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PubMed1995

Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus.

We determined the 16S rRNA sequences of the type strains of Streptococcus mitis and Streptococcus gordonii and calculated the phylogenetic distances between those organisms and other members of the genus Streptococcus. The viridans group streptococci were separated into five phylogenetic groups; we named these groups the anginosus group, the mitis group, the salivarius group, the bovis group, and the mutans group. S. mitis and S. gordonii clustered in the mitis group together with Streptococcus pneumoniae, Streptococcus oralis, Streptococcus sanguis, and Streptococcus parasanguis at levels of sequence homology of more than 96%. Within this group, S. mitis, S. oralis, and S. pneumoniae exhibited more than 99% sequence homology with each other, although the DNA-DNA similarity values for their total chromosome DNAs were less than 60%.

DNA, Bacterial↗
PubMedDate not supplied

Construction of phylogenetic tree based on G + C contents in DNA and 16S rRNA sequences: example for group 1 of genus Bacillus.

The applicability of the G + C content in DNA in the construction of phylogenetic tree was studied. The group 1 of the genus Bacillus was selected as an object for study. Statistically reliable correlation between evolutionary distances of 16S rRNA sequences (Ei) and parameter Pi named as "GC evolutionary distance" was shown. The value of Pi is the difference between the G + C content in DNA of two species branching from one phylogenetic line. The coefficient of correlation between Ei and Pi equals 0.97 for the representatives of group 1, including Bacillus anthracis, B. cereus, B. circulans, B. firmus, B. lautus, and B. subtilis. Phylogenetic studies of the G + C content in DNA in the genus Bacillus, group 1 representatives has shown that this character can be used in molecular systematics and phylogeny as additional data altogether with the data on 16S rRNA sequences.

Bacillus↗
PubMed1993

Phylogenetic relationship of Gemella morbillorum to Gemella haemolysans.

Partial 16S rRNA gene sequences (16S rDNA) of Gemella morbillorum and Gemella haemolysans were determined by sequencing polymerase chain reaction-amplified DNA. A phylogenetic analysis of 53 eubacterial 16S rRNA sequences grouped the gemellae on a distinct branch separate from the 18 members of the genus Streptococcus. DNA-DNA hybridization results indicate that the two gemellae are related at the genus level but are not a single species.

Base Sequence↗
PubMed1999

16S rDNA sequencing of Ruminococcus albus and Ruminococcus flavefaciens: design of a signature probe and its application in adult sheep.

The ruminococci are an important group of fibrolytic bacteria inhabiting the rumen. Seventeen strains of presumptively identified Ruminococcus were evaluated by a combination of nearly complete and partial 16S rDNA sequence that identified all strains as either Ruminococcus albus or Ruminococcus flavefaciens. All sequences fell into cluster IV of the clostridia, while other species of ruminococci (e.g. Ruminococcus obeum, Ruminococcus gnavus, Ruminococcus lactaris) fall into cluster XIVa of the clostridia. Ruminococcus cluster IV sequences were used to design a 16S rRNA oligonucleotide probe to assess the relative abundance of target populations in a stable ruminal environment. A stable population (animals fed eight times per day) was established in sheep so that statistically robust comparisons could be made in the absence of variation due to diurnal rumen fluctuations. The steady state populations were sampled six times over a 24 d period and direct microscopic counts (DC), total culturable counts (TCC), and total cellulolytic counts (CEL) were determined. DC and culturable data (TCC and CEL) were compared with relative abundance estimates of Ruminococcus IV and Fibrobacter succinogenes. A combination of the Ruminococcus and F. succinogenes probes accounted for 4.0% of the bacterial population and cellulolytic bacteria (measured by most-probable numbers) were 5.2% of the total culturable count. These data suggest that a major portion of the Ruminococcus and Fibrobacter diversity has been cultured and is represented by available sequences. Steady state populations were measured over several days in three sheep and an estimate of variation in DC, TCC, CEL and 16S-based data were obtained. These variance estimates could be used to determine the theoretical sample sizes required to obtain statistically significant differences under different experimental conditions.

