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At least 343 records · Page 19Linked to original sources
PubMed2001

Development of a PCR test to diagnose Haemophilus parasuis infections.

A polymerase chain reaction (PCR) test was developed in order to improve the accuracy and speed of diagnosis of Haemophilus parasuis, an economically important respiratory pathogen that affects swine. The gene sequence of the 16S small subunit ribosomal RNA of H. parasuis (GenBank M75065) was compared with 56 16S sequences of related bacteria, including those frequently isolated from pig tissues. Two species-specific primers were designed: HPS forward and HPS reverse. The predicted size of the amplified PCR product was 821 bp. The PCR test could detect a minimum of 102 bacteria and 0.69 pg of DNA. Thirty-one H. parasuis isolates, including 12 different serovars and 19 field isolates, were positive using the PCR test. No amplification was observed when the test was run using DNA from 15 other bacterial species commonly isolated from swine tissues. A weak band was observed when the PCR test was performed using Actinobacillus indolicus DNA as template. Clinical samples tested by PCR included tissues and swabs from 5 animals naturally infected with H. parasuis and 1 experimentally infected animal. The PCR was positive in 26 of 30 clinical samples. Four samples showed weak bands, and these results were not considered positive. Haemophilus parasuis was isolated from 18 of 30 of these samples. Tissues from specific pathogen-free (SPF) pigs and from unrelated species were negative for H. parasuis isolation and PCR. The developed PCR was successfully used in the diagnosis of H. parasuis infection, especially when compared with traditional microbiology techniques.

Animals↗
PubMed2002

[Phylogenetic analysis of intestinal bacterium using the distribution of intestinal bacterium in cyprinidate fishes and 16S DNA sequence data set].

There is a complex- and multi-effect for interdependent survival between intestinal- microorganisms and hosts. The symbiosis or coevolution that results from this effect for interdependent survival is used to reveal the phylogenies of hosts as well as intestinal microorganisms. The symbiosis or coevolution between intestinal microorganisms and hosts has been generated by interactive natural selection occurred between them. The symbiosis information that has been formed by interactive natural selection during a long evolutionary process must be recorded in DNA sequences. According to this point of view,we analyzed the phylogeny of 9 intestinal bacteria genera using their contents in intestines of 8 Cyrinidate species. At the same time,we fetched the 16S rRNA gene DNA sequences of 43 intestinal bacteria species being included in these nine genera of six intestinal families from GeneBank and constructed phylogenetic trees by NJ and MP methods. The NJ tree and MP tree have the same topologic configuration and are identical with the classical phylogenetic tree. Both the trees of 16S rRNA gene separated 43 bacteria species into gram-negative bacteria group and the gram-positive bacteria group,which are the first branches. Each of the first branches (groups) made again 6 subbranches (subgroups) where each subbranch is a family.Especially,the subbranch (subgroup) of enterobacteriaceace made again four small branches as genus taxon. This tree also shows that bacilliform bacterium is distinct from each other in the NJ and MP trees. After all species on the tree are merged,the topological configuration of the unrooted tree of 16S gene is closed to that of the host range unrooted tree.However,the position of bacillus is greatly changed on both the unrooted trees. The difference can be found if we increase the examination level and extend the hosts examed.

English Abstract↗
PubMed1981

The sequence of the ribosomal 16S RNA from Proteus vulgaris. Sequence comparison with E. coli 16S RNA and its use in secondary model building.

The complete nucleotide sequence of the 16S RNA from Proteus vulgaris has been determined. The molecule (1544 nucleotides) shows 93% homology with the sequence of E. coli 16S RNA. Six methylated nucleotides have been localized in positions homologous to those observed in the E. coli RNA molecule. Both E. coli and P. vulgaris 16S RNA chains can be folded up into a common secondary structure scheme. Comparative sequence analysis of the two molecules has provided a valuable contribution to 16S RNA secondary structure model building.

Base Sequence↗
PubMed2003

Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis.

