Species‐specific Identification of Vibrio sp. based on 16S‐23S rRNA gene internal transcribed spacer

2020 ◽  
Vol 129 (3) ◽  
pp. 738-752
Author(s):  
J. Yu ◽  
B. Zhu ◽  
T. Zhou ◽  
Y. Wei ◽  
X. Li ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
Specific Identification ◽  
23S Rrna Gene ◽  
Species Specific

scholarly journals 16S–23S rRNA gene internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Porphyromonas

2005 ◽  
Vol 55 (2) ◽  
pp. 607-613 ◽  
Author(s):  
Georg Conrads ◽  
Diane M. Citron ◽  
Kerin L. Tyrrell ◽  
Hans-Peter Horz ◽  
Ellie J. C. Goldstein
Keyword(s):  
Internal Transcribed Spacer ◽  
Type Strain ◽  
Distinct Species ◽  
Genetic Identification ◽  
23S Rrna ◽  
Rrna Gene ◽  
23S Rrna Gene ◽  
Internal Transcribed Spacer Sequences ◽  
Tannerella Forsythensis ◽  
Reference Strains

The 16S–23S rRNA gene internal transcribed spacer (ITS) regions of 11 reference strains of Porphyromonas species, together with Bacteroides distasonis and Tannerella forsythensis, were analysed to examine interspecies relationships. Compared with the phylogenetic tree generated using 16S rRNA gene sequences, the resolution of the ITS sequence-based tree was higher, but species positioning and clustering were similar with both approaches. The recent separation of Porphyromonas gulae and Porphyromonas gingivalis into distinct species was confirmed by the ITS data. In addition, analysis of the ITS sequences of 24 clinical isolates of Porphyromonas asaccharolytica plus the type strain ATCC 25260T divided the sequences into two clusters, of which one was α-fucosidase-positive (like the type strain) while the other was α-fucosidase-negative. The latter resembled the previously studied unusual extra-oral isolates of ‘Porphyromonas endodontalis-like organisms' (PELOs) which could therefore be called ‘Porphyromonas asaccharolytica-like organisms' (PALOs), based on the genetic identification. Moreover, the proposal of α-fucosidase-negative P. asaccharolytica strains as a new species should also be considered.

scholarly journals Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

2020 ◽  
Author(s):  
Eiseul Kim ◽  
Seung-Min Yang ◽  
Bora Lim ◽  
Si Hong Park ◽  
Bryna Rackerby ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genomic Analysis ◽  
23S Rrna ◽  
Lactobacillus Species ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
23S Rrna Gene ◽  
Species Specific

Abstract Background Lactobacillus species are used as probiotics and play an important role in fermented food production. However, use of 16S rRNA gene sequences as standard markers for the differentiation of Lactobacillus species offers a very limited scope, as several species of Lactobacillus share similar 16S rRNA gene sequences. In this study, we developed a rapid and accurate method based on comparative genomic analysis for the simultaneous identification of 37 Lactobacillus species that are commonly used in probiotics and fermented foods. Results To select species-specific sequences or genes, a total of 180 Lactobacillus genome sequences were compared using Python scripts. In 14 out of 37 species, species-specific sequences could not be found due to the similarity of the 16S–23S rRNA gene. Selected unique genes were obtained using comparative genomic analysis and all genes were confirmed to be specific for 52,478,804 genomes via in silico analysis; they were found not to be strain-specific, but to exist in all strains of the same species. Species-specific primer pairs were designed from the selected 16S–23S rRNA gene sequences or unique genes of species. The specificity of the species-specific primer pairs was confirmed using reference strains, and the accuracy and efficiency of the polymerase chain reaction (PCR) with the standard curve were confirmed. The PCR method developed in this study is able to accurately differentiate species that were not distinguishable using the 16S rRNA gene alone. This PCR assays were designed to detect and identify 37 Lactobacillus species. The developed method was then applied in the monitoring of 19 probiotics and 12 dairy products. The applied tests confirmed that the species detected in 17 products matched those indicated on their labels, whereas the remaining products contained species other than those appearing on the label. Conclusions The method developed in this study is able to rapidly and accurately distinguish different species of Lactobacillus , and can be used to monitor specific Lactobacillus species in foods such as probiotics and dairy products.

scholarly journals Identification and Detection ofStenotrophomonas maltophilia by rRNA-Directed PCR