Animals↗
PubMed1995

Phylogenetic analysis of polycyclic aromatic hydrocarbon degrading mycobacteria by 16S rRNA sequencing.

Mycobacterium sp. PYR-1 was previously isolated in our laboratory and was shown to be able to mineralize high molecular mass polycyclic aromatic hydrocarbons (PAHs) [Heitkamp and Cerniglia, (1988) Appl. Environ. Microbiol. 54, 1612-1614]. In this research, the 16S rRNA gene (rDNA) of this strain was amplified by polymerase chain reaction (PCR) and directly sequenced by cycle sequencing method. We compared this sequence with all known mycobacterial 16S rDNA sequences available from GenBank and found that Mycobacterium sp. PYR-1 16S rDNA differs from the other mycobacteria, especially in the region of nucleotides 168-200 (in the Escherichia coli numbering system). Using the 16S rDNA sequences of the mycobacteria, a phylogenetic tree was constructed. The data from the phylogenetic tree and similarity values suggest that Mycobacterium sp. PYR-1 is closer to M. aurum and M. vaccae. Using the same approach, we also determined the 16S rDNA from an another PAH-degrading Mycobacterium sp. PAH135, isolated by Grosser and colleagues (1991) (Appl. Environ. Microbiol. 57, 3462-3469). Mycobacterium sp. PAH135 was found to be closer to M. aichiense, and different from our Mycobacterium sp. PYR-1.

Base Sequence↗
PubMed2001

16S rDNA sequence analysis of bacterial isolates from biodeteriorated mural paintings in the Servilia tomb (Necropolis of carmona, Seville, Spain).

Bacteria were isolated from damaged mural paintings of the Servilia tomb (necropolis of Carmona, Seville, Spain). Selected strains, representative for different clusters of isolates with similar fatty acid profiles, were analysed by 16S rDNA sequence analysis. Bacillus is the dominant genus among the isolates: members of the rRNA species complexes of B. megaterium, B. pumilus and B. firmus were found as well as several other Bacillus species. One group of halotolerant isolates falls in the Bacillus sensu lato group, with closest relatedness to the genera Salibacillus and Virgibacillus. Other genera found are Artbrobacter, Micrococcus, Streptomyces, Sphingomonas, Paenibacillus, and a genus closely related to Paracraurococcus. Many isolates showed low 16S rDNA sequence similarities with the closest related database entries, a strong indication for the presence of several new species among the isolates.

Biodegradation, Environmental↗
PubMed1999

Characterisation of rhizobia from African acacias and other tropical woody legumes using Biolog and partial 16S rRNA sequencing.

A Biolog (sole carbon source utilisation) user database of tropical and temperature rhizobial strains was created and used in conjunction with the partial 16S rRNA sequencing method to characterise 12 rhizobial isolates from African acacias and other tropical woody legumes. There was close agreement between the two methods but also some significant discrepancies. A high degree of diversity was shown in the relatively small sample of isolates, with 4 out of 5 of the currently proposed rhizobial genera represented. This is the first time Biolog has shown congruence with genotypic fingerprinting using a wide selection of rhizobial reference and test strains.

Acacia↗
PubMed2006

[Analysis of DNA homology and 16S rDNA sequence of rhizobia, a new phenotypic subgroup, isolated from Xizang Autonomous Region of China].

