Use of PCR-Based Methods for Rapid Differentiation of Lactobacillus delbrueckii subsp.bulgaricus and L. delbrueckii subsp.lactis

1999 ◽  
Vol 65 (10) ◽  
pp. 4351-4356 ◽  
Author(s):  
Sandra Torriani ◽  
Giacomo Zapparoli ◽  
Franco Dellaglio
Keyword(s):  
Numerical Analysis ◽  
Dairy Products ◽  
Lactobacillus Delbrueckii ◽  
Randomly Amplified Polymorphic Dna ◽  
Specific Pcr ◽  
Single Colony ◽  
Rapd Pcr ◽  
Reliable Differentiation ◽  
Dna Pcr ◽  
Proline Iminopeptidase

ABSTRACT Two PCR-based methods, specific PCR and randomly amplified polymorphic DNA PCR (RAPD-PCR), were used for rapid and reliable differentiation of Lactobacillus delbrueckii subsp.bulgaricus and L. delbrueckii subsp.lactis. PCR with a single combination of primers which targeted the proline iminopeptidase (pepIP) gene ofL. delbrueckii subsp. bulgaricus allowed amplification of genomic fragments specific for the two subspecies when either DNA from a single colony or cells extracted from dairy products were used. A numerical analysis of the RAPD-PCR patterns obtained with primer M13 gave results that were consistent with the results of specific PCR for all strains except L. delbrueckii subsp.delbrueckii LMG 6412T, which clustered withL. delbrueckii subsp. lactis strains. In addition, RAPD-PCR performed with primer 1254 provided highly polymorphic profiles and thus was superior for distinguishing individual L. delbrueckii strains.

scholarly journals Phenotypic and Genotypic Characterization ofStaphylococcus aureusStrains from Italian Dairy Products

2009 ◽  
Vol 2009 ◽  
pp. 1-7 ◽  
Author(s):  
Stefano Morandi ◽  
Milena Brasca ◽  
Cristian Andrighetto ◽  
Angiolella Lombardi ◽  
Roberta Lodi
Keyword(s):  
Dairy Products ◽  
Animal Species ◽  
Randomly Amplified Polymorphic Dna ◽  
Foodborne Illnesses ◽  
Phenotypic Properties ◽  
Rapd Pcr ◽  
Genes Encoding ◽  
Dna Pcr ◽  
Phenotypic And Genotypic Characterization ◽  
Milk And Dairy Products

Staphylococcus aureusis a known major cause of foodborne illnesses, and milk and dairy products are often contaminated by enterotoxigenic strains of this bacterium. In the present study, 122S. aureusisolates collected from different dairy products were characterised by phenotypic properties, by the distribution of genes encoding staphylococcal enterotoxins (sea,sec,sed,seg,seh,sei,sej, andsel) and by randomly amplified polymorphic DNA PCR (RAPD-PCR). Moreover, strain resistance to vancomycin and methicillin (oxacillin) was studied. The differences in the RAPD-PCR profiles obtained with the primers M13 and AP4 revealed the presence of a great genetic heterogeneity among the differentS. aureusstrains. Using the primer AP4 and M13, eight groups were distinguished by RAPD-PCR cluster analysis, although, except in few cases, it was not possible to correlate the isolates of different animal species (cow or ovine) with the presence ofsegenes. None of the isolates showed resistance to vancomycin or methicillin.

scholarly journals A Pseudomonas syringae Diversity Survey Reveals a Differentiated Phylotype of the Pathovar syringae Associated with the Mango Host and Mangotoxin Production

2013 ◽  
Vol 103 (11) ◽  
pp. 1115-1129 ◽  
Author(s):  
José A. Gutiérrez-Barranquero ◽  
Víctor J. Carrión ◽  
Jesús Murillo ◽  
Eva Arrebola ◽  
Dawn L. Arnold ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Randomly Amplified Polymorphic Dna ◽  
Chain Reaction ◽  
Catabolic Diversity ◽  
Rapd Pcr ◽  
Geographical Regions ◽  
Extensive Collection ◽  
Polymerase Chain ◽  
Apical Necrosis ◽  
Dna Pcr

Pseudomonas syringae pv. syringae, the causal agent of bacterial apical necrosis (BAN) in mango crops, has been isolated in different mango-producing areas worldwide. An extensive collection of 87 P. syringae pv. syringae strains isolated from mango trees affected by BAN from different countries, but mainly from Southern Spain, were initially examined by repetitive sequence-based polymerase chain reaction (rep-PCR) to analyze the genetic diversity with an epidemiological aim. rep-PCR was powerful in assessing intrapathovar distribution and also allowing clustering of the P. syringae pv. syringae strains isolated from mango, depending on the isolation area. A clear pattern of clustering was observed for all the P. syringae pv. syringae strains isolated from mango distinct from strains from other hosts, including strains for the same geographical regions as the mango isolates. For this reason, a representative group of 51 P. syringae pv. syringae strains isolated from mango and other hosts, as well as some P. syringae strains from other pathovars, were further characterized to determine their possible genetic, phenotypic, and phylogenetic relationships. Similar to the rep-PCR results, the randomly amplified polymorphic DNA PCR (RAPD-PCR) and catabolic diversity analysis using the Biolog GN2 profile grouped 90% of the mango isolates together in a unique cluster. Interestingly, the majority of P. syringae pv. syringae strains isolated from mango produced mangotoxin. The analysis of the phylogenetic distribution using the multilocus sequence typing analysis strongly supports the existence of a differentiated phylotype of the pathovar syringae mainly associated with the mango host and characterized by the mangotoxin production.

