A nested PCR-based method for detection ofStreptococcus agalactiae16S rRNA in milk and its application

2006 ◽  
Vol 3 (2) ◽  
pp. 115-118
Author(s):  
Jia Yu-Ping ◽  
Zhou Dong-Shun ◽  
Zhao Hong-Kun ◽  
Wan Ren-Zhong ◽  
Liu Wen-Qiang ◽  
...  
Keyword(s):  
16S Rrna ◽  
Simple Procedure ◽  
Bovine Mastitis ◽  
Dairy Herd ◽  
Raw Milk ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nested Polymerase Chain Reaction ◽  
Specific Pcr ◽  
And Control

AbstractBovine mastitis caused byStreptococcus agalactiaeis mainly subclinical and therefore can be diagnosed only in the laboratory. A nested polymerase chain reaction (PCR)-based method for specific, sensitive and rapid detection ofS. agalactiaein raw milk was developed. The general streptococci primers, which anneal to conserved areas within the 16S rRNA subunit gene, were used as positive controls. The specificity ofS. agalactiaeprimers is based on various areas within conserved areas of the 16S rRNA genes ofS. agalactiae. Results have indicated that the method enables the detection of 1 CFU/ml ofS. agalactiaein raw milk after enrichment, followed by DNA extraction using a rapid and simple procedure developed for this purpose, and specific PCR reaction. The method developed can be used efficiently in the early infectious status investigation ofS. agalactiaein the dairy herd and in prevention and control ofS. agalactiaespread in a herd.

scholarly journals Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment

2002 ◽  
Vol 68 (10) ◽  
pp. 5064-5081 ◽  
Author(s):  
Alexander Loy ◽  
Angelika Lehner ◽  
Natuschka Lee ◽  
Justyna Adamczyk ◽  
Harald Meier ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Pcr Amplification ◽  
Oligonucleotide Microarray ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Specific Pcr

ABSTRACT For cultivation-independent detection of sulfate-reducing prokaryotes (SRPs) an oligonucleotide microarray consisting of 132 16S rRNA gene-targeted oligonucleotide probes (18-mers) having hierarchical and parallel (identical) specificity for the detection of all known lineages of sulfate-reducing prokaryotes (SRP-PhyloChip) was designed and subsequently evaluated with 41 suitable pure cultures of SRPs. The applicability of SRP-PhyloChip for diversity screening of SRPs in environmental and clinical samples was tested by using samples from periodontal tooth pockets and from the chemocline of a hypersaline cyanobacterial mat from Solar Lake (Sinai, Egypt). Consistent with previous studies, SRP-PhyloChip indicated the occurrence of Desulfomicrobium spp. in the tooth pockets and the presence of Desulfonema- and Desulfomonile-like SRPs (together with other SRPs) in the chemocline of the mat. The SRP-PhyloChip results were confirmed by several DNA microarray-independent techniques, including specific PCR amplification, cloning, and sequencing of SRP 16S rRNA genes and the genes encoding the dissimilatory (bi)sulfite reductase (dsrAB).

scholarly journals Design and Evaluation of Useful Bacterium-Specific PCR Primers That Amplify Genes Coding for Bacterial 16S rRNA

1998 ◽  
Vol 64 (2) ◽  
pp. 795-799 ◽  
Author(s):  
Julian R. Marchesi ◽  
Takuichi Sato ◽  
Andrew J. Weightman ◽  
Tracey A. Martin ◽  
John C. Fry ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Amplification ◽  
Environmental Samples ◽  
Bacterial Species ◽  
Pcr Primers ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Specific Pcr

ABSTRACT We report the design and evaluation of PCR primers 63f and 1387r for amplification of 16S rRNA genes from bacteria. Their specificity and efficacy were tested systematically with a variety of bacterial species and environmental samples. They were found to be more useful for 16S rRNA gene amplification in ecological and systematic studies than PCR amplimers that are currently more generally used.

scholarly journals Species-Specific PCR for Identification of Common Contaminant Mollicutes in Cell Culture

2001 ◽  
Vol 67 (7) ◽  
pp. 3195-3200 ◽  
Author(s):  
Fanrong Kong ◽  
Gregory James ◽  
Susanna Gordon ◽  
Anna Zelynski ◽  
Gwendolyn L. Gilbert
Keyword(s):  
16S Rrna ◽  
Cell Cultures ◽  
Bacterial Species ◽  
Intergenic Spacer ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Species Specific

ABSTRACT Mycoplasma arginini, M. fermentans, M. hyorhinis, M. orale, and Acholeplasma laidlawii are the members of the class Mollicutes most commonly found in contaminated cell cultures. Previous studies have shown that the published PCR primer pairs designed to detect mollicutes in cell cultures are not entirely specific. The 16S rRNA gene, the 16S-23S rRNA intergenic spacer region, and the 5′ end of the 23S rRNA gene, as a whole, are promising targets for design of mollicute species-specific primer pairs. We analyzed the 16S rRNA genes, the 16S-23S rRNA intergenic spacer regions, and the 5′ end of the 23S rRNA genes of these mollicutes and developed PCR methods for species identification based on these regions. Using high melting temperatures, we developed a rapid-cycle PCR for detection and identification of contaminant mollicutes. Previously published, putative mollicute-specific primers amplified DNA from 73 contaminated cell lines, but the presence of mollicutes was confirmed by species-specific PCR in only 60. Sequences of the remaining 13 amplicons were identified as those of gram-positive bacterial species. Species-specific PCR primers are needed to confirm the presence of mollicutes in specimens and for identification, if required.