Based on the studies of numerical taxonomy, the seven rhizobial strains isolated from the root nodules of leguminous plants Trigonella spp. and Astragalus spp. growing in the Xizang Autonomous Region of China constituted a new phenotypic subgroup, where wide phenotypic and genotypic diversity among legume crops had been reported due to complex terrain and various climate. The new phenotypic subgroup were further identified to clarify its taxonomic position by DNA homology analysis and 16S rDNA gene sequencing. The mol% G + C ratio of the DNA among members of the new subgroup ranged from 59.5 to 63.3 mol% as determined by T (m) assay. The levels of DNA relatedness, determined by using the DNA liquid hybridization method, among the members of the new subgroup were between 74.3% and 92.3%, while level of DNA relatedness between the central strains XZ2-3 of the new subgroup and the type strains of known species of Rhizobium was less than 47.4%. These results indicated that the new phenotypic subgroup is a DNA homological group different from described species of Rhizobium. Therefore, this new phenotypic subgroup was supposed to be a new species in the genus of Rhizobium since the strains in the same species generally exhibit levels of DNA homology ranging from 70 to 100%. A systematic identification method-16S rDNA gene sequence comparison was carried out to determine the phylogenetic relationships of the new subgroup with the described species of Rhizobium. The GenBank accession number for the 16S rDNA sequence of the central strain XZ2-3 of the new subgroup is DQ099745. The full-length 16S rDNA gene sequence were sequenced by chain terminator techniques and analyzed with PHYLIP. The phylogenetic trees were constructed by using the programs DRAWTREE. The phylogenetic analysis indicated that new subgroup occupy a independent sub-branch in phylogenetic tree. The sequence similarities between the center strain XZ2-3 and the closest relatives, strain R. leguminosarum USDA2370T and R. etli CFN42T, were 96.55% and 96.62% respectively. Both the 16S rDNA sequence data and the DNA relatedness data suggested that the new phenotypic subgroup isolated from the root nodules of leguminous plants Trigonella spp. and Astragalus spp. obtained from the Xizang Autonomous Region of China represents a new rhizobial species in the genus of Rhizobium according to the minimal standards for the description of new genera and species of root-and stem-nodulating bacteria.

Base Sequence↗
PubMed1993

A Staphylococcus aureus-specific oligonucleotide probe derived from 16S rRNA gene sequences.

Genes encoding 16S rRNA were sequenced from 16 species of Staphylococcus. Sequence analysis highlighted a potential Staph. aureus-specific region and a complementary oligonucleotide probe was synthesized and its specificity tested. Northern blotting indicated molecular specificity, and dot blots to RNA from Staph. aureus, Staph. capitis, Staph. caprae, Staph. carnosus, Staph. caseolyticus, Staph. cohnii, Staph. epidermidis, Staph. gallinarum, Staph. haemolyticus, Staph. hominis, Staph. hyicus, Staph. saprophyticus, Staph. sciuri, Staph. simulans, Staph. warneri and Staph. xylosus indicated species-specificity.

Base Composition↗
PubMed2002

Development of a PCR test for the identification of Staphylococcus intermedius based on the 16S rDNA sequence.

The development of a PCR assay based on the 16S ribosomal RNA gene (rDNA) sequence was carried out for the identification of Staphylococcus intermedius. Sixty-six strains of S. intermedius, 70 of Staphylococcus aureus and 2 of Staphylococcus hyicus were examined for the assay. The 16S rDNA, of which the PCR target fragment makes up 901 bp corresponding to the sequence data of the gene, was detected in all strains of S. intermedius, but it was not detected in any strains of either S. aureus or S. hyicus. These results suggest that the PCR allows a simple and precise identification of S. intermedius.

Coagulase↗
PubMed2006

Bifidobacterial diversity determined by culturing and by 16S rDNA sequence analysis in feces and mucosa from ten healthy Spanish adults.

This study aimed to identify the numerically predominant bifidobacterial species in feces and mucosa of healthy Spanish people and to determine their phenotypic and genetic diversity. To this end, both traditional culturing and molecular methods were used. A set of 196 bifidobacterial colonies was identified from the counting plates by sequencing of a stretch of their 16S rRNA gene. Representative isolates were phenotypically characterized by their carbohydrate fermentation profile and genotypically typed by RAPD-PCR. Four 16S rDNA libraries composed of 113 clones from two fecal and two mucosal samples were independently analyzed. Seven bifidobacterial species were identified by culturing, and six by 16S rDNA analysis. Both methodologies showed Bifidobacterium longum and B. pseudocatenulatum to predominate in feces and mucosa, although high interindividual variability was noted. High phenotypic variation was observed in the fermentation profile of different isolates from the same species. RAPD analysis showed that two to five strains made up the subjects' personal bifidobacterial communities. The identification of the dominant bifidobacterial species could be useful for the rational design, use, and evaluation of probiotics in our community.