AIM: The aim of this study was to characterize the bacterial community adhering to the mucosa of the terminal ileum, and proximal and distal colon of the human digestive tract. METHODS AND RESULTS: Pinch samples of the terminal ileum, proximal and distal colon were taken from a healthy 35-year-old, and a 68-year-old subject with mild diverticulosis. The 16S rDNA genes were amplified using a low number of PCR cycles, cloned, and sequenced. In total, 361 sequences were obtained comprising 70 operational taxonomic units (OTU), with a calculated coverage of 82.6%. Twenty-three per cent of OTU were common to the terminal ileum, proximal colon and distal colon, but 14% OTU were only found in the terminal ileum, and 43% were only associated with the proximal or distal colon. The most frequently represented clones were from the Clostridium group XIVa (24.7%), and the Bacteroidetes (Cytophaga-Flavobacteria-Bacteroides) cluster (27.7%). CONCLUSION: Comparison of 16S rDNA clone libraries of the hindgut across mammalian species confirms that the distribution of phylogenetic groups is similar irrespective of the host species. Lesser site-related differences within groups or clusters of organisms, are probable. SIGNIFICANCE AND IMPACT: This study provides further evidence of the distribution of the bacteria on the mucosal surfaces of the human hindgut. Data contribute to the benchmarking of the microbial composition of the human digestive tract.

Adult↗
PubMed2006

Structure analysis of 16S rDNA sequences from strains of Acidithiobacillus ferrooxidans.

Four strains of Acidithiobacillus ferrooxidans with different iron oxidation capacity were isolated from different mine drainage stations. The 16S rRNA gene of these strains were cloned and sequenced. Based on our sequences analysis on the four strain and the data on the other strains deposited in Genbank, all A. ferrooxidans may be classified into three phylogenetic groups. The analysis data showed that nucleotide variables (signature sites) were detected in 21 positions, and most of them were found in the first 800 bp from 5' terminal except position 970 and 1375. Interestingly, the first 13 signature sites were located in two main regions: the first region (position 175-234) located in V2 while the second region (position 390-439) were detected in constant region between V2 and V3. Furthermore, the secondary structure and minimal free energy were determined in two regions among strains of three groups. These results may be useful in characterizing the microevolutionary mechanisms of species formation and monitoring in biohydrometallurgical application.

Acidithiobacillus↗
PubMed1994

The phylogenetic position of Hydrogenobacter acidophilus based on 16S rRNA sequence analysis.

Hydrogenobacter acidophilus strain 3H-1 is a thermoacidophilic, obligately chemolithoautotrophic, hydrogen-oxidizer isolated from a Japanese solfataric field. Strain 3H-1 requires elemental sulfur for growth. We used PCR to amplify the 16S rRNA gene of strain 3H-1, and sequenced the amplification product directly. Phylogenetic analyses show strain 3H-1 is closely related to Aquifex pyrophilus and may be located in the deepest branch within the eubacterial phylogenetic tree. Sulfur-dependency of the ancestral eubacterium is also discussed.

Archaea↗
PubMed1994

Phylogenetic relationships between some members of the genera Neisseria, Acinetobacter, Moraxella, and Kingella based on partial 16S ribosomal DNA sequence analysis.

