRNA gene regions, Nod factors, and nodulation abilities of Brady rhizobium strains isolated from tropical Thai Vigna species is reported. A total of 55 Bradyrhizobium strains isolated from two cultivated and six wild Vigna species growing in central and northern Thailand were evaluated. Thai Vigna spp. Bradyrhizobium strains showed higher levels of nod gene RFLP diversity compared with Thai soybean Brady rhizobium strains or temperate strains of Bradyrhizobium japonicum and Bradyrhizobium elkanii. Analysis of the 16S rRNA gene region using selected strains also suggests a high genetic diversity of the Thai Vigna-Bradyrhizobium association. Based on thin-layer chromatography analysis, Nod factors produced by tropical Thai Vigna spp. Brady rhizobium strains are more diverse than temperate Japanese and US strains of B. japonicum and B. elkanii. Thai Vigna spp. Bradyrhizobium strains showed variation in nodulation ability and affinity, estimated by the number of normal nodules versus green nodules in an inoculation study. There are some Bradyrhizobium-host combinations that could not form any nodules, suggesting that some genetic differentiation has evolved in their host range. However, most of the Thai Vigna spp. Bradyrhizobium strains formed nodules on the cultigens soybean (Glycine max), mungbean (Vigna radiata), azuki bean (Vigna angularis), and cowpea (Vigna unguiculata). This is the first study on Bradyrhizobium strains associated with a range of cultivated and wild Vigna and reveals that these Bradyrhizobium strains are diverse and may provide novel sources of useful variation for the improvement of symbiotic systems.

Bradyrhizobium↗
PubMed1993

Identification of mycobacteria from animals by restriction enzyme analysis and direct DNA cycle sequencing of polymerase chain reaction-amplified 16S rRNA gene sequences.

Two methods, based on analysis of the polymerase chain reaction-amplified 16S rRNA gene by restriction enzyme analysis (REA) or direct cycle sequencing, were developed for rapid identification of mycobacteria isolated from animals and were compared to traditional phenotypic typing. BACTEC 7H12 cultures of the specimens were examined for "cording," and specific polymerase chain reaction amplification was performed to identify the presence of tubercle complex mycobacteria. Combined results of separate REAs with HhaI, MspI, MboI, and ThaI differentiated 12 of 15 mycobacterial species tested. HhaI, MspI, and ThaI restriction enzyme profiles differentiated Actinobacillus species from mycobacterial species. Mycobacterium bovis could not be differentiated from M. bovis BCG or Mycobacterium tuberculosis. Similarly, Mycobacterium avium and Mycobacterium paratuberculosis could not be distinguished from each other by REA but were differentiated by cycle sequencing. Compared with traditional typing, both methods allowed rapid and more accurate identification of acid-fast organisms recovered from 21 specimens of bovine and badger origin. Two groups of isolates were not typed definitively by either molecular method. One group of four isolates may constitute a new species phylogenetically very closely related to Mycobacterium simiae. The remaining unidentified isolates (three badger and one bovine) had identical restriction enzyme profiles and shared 100% nucleotide identify over the sequenced signature region. This nucleotide sequence most closely resembled the data base sequence of Mycobacterium senegalense.

Animals↗
PubMed1995

Taxonomy of the feline mycoplasmas Mycoplasma felifaucium, Mycoplasma feliminutum, Mycoplasma felis, Mycoplasma gateae, Mycoplasma leocaptivus, Mycoplasma leopharyngis, and Mycoplasma simbae by 16S rRNA gene sequence comparisons.

The nucleotide sequence of the 16S rRNA gene of eight mycoplasmas isolated from felids was determined and used for taxonomic comparisons. A signature nucleotide sequence motif and overall sequence similarity to other mollicutes positioned Mycoplasma felifaucium, Mycoplasma felis, Mycoplasma leocaptivus, Mycoplasma leopharyngis, and Mycoplasma simbae in the Mycoplasma fermentans phylogenetic group of mollicutes. Mycoplasma arginini and Mycoplasma gateae were positioned in the Mycoplasma hominis phylogenetic group of mollicutes, and Mycoplasma feliminutum was positioned in the phylogenetically distant Acholeplasma group of mollicutes, showing that host family preference does not necessarily derive from bacterial phylogenetic closeness.

Acholeplasma↗
PubMed1999

[Amplification of phytoplasma 16S rDNA from banana bunchy top disease, RFLP and sequence analysis of 16S rDNA fragment].

Extract DNA from banana plants with banana bunchy top disease and amplify the phytoplasma 16S rDNA fragment by nested PCR. The classification of the phytoplasma established on the basis of 16S rDNA restriction patterns was examined by performing a sequence analysis of 16S rDNA fragment. The RFLP pattern, sequence data and phylogenic tree showed that this phytoplasma should belong to Group I(Phytoplasma asteri).

Base Sequence↗
PubMed1995

Taxonomic analysis of the tortoise mycoplasmas Mycoplasma agassizii and Mycoplasma testudinis by 16S rRNA gene sequence comparison.

The nucleotide sequences of the 16S rRNA genes of two mycoplasmas, Mycoplasma agassizii (proposed sp. nov.) and Mycoplasma testudinis, isolated from tortoises were determined and used for taxonomic comparisons. Signature nucleotide sequence motifs and overall sequence similarities to other mollicutes positioned these mycoplasmas in the M. hyorhinis and M. pneumoniae phylogenetic groups, respectively. A third, previously unrecognized tortoise mycoplasma was detected by 16S rRNA gene amplification and sequence analysis and was positioned in the M. fermentans phylogenetic group. The 16S rRNA gene of Acholeplasma laidlawii was similarly detected in a tortoise isolate, showing that diverse mollicutes can share the same family of reptilian host.

Animals↗
PubMed1993

Phylogenic homogeneity of Coxiella burnetii strains as determinated by 16S ribosomal RNA sequencing.

DNA coding for the 16S rRNA of six strains of the obligate intracellular bacterium Coxiella burnetii was directly amplified from lysed host cells using the polymerase chain reaction. The amplification product was sequenced using a linear-PCR procedure and compared with other published 16S rRNA sequences. The results of this analysis confirm the position of C. burnetii in the gamma subgroup of the proteobacteria. The data show that all of the C. burnetii strains are highly related (> 99%) on the basis of 16S rRNA sequences although they had different geographic origins and phenotypic characteristics. The data support a phylogenetic homogeneity of the genus Coxiella with only one species which is C. burnetii.

Base Sequence↗
PubMed1998

Three cases of Anaerobiospirillum succiniciproducens bacteremia confirmed by 16S rRNA gene sequencing.

We describe three cases of Anaerobiospirillum succiniciproducens bacteremia from Australia. We believe one of these cases represents the first report of A. succiniciproducens bacteremia in a human immunodeficiency virus (HIV)-infected individual. The other two patients had an underlying disorder (one patient had bleeding esophageal varices complicating alcohol liver disease and one patient had non-Hodgkin's lymphoma). A motile, gram-negative, spiral anaerobe was isolated by culturing blood from all patients. Electron microscopy showed a curved bacterium with bipolar tufts of flagella resembling Anaerobiospirillum spp. Sequencing of the 16S rRNA genes of the isolates revealed no close relatives (organisms likely to be in the same genus) in the sequence databases, nor were any sequence data available forA. succiniciproducens. This report presents for the first time the 16S rRNA gene sequence of the type strain of A. succiniciproducens, strain ATCC 29305. Two of the three clinical isolates have sequences identical to that of the type strain, while the sequence of the other strain differs from that of the type strain at 4 nucleotides.

AIDS-Related Opportunistic Infections↗