Adult↗
PubMed2000

Infectivity, transmission and 16S rRNA sequencing of a rickettsia, Coxiella cheraxi sp. nov., from the freshwater crayfish Cherax quadricarinatus.

A rickettsia-like organism isolated from infected, farm-reared Cherax quadricarinatus was cultured in the yolk sac of developing chicken eggs, but could not be cultured in 3 continuous cell lines, bluegill fry (BF-2), fathead minnow (FHM), and Spodoptera frugiperda (Sf-9). The organism was confirmed by fulfilling Koch's postulates as the aetiological agent of mortalities amongst C. quadricarinatus. When C. quadricarinatus was inoculated with the organism, mortality was 100% at 28 degrees C and 80% at an ambient temperature of 24 degrees C. Horizontal transmission with food and via the waterborne route was demonstrated, but mortalities were lower at 30 and 10% respectively over a 4 wk period. The 16S rRNA sequence of 1325 base pairs of the Gram-negative, obligate intracellular organism was 95.6% homologous to Coxiella burnetii. Of 18 species compared to this rickettsia, the next most closely related bacterium was Legionella pneumophila at 86.7%. The suggested classification of this organism is Order Rickettsiales, family Rickettsiaceae, tribe Rickettsieae, within the genus Coxiella. We suggest it should be named Coxiella cheraxi sp. nov.

Animals↗
PubMed2003

Advantages of using mitochondrial 16S rDNA sequences to classify clinical isolates of Acanthamoeba.

PURPOSE: This work was intended to test the classification of Acanthamoeba into genotypes based on nuclear ribosomal RNA gene (18S rDNA, Rns) sequences. Nearly all Acanthamoeba keratitis (AK) isolates are genotype RnsT4. This marked phylogenetic localization is presumably either due to an innate potential for pathogenicity or to a peculiarity of the gene sequences used. To differentiate between these possibilities, relationships among isolates have been reexamined, using a second gene. METHODS: Phylogenetic relationships among isolates of Acanthamoeba were studied, using sequences of the mitochondrial small subunit ribosomal RNA gene (16S rDNA; rns). Genotypes based on complete sequences of approximately 1540 bp were determined for 68 strains, by using multiple phylogenetic analyses. RESULTS: Each strain's mitochondria contained a single intron-free rns sequence (allele). The 68 strains had 35 different sequences. Twenty-eight strains had unique sequences, and 40 strains each shared one of the seven remaining sequences. Eleven mitochondrial rns genotypes corresponding to 11 of 12 previously described nuclear Rns genotypes were identified. Genotype rnsT4 was subdivided into eight distinct clades, with seven including Acanthamoeba keratitis (AK) isolates. CONCLUSIONS: The phylogenetic clustering of AK isolates was confirmed and thus is not specific to the nuclear gene. Rns and rns sequences are both suitable for genotyping of ACANTHAMOEBA: However, the mitochondrial sequences are shorter and more consistent in length, have a higher percentage of alignable bases for sequence comparisons, and have none of the complications caused by multiple alleles or introns, which are occasionally found in Rns. In addition, the more common occurrence of strains with identical rns sequences simplifies identification and clustering of isolates.

Acanthamoeba↗
PubMed2004

Vibrio alginolyticus infection in the white shrimp Litopenaeus vannamei confirmed by polymerase chain reaction and 16S rDNA sequencing.