We obtained 16S ribosomal DNA (rDNA) sequence data for strains belonging to 11 species of Proteobacteria, including the type strains of Kingella kingae, Neisseria lactamica, Neisseria meningitidis, Moraxella lacunata subsp. lacunata, [Neisseria] ovis, Moraxella catarrhalis, Moraxella osloensis, [Moraxella] phenylpyruvica, and Acinetobacter lwoffii, as well as strains of Neisseria subflava and Acinetobacter calcoaceticus. The data in a distance matrix constructed by comparing the sequences supported the proposal that the genera Acinetobacter and Moraxella and [N.] ovis should be excluded from the family Neisseriaceae. Our results are consistent with hybridization data which suggest that these excluded taxa should be part of a new family, the Moraxellaceae. The strains that we studied can be divided into the following five groups: (i) M. lacunata subsp. lacunata, [N.] ovis, and M. catarrhalis; (ii) M. osloensis; (iii) [M.] phenylpyruvica; (iv) A. calcoaceticus and A. lwoffii; and (v) N. meningitidis, N. subflava, N. lactamica, and K. kingae. We agree with the previous proposal that [N.] ovis should be renamed Moraxella ovis, as this organism is closely related to Moraxella species and not to Neisseria species. The generically misnamed taxon [M.] phenylpyruvica belongs to the proposed family Moraxellaceae, but it is sufficiently different to warrant exclusion from the genus Moraxella. Further work needs to be done to investigate genetically similar species, such as Psychrobacter immobilis, before the true generic position of this organism can be determined. Automated 16S rDNA sequencing with the PCR allows workers to accurately determine phylogenetic relationships between groups of organisms.(ABSTRACT TRUNCATED AT 250 WORDS)

Acinetobacter↗
PubMed2026

Oral bacteriome in pediatric patients with malignancies prior to chemotherapy: a pilot study using full-length 16S rRNA sequencing.

OBJECTIVE: To characterize the composition, diversity, and ecological features of the oral bacteriome in pediatric patients with malignancies prior to chemotherapy initiation. METHODS: In this prospective pilot study,supragingival plaque samples were collected from 10 pediatric cancer patients prior to the initiation of chemotherapy. Bacterial genomic DNA was extracted from each sample, and the full-length 16S rRNA gene was amplified and sequenced on the PacBio Sequel II platform using circular consensus sequencing (CCS). Raw CCS reads were quality-filtered and denoised into amplicon sequence variants (ASVs) using DADA2, and taxonomic assignment was performed against the SILVA 138 reference database. Alpha diversity was assessed using the Chao1, Shannon, Simpson, and Faith's phylogenetic diversity (PD whole tree) indices, while beta diversity was evaluated through principal coordinate analysis (PCoA), and non-metric multidimensional scaling (NMDS). Microbial co-occurrence networks were constructed to characterize bacterial interactions, and functional potential was predicted using PICRUSt2, and BugBase. RESULTS: A total of 614,473 high-quality CCS reads were generated, yielding 1,697 ASVs. Alpha diversity analysis revealed substantial inter-individual variation in microbial richness and diversity among the pediatric cancer patients. The bacterial community was dominated by the phyla Firmicutes, Proteobacteria, Bacteroidota, Actinobacteriota. At the genus level, Streptococcus, Prevotella, Neisseria, and Haemophilus were the most abundant taxa. Beta diversity analysis revealed distinct clustering patterns, indicating highly individualized microbial profiles. Co-occurrence network analysis identified several keystone taxa and potential pathogenic associations within the supragingival plaque community. Functional prediction indicated that the dominant metabolic pathways were related to amino acid metabolism, carbohydrate metabolism, and membrane transport. CONCLUSION: These preliminary findings reveal a taxonomically diverse, highly individualized pre-chemotherapy oral bacteriome, providing foundational baseline profiles to guide future longitudinal investigations of chemotherapy-induced dysbiosis and personalized interventions.

Humans↗
PubMed2006

The phylogenetic position of Ixodes stilesi Neumann, 1911 (Acari: Ixodidae): morphological and preliminary molecular evidences from 16S rDNA sequences.