scholarly journals Monitoring Bacterial Communities in Raw Milk and Cheese by Culture-Dependent and -Independent 16S rRNA Gene-Based Analyses

2007 ◽  
Vol 73 (6) ◽  
pp. 1882-1891 ◽  
Author(s):  
Céline Delbès ◽  
Leila Ali-Mandjee ◽  
Marie-Christine Montel
Keyword(s):  
16S Rrna ◽  
Culture Media ◽  
Raw Milk ◽  
Single Strand Conformation Polymorphism ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Plate Count ◽  
Rrna Gene ◽  
Dual Culture ◽  
Culture Dependent

ABSTRACT The diversity and dynamics of bacterial populations in Saint-Nectaire, a raw-milk, semihard cheese, were investigated using a dual culture-dependent and direct molecular approach combining single-strand conformation polymorphism (SSCP) fingerprinting and sequencing of 16S rRNA genes. The dominant clones, among 125 16S rRNA genes isolated from milk, belonged to members of the Firmicutes (58% of the total clones) affiliated mainly with the orders Clostridiales and the Lactobacillales, followed by the phyla Proteobacteria (21.6%), Actinobacteria (16.8%), and Bacteroidetes (4%). Sequencing the 16S rRNA genes of 126 milk isolates collected from four culture media revealed the presence of 36 different species showing a wider diversity in the Gammaproteobacteria phylum and Staphylococcus genus than that found among clones. In cheese, a total of 21 species were obtained from 170 isolates, with dominant species belonging to the Lactobacillales and subdominant species affiliated with the Actinobacteria, Bacteroidetes (Chryseobacterium sp.), or Gammaproteobacteria (Stenotrophomonas sp.). Fingerprinting DNA isolated from milk by SSCP analysis yielded complex patterns, whereas analyzing DNA isolated from cheese resulted in patterns composed of a single peak which corresponded to that of lactic acid bacteria. SSCP fingerprinting of mixtures of all colonies harvested from plate count agar supplemented with crystal violet and vancomycin showed good potential for monitoring the subdominant Proteobacteria and Bacteroidetes (Flavobacteria) organisms in milk and cheese. Likewise, analyzing culturable subcommunities from cheese-ripening bacterial medium permitted assessment of the diversity of halotolerant Actinobacteria and Staphylococcus organisms. Direct and culture-dependent approaches produced complementary information, thus generating a more accurate view of milk and cheese microbial ecology.

scholarly journals Quantifying Microbial Diversity: Morphotypes, 16S rRNA Genes, and Carotenoids of Oxygenic Phototrophs in Microbial Mats

1999 ◽  
Vol 65 (2) ◽  
pp. 422-430 ◽  
Author(s):  
Ulrich Nübel ◽  
Ferran Garcia-Pichel ◽  
Michael Kühl ◽  
Gerard Muyzer
Keyword(s):  
16S Rrna ◽  
Microbial Mats ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Morphological Diversity ◽  
Numerical Approach ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Phototrophic Microorganisms

ABSTRACT We quantified the diversity of oxygenic phototrophic microorganisms present in eight hypersaline microbial mats on the basis of three cultivation-independent approaches. Morphological diversity was studied by microscopy. The diversity of carotenoids was examined by extraction from mat samples and high-pressure liquid chromatography analysis. The diversity of 16S rRNA genes from oxygenic phototrophic microorganisms was investigated by extraction of total DNA from mat samples, amplification of 16S rRNA gene segments from cyanobacteria and plastids of eukaryotic algae by phylum-specific PCR, and sequence-dependent separation of amplification products by denaturing-gradient gel electrophoresis. A numerical approach was introduced to correct for crowding the results of chromatographic and electrophoretic analyses. Diversity estimates typically varied up to twofold among mats. The congruence of richness estimates and Shannon-Weaver indices based on numbers and proportional abundances of unique morphotypes, 16S rRNA genes, and carotenoids unveiled the underlying diversity of oxygenic phototrophic microorganisms in the eight mat communities studied.

scholarly journals ‘Candidatus Mycoplasma haemoalbiventris’ and tick-borne pathogens screening in white-eared opossums (Didelphis albiventris) from Curitiba and Foz do Iguaçu Cities, Paraná State, southern Brazil

2021 ◽  
Vol 30 (4) ◽  
Author(s):  
Renata Prestes Antonangelo de Oliveira ◽  
Flávia Carolina Meira Collere ◽  
Larissa Dantas Roeder Ferrari ◽  
Vanessa dos Santos Coradi ◽  
Nathália de Albuquerque Soares ◽  
...  
Keyword(s):  
16S Rrna ◽  
Clinical Signs ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Southern Brazil ◽  
Specific Pcr ◽  
Gapdh Gene ◽  
Didelphis Albiventris