2000 ◽  
Vol 38 (12) ◽  
pp. 4305-4309 ◽  
Author(s):  
Paul W. Whitby ◽  
Karen B. Carter ◽  
Jane L. Burns ◽  
James A. Royall ◽  
John J. LiPuma ◽  
...  
Keyword(s):  
Burkholderia Cepacia ◽  
Direct Detection ◽  
Pcr Primers ◽  
Laboratory Culture ◽  
23S Rrna ◽  
Rrna Gene ◽  
Specific Pcr ◽  
23S Rrna Gene ◽  
Susceptible Populations ◽  
Species Specific

Stenotrophomonas maltophilia has recently emerged as an important nosocomial pathogen in immunocompromised patients, in transplant recipients, and in persons with cystic fibrosis (CF). While this organism is nonpathogenic in healthy individuals, it is increasingly associated with morbidity and mortality in susceptible populations. Recent studies have indicated that for approximately 10% of CF patients with moderate lung disease, S. maltophiliacan be cultured from respiratory tract secretions. Identification ofS. maltophilia can be problematic, and analysis of isolates from the Burkholderia cepacia Research Laboratory and Repository showed that several isolates presumptively identified asB. cepacia by clinical microbiology laboratories were in fact S. maltophilia. To overcome the problems associated with definitive identification, we developed species-specific PCR (SS-PCR) primers, designated SM1 and SM4, directed to the 23S rRNA gene, and tested their utility to accurately identify S. maltophilia directly from sputum. The SS-PCR was developed and tested against a panel of 112 S. maltophilia isolates collected from diverse geographic locations. To test for specificity, 43 isolates from 17 different species were analyzed. PCR with the SM1-SM4 primer pair and isolated genomic DNA as a template resulted in amplification of a band from all S. maltophilia isolates and was uniformly negative for all other species tested, yielding a sensitivity and a specificity of 100% for the SS-PCR. The utility of the SS-PCR to directly identify S. maltophilia in sputum was examined. Thirteen expectorated sputum samples from CF patients were analyzed by SS-PCR. Three samples were PCR positive, in complete concordance with the conventional laboratory culture. Thus, we have developed an SS-PCR protocol that can rapidly and accurately identifyS. maltophilia isolates and which can be used for the direct detection of this organism in CF patient sputum.

scholarly journals Identification of the genusGeobacillususing genus-specific primers, based on the 16S–23S rRNA gene internal transcribed spacer

2007 ◽  
Vol 277 (2) ◽  
pp. 165-172 ◽  
Author(s):  
Nomeda Kuisiene ◽  
Juozas Raugalas ◽  
Milda Stuknyte ◽  
Donaldas Chitavichius
Keyword(s):  
Internal Transcribed Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
Specific Primers ◽  
23S Rrna Gene

scholarly journals Differentiation Among Rodentibacter Species Based on 16S–23S rRNA Internal Transcribed Spacer Analysis

2020 ◽  
Vol 70 (6) ◽  
pp. 487-491
Author(s):  
Laurentiu Benga ◽  
Peter M Benten ◽  
Eva Engelhardt ◽  
Karl Köhrer ◽  
Barbara Hueber ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Reliable Method ◽  
Species Level ◽  
23S Rrna ◽  
Its Sequence ◽  
Specific Identification ◽  
Laboratory Rodents ◽  
Sequence Variations ◽  
Species Specific ◽  
Type Strains

The internal transcribed spacer (ITS) regions of Rodentibacter pneumotropicus, R. heylii, R. rarus, R. ratti, and R. heidelbergensis and of a Rodentibacter- related β-hemolytic Pasteurellaceae taxon isolated from laboratory rodents were studied for their feasibility to discriminate among these species. The 6 species analyzed showed species-specific ITS patterns that were shared by the type strains and clinical isolates and that allowed their identification. Nevertheless, differentiating between the ITS band patterns of R. pneumotropicus and R. ratti is visually challenging. In all species tested, sequence analysis of the ITS fragments revealed a larger ITSile+ala, which contained the genes for tRNAIle(GAU) and tRNA Ala(UGC), and a smaller ITSglu with the tRNAGlu(UUC) gene. The ITS sequences varied among the 6 species evaluated, displaying identity levels ranging from 62% to 86% for ITSile+ala and 68% to 90% for ITSglu. Overall, ITS amplification proved to be a reliable method to differentiate among these important Pasteurellaceae species of laboratory rodents. Moreover, the ITS sequence variations recorded here might facilitate the design of probes for specific identification of these species. The ability to diagnose these organisms to the species level could increase our understanding of their clinical significance.

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