A gram-negative, rod-shaped bacterium identified as Vibrio alginolyticus was isolated from diseased Litopenaeus vannamei (also called Penaeus vannamei) in Taiwanese culture ponds. The diseased shrimp displayed poor growth, anorexia, inactivity, reddish pleural borders of antennae, uropods and telson, opaque and whitish musculature, and mortality. In histological preparations, melanized hemocytic granulomas were observed in the connective tissue around hemal sinuses together with hemocytic aggregation in necrotic musculature. Six isolates of Vibrio were collected from diseased shrimp at 3 farms, and these were evaluated for characteristics including morphology, physiology, biochemistry and sensitivity to antibiotics. The results indicated that the isolates belonged to a single species that grew in 1 to 8% NaCl, at 10 to 40 degrees C and on TCBS (thiosulfatecitrate-bile sucrose) agar, and that gave positive catalase, O/F (Oxidation/Fermentation), lysine decarboxylase, gelatinase and cytochrome-oxidase tests. Identification of CH003 (1 of 6 isolates) was confirmed by PCR assay for V. alginolyticus (expected amplicon 1486 bp). The 16S rDNA sequence (GenBank accession number AY373027) gave 99.9% sequence identity to V. alginolyticus (GenBank accession number X74690). The calculated 96 h LD50 dose of the isolated strain was 3.0 x 10(5) colony forming units (CFU) shrimp(-1) (6.6 x 10(4) CFU g(-1)).

Animals↗
PubMed2005

Phylogenetic analysis of six species of pacific abalone (Haliotidae) based on DNA sequences of 16s rRNA and cytochrome c oxidase subunit I mitochondrial genes.

Six species of abalones (Haliotidae) are found on the Korean coasts. Identification and characterization of these abalones are usually based on morphologic characters. In this research we compared the partial sequences of the mitochondrial 16S ribosomal RNA and cytochrome c oxidase subunit I genes to identify species using molecular data and to determine their phylogenetic relationships. Sequence alignments and phylogenetic analysis revealed that the 6 species fell into 2 distinct groups which were genetically distant from each other and exhibited little internal phylogenetic resolution. One group included Haliotis discus hannai, H. discus discus, H. madaka, and H. gigantea, while the other group contained H. diversicolor supertexta and H. diversicolor diversicolor. The 16S rRNA sequences were relatively more conserved than to the COI sequences, but both gene sequences provided sufficient phylogenetic information to distinguish among the 6 species of Pacific abalone, and thus could be valuable molecular characters for species identification.

Animals↗
PubMed2002

16S rRNA sequence analysis of bacteria present in foaming activated sludge.

The formation of a stable viscous foam on activated sludge aeration basin surfaces is a world wide problem. Foam is usually comprised of filamentous bacteria occurring predominantly in the mixed liquor. The lack of availability of pure cultures of most filaments and the limited amount of characterisation data available for them, means that our current understanding of their taxonomic position is very poor and their relationship to other bacteria are not known. 16S rDNA sequencing was used in an attempt to identify the bacteria in a foaming sample from the Centurion Waste Water Treatment Plant in Gauteng South Africa.

Actinobacteria↗
PubMed1999

Diversity of Pseudomonas strains isolated with King's B and Gould's S1 agar determined by repetitive extragenic palindromic-polymerase chain reaction, 16S rDNA sequencing and Fourier transform infrared spectroscopy characterisation.

King's B and Gould's S1 agar were compared with regard to the isolation of Pseudomonas from four environmental samples. In all samples, King's B gave the highest number of colony-forming units, and in some environments, there were more fluorescent colony-forming units on King's B as well. However, almost all types grew on Gould's S1, which enabled us to isolate a greater variety of groups than with King's B, fluorescent as well as non-fluorescent members of Pseudomonas. The Pseudomonas isolates were comparatively typed by repetitive extragenic palindromic-polymerase chain reaction and Fourier transform infrared spectroscopy, not previously used for environmental Pseudomonas. The two typing methods were similar in resolution, thus Fourier transform infrared spectroscopy proved fast and reproducible and is a good method for discrimination at subspecies level. Representative strains were identified by partial 16S rDNA sequencing. Thus, we suggest Gould's S1 agar be used for isolation of Pseudomonas because the results are reproducible, specific and give the most diverse recovery and the least work.

Agar↗