Abstract Hemoplasmas are epierythrocytic bacteria that infect mammals. ‘Candidatus Mycoplasma haemoalbiventris’ was detected in white-eared opossums (Didelphis albiventris) from southern and central-western Brazil. The present study aimed at: i) screening opossums for tick-borne (TBP) pathogens (Piroplasmida and Anaplasmataceae) and ii) detecting and characterizing hemoplasma species infecting opossums from Curitiba and Foz do Iguaçu cities in the Paraná State, southern Brazil. Thirty blood samples from white-eared opossums were evaluated by PCR assays. Animals were not infested by ectoparasites. The mammalian endogenous gapdh gene was consistently amplified in all samples. All opossums tested negative for Theileria/Babesia spp. and Ehrlichia/Anaplasma spp. by PCR based on 18S rRNA and 16S rRNA genes, respectively. A genus-specific PCR assay based on the 16S rRNA gene of hemoplasmas showed that three/13 (23.08%; CI 95%: 8.18-50.26%) opossums from Foz do Iguaçu were positive for hemotropic Mycoplasma sp. All opossums from Curitiba tested negative for hemoplasmas. Sequencing of both the 16S and 23S rRNA genes revealed that the animals were infected by ‘Ca. M. haemoalbiventris’. Although ‘Ca. M. haemoalbiventris’ is prevalent in opossums in Brazil, clinical signs associated with its infection and its putative vectors remain unknown.

scholarly journals Homozygous Triplicate Mutations in Three 16S rRNA Genes Responsible for High-Level Aminoglycoside Resistance in Nocardia farcinica Clinical Isolates from a Canada-Wide Bovine Mastitis Epizootic

2010 ◽  
Vol 54 (6) ◽  
pp. 2385-2390 ◽  
Author(s):  
Takahisa Kogure ◽  
Reona Shimada ◽  
Jun Ishikawa ◽  
Katsukiyo Yazawa ◽  
June M. Brown ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bovine Mastitis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Triple Mutant ◽  
Aminoglycoside Resistance ◽  
Nocardia Farcinica ◽  
High Level

ABSTRACT Nocardia farcinica strains showing high-level resistance to amikacin were isolated from clinical cases in a Canada-wide bovine mastitis epizootic. Shotgun cloning of the resistance genes in the amikacin-resistant mastitis isolate N. farcinica IFM 10580 (W6220 [Centers for Disease Control and Prevention]) using a multicopy vector system revealed that the 16S rRNA gene with an A-to-G single-point mutation at position 1408 (in Escherichia coli numbering) conferred “moderate” cross-resistance to amikacin and other aminoglycosides to an originally susceptible N. farcinica strain IFM 10152. Subsequent DNA sequence analyses revealed that, in contrast to the susceptible strain, all three chromosomal 16S rRNA genes of IFM 10580, the epizootic clinical strain, contained the same A1408G point mutations. Mutant colonies showing high-level aminoglycoside resistance were obtained when the susceptible strain N. farcinica IFM 10152 was transformed with a multicopy plasmid carrying the A1408G mutant 16S rRNA gene and was cultured in the presence of aminoglycosides for 3 to 5 days. Of these transformants, at least two of the three chromosomal 16S rRNA genes contained A1408G mutations. A triple mutant was easily obtained from a strain carrying the two chromosomal A1408G mutant genes and one wild-type gene, even in the absence of the plasmid. The triple mutant showed the highest level of resistance to aminoglycosides, even in the absence of the plasmid carrying the mutant 16S rRNA gene. These results suggest that the homozygous mutations in the three 16S rRNA genes are responsible for the high-level aminoglycoside resistance found in N. farcinica isolates of the bovine mastitis epizootic.

scholarly journals Evaluations of Different Hypervariable Regions of Archaeal 16S rRNA Genes in Profiling of Methanogens by Archaea-Specific PCR and Denaturing Gradient Gel Electrophoresis

2007 ◽  
Vol 74 (3) ◽  
pp. 889-893 ◽  
Author(s):  
Zhongtang Yu ◽  
Rubén García-González ◽  
Floyd L. Schanbacher ◽  
Mark Morrison
Keyword(s):  
16S Rrna ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis ◽  
V Region

ABSTRACT Different hypervariable (V) regions of the archaeal 16S rRNA gene (rrs) were compared systematically to establish a preferred V region(s) for use in Archaea-specific PCR-denaturing gradient gel electrophoresis (DGGE). The PCR products of the V3 region produced the most informative DGGE profiles and permitted identification of common methanogens from rumen samples from sheep. This study also showed that different methanogens might be detected when different V regions are targeted by PCR-DGGE. Dietary fat appeared to transiently stimulate Methanosphaera stadtmanae but inhibit Methanobrevibacter sp. strain AbM4 in rumen samples.

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