The female of Ixodes stilesi Neumann, 1911 (Acari Ixodidae) is redescribed and the male and nymph are described from specimens collected from Pudu puda (Molina) (Artiodactyla: Cervidae) in Chile. Both sexes of I. stilesi have characteristics of the subgenera Ixodes Latreille, 1795 and Ixodiopsis Filippova, 1957. The females of I. stilesi are peculiar in having the combination of the sinuous scutum outline, rounded porose areas with distinct borders separated by the width of one area, slender and long palpi, and two subequal spurs on coxa I. The male is unique in having a combination of a posteriorly wrinkled marginal folder, a basis capituli longer than wide, a non-crenulate hypostome toothed portion, two spurs on coxa II to IV and the presence of a pseudoscutum. The nymph of I. stilesi has blunt anterior and posterior processes on palpal article I (characteristics of the subgenus Ixodiopsis and some Pholeoixodes Schulze, 1942) and a wing-shaped basis capituli with a prominent triangular cornua. Phylogenetic analyses based on 16S mitochondrial rDNA sequences of 12 Neotropical and two Australian Ixodes species, plus three argasids, were carried out to clarify the position of I. stilesi. The results of phylogenetic analyses and morphological characters indicate a close relationships between I. stilesi and two other Neotropical species of uncertain subgeneric status, I. neuquenensis Ringuelet, 1947 and I. sigelos Keirans, Clifford & Corwin, 1976.

Animals↗
PubMed2000

Comparative phylogenetic analyses of members of the order Planctomycetales and the division Verrucomicrobia: 23S rRNA gene sequence analysis supports the 16S rRNA gene sequence-derived phylogeny.

Almost complete 23S rRNA gene sequences were obtained from 13 planctomycete strains, the fimbriated, prosthecate bacterium Verrucomicrobium spinosum and two strains of the genus Prosthecobacter. The 23S rRNA genes were amplified by the PCR, using modified primers. The majority of the planctomycete strains investigated were shown to have 23S rRNA genes that were not linked to the 16S rRNA genes. Amplification of the 5'-termini of these genes was achieved using a novel primer-design strategy. Comparative phylogenetic analyses were performed using the 23S rRNA gene sequences determined in this study and previously determined 16S rRNA gene sequences. The phylogenetic dendrograms constructed from both datasets showed that the planctomycetes form a coherent group and distinct lineage within the domain Bacteria. Analysis of 23S rRNA gene sequences of Verrucomicrobium spinosum, Prosthecobacter fusiformis and Prosthecobacter sp. strain FC-2 showed that these organisms cluster together, as was also shown here and previously by analysis of 16S rRNA gene sequences. The distinct phylogenetic position of the division Verrucomicrobia was also supported by analysis of the 23S rRNA gene sequences, and no statistically significant phylogenetic relationship between the division Verrucomicrobia and the planctomycetes was found. The analyses presented in this study also provide further evidence that the chlamydiae are no more related to members of the order Planctomycetales and the division Verrucomicrobia than they are to members of other bacterial lineages.

Bacteria↗
PubMed2002

Detection of 16S rDNA sequences representing the novel phylum "Nanoarchaeota": indication for a wide distribution in high temperature biotopes.

We screened samples from high temperature biotopes for 16S rRNA genes of the novel archaeal phylum "Nanoarchaeota". Positive PCR amplifications were obtained from Yellowstone National Park, Uzon Caldera, and an abyssal vent system. These sequences form a cluster with the sequence of "Nanoarchaeum equitans", indicating a wide distribution of this phylum.

Archaea↗
PubMed1992

Towards a phylogeny of the genus Vibrio based on 16S rRNA sequences.

The inter- and intrageneric relationships of the genus Vibrio were investigated by performing a comparative analysis of the 16S rRNAs of 10 species, including four pathogenic representatives. The results of immunological and 5S rRNA studies were confirmed in that the genus is a neighboring taxon of the family Enterobacteriaceae. With regard to the intrageneric structure, Vibrio alginolyticus, Vibrio campbellii, Vibrio natriegens, Vibrio harveyi, Vibrio proteolyticus, Vibrio parahaemolyticus, and Vibrio vulnificus form the core of the genus, while Vibrio (Listonella) anguillarum, Vibrio diazotrophicus, and Vibrio hollisae are placed on the outskirts of the genus. Variable regions around positions 80, 180, and 450 could be used as target sites for genus- and species-specific oligonucleotide probes and polymerase chain reaction primers to be used in molecular identification.

Base Sequence↗
PubMed2005

[Detection of Mobiluncus species by special primer amplification and 16S DNA sequence analysis].