scholarly journals Seasonal Dynamics and Metagenomic Characterization of Estuarine Viriobenthos Assemblages by Randomly Amplified Polymorphic DNA PCR

2009 ◽  
Vol 75 (8) ◽  
pp. 2259-2265 ◽  
Author(s):  
Rebekah R. Helton ◽  
K. Eric Wommack
Keyword(s):  
Chesapeake Bay ◽  
Oligonucleotide Primer ◽  
Viral Diversity ◽  
Randomly Amplified Polymorphic Dna ◽  
Aquatic Sediments ◽  
Banding Patterns ◽  
Rapd Pcr ◽  
Viral Sequences ◽  
Dna Pcr

ABSTRACT Direct enumeration and genetic analyses indicate that aquatic sediments harbor abundant and diverse viral communities. Thus far, synecological analysis of estuarine sediment viral diversity over an annual cycle has not been reported. This oversight is due in large part to a lack of molecular genetic approaches for assessing viral diversity within a large collection of environmental samples. Here, randomly amplified polymorphic DNA PCR (RAPD-PCR) was used to examine viral genotypic diversity within Chesapeake Bay sediments. Using a single 10-mer oligonucleotide primer for all samples, RAPD-PCR analysis of sediment viral assemblages yielded unique banding patterns across spatial and temporal scales, with the occurrence of specific bands varying among the sample set. Cluster analysis of RAPD-PCR amplicon banding patterns indicated that sediment viral assemblages changed with season and to a lesser extent with geographic location. Sequence analysis of RAPD-PCR amplicons revealed that 76% of sediment viral sequences were not homologous to any sequence in the GenBank nonredundant protein database. Of the GenBank sequence homologs, the majority belonged to viruses within the Podoviridae (24%) and Myoviridae (22%) viral families, which agrees with the previously observed frequencies of these morphological families in Chesapeake Bay sediments. Furthermore, the majority of the sediment viral sequences homologous to GenBank nonredundant protein sequences were phages or prophages (57%). Hence, RAPD-PCR proved to be a reliable and useful approach for characterization of viral assemblages and the genetic diversity of viruses within aquatic sediments.

Randomly amplified polymorphic DNA (RAPD) PCR for the identification of yeasts isolated from dairy products

2000 ◽  
Vol 30 (1) ◽  
pp. 5-9 ◽  
Author(s):  
C. Andrighetto ◽  
E. Psomas ◽  
N. Tzanetakis ◽  
G. Suzzi ◽  
A. Lombardi
Keyword(s):  
Dairy Products ◽  
Randomly Amplified Polymorphic Dna ◽  
Rapd Pcr

Differentiation of faecal Escherichia coli from human and animal sources by random amplified polymorphic DNA-PCR (RAPD-PCR)

2004 ◽  
Vol 50 (1) ◽  
pp. 193-198 ◽  
Author(s):  
D. Venieri ◽  
A. Vantarakis ◽  
G. Komninou ◽  
M. Papapetropoulou
Keyword(s):  
Escherichia Coli ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Hierarchical Cluster ◽  
Group Method ◽  
Randomly Amplified Polymorphic Dna ◽  
Arbitrary Primers ◽  
E Coli ◽  
Rapd Pcr ◽  
Dna Pcr

In this study the assessment of randomly amplified polymorphic DNA (RAPD) analysis was established as a molecular epidemiological tool. RAPD analysis was performed to differentiate faecal Escherichia coli isolates from human and animal sources. E. coli strains (128) were isolated from human and animal faeces (from cattle and sheep). Genomic DNA was extracted and randomly amplified polymorphic DNA-PCR (RAPD-PCR) fingerprinting was performed. Seven arbitrary primers were tested with a view to discriminating between E. coli isolates from humans and E. coli isolates from animals. RAPD profiles were analysed with hierarchical cluster analysis using an unweighted pair group method. RAPD profiles obtained with three of the tested primers (1247, 1290 and 1254) established a distinct differentiation between E. coli isolates from humans and E. coli from animals. Low levels of misclassification and high levels of specificity make RAPD a sensitive, efficient and reliable means of distinguishing closely related strains.

scholarly journals Lactobacillus delbrueckii subsp. indicus subsp. nov., isolated from Indian dairy products

2005 ◽  
Vol 55 (1) ◽  
pp. 401-404 ◽  
Author(s):  
Franco Dellaglio ◽  
Giovanna E. Felis ◽  
Anna Castioni ◽  
Sandra Torriani ◽  
Jacques-Edouard Germond
Keyword(s):  
Dairy Products ◽  
Type Strain ◽  
Lactobacillus Delbrueckii ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Rapd Pcr ◽  
Total Dna ◽  
Type Strains ◽  
Lactobacillus Delbrueckii Subsp

Four strains isolated from Indian dairy products and initially identified as Lactobacillus delbrueckii could not be assigned to a definite subspecies because molecular identification and phenotypic traits did not agree with those of recognized subspecies of L. delbrueckii. Hybridization of total DNA (78–86 % against type strains of the other three subspecies), AFLP and RAPD-PCR fingerprints, phylogenetic analysis based on 16S rRNA gene sequences and sequence analysis of two coding genes (recA and hsp60), together with phenotypic profiles, indicated that the four strains form a coherent cluster and represent a novel subspecies, for which the name Lactobacillus