Bacterial Vaginosis (BV), a microecological disease leaded by overgrowth of the vaginal bacteria, is one of the Polymicrobial Diseases. The close relationship between BV and Mobiluncus ssp. was recognized gradually. But it is difficult to get the pure culture of this anaerobic bacterium because of its rigorous requirement for growth conditions. The vaginal discharge came from the BV animal model--Rhesus monkey was cultured in anaerobic environment. The 16S rRNA gene was amplified and sequenced using mobiluncus-specific primers. Mobiluncus ssp, closely related to Mobiluncus mulieris, were detected, by comparing with the 16S rRNA genes in the GenBank.

Animals↗
PubMed2005

Genetic characterization of the lobster pathogen Aerococcus viridans var. homari by 16S rRNA gene sequence and RAPD.

A combination of 16S rRNA sequencing and random amplified polymorphic DNA (RAPD) analysis was used to evaluate the genetic diversity within Aerococcus viridans var. homari, the causative agent of gaffkemia in lobsters. A collection of 7 A. viridans var. homari strains and 2 avirulent A. viridans-like cocci isolated from homarid lobsters harvested from different regions on the Atlantic Coast of North America were analyzed. The isolates are separated geographically and temporally between the years 1947 and 2000. Sequencing of 16S rRNA genes confirmed the inclusion of all 9 isolates in the monophyletic A. viridans clade (99.8 to 100% similarity). RAPD analysis revealed that the 9 A. viridans var. homari isolates could be separated into 2 distinct subtypes. Subtype 1 included the 7 pathogenic lobster isolates and constituted a homogeneous group regardless of their geographical, temporal or virulence differences. Subtype 2 contained the 2 avirulent A. viridans-like cocci that had distinct RAPD patterns and clustered separately with the non-marine A. viridans. RAPD analysis represented a useful method for determining molecular subtyping for the intraspecific classification and epidemiological investigations of A. viridans var. homari.

Animals↗
PubMed1998

Phylogenetic relationships of terrestrial Australo-Papuan elapid snakes (subfamily Hydrophiinae) based on cytochrome b and 16S rRNA sequences.

Phylogenetic relationships among the venomous Australo-Papuan elapid snake radiation remain poorly resolved, despite the application of diverse data sets. To examine phylogenetic relationships among this enigmatic group, portions of the cytochrome b and 16S rRNA mitochondrial DNA genes were sequenced from 19 of the 20 terrestrial Australian genera and 6 of the 7 terrestrial Melanesian genera, plus a sea krait (Laticauda) and a true sea snake (Hydrelaps). These data clarify several significant issues in elapid phylogeny. First, Melanesian elapids form sister groups to Australian species, indicating that the ancestors of the Australian radiation came via Asia, rather than representing a relict Gondwanan radiation. Second, the two major groups of sea snakes (sea kraits and true sea snakes) represent independent invasions of the marine environment. Third, the radiation of viviparous Australian elapids is much older than has been suggested from immunological data. Parsimony analyses were unable to resolve relationships among the Australian radiation, a problem previously encountered with analyses of other (morphological, electrophoretic, karyotypic, immunological) data sets on these species. These data suggest that the reason for this continued difficulty lies in the timing of speciation events: the elapids apparently underwent a spectacular adaptive radiation soon after reaching Australia, such that divergences are ancient even within genera. Indeed, intrageneric divergences are almost as large as intergeneric divergences. Although this timing means that our sequence data cannot fully resolve phylogenetic relationships among the Australian elapids, the data suggest a close relationship of the following clades: Pseudonaja with Oxyuranus; Ogmodon with Toxicocalamus; Demansia with Aspidomorphus; Echiopsis with Denisonia; the "Notechis" lineage with Drysdalia coronoides; and Rhinoplocephalus and Suta with Drysdalia coronata. At least two of the Australian genera (Drysdalia and Simoselaps) appear to be paraphyletic. These sequence data support many of the conclusions reached by earlier studies using other types of data, but additional information will be needed before the phylogeny of the Australian elapids can be fully resolved.

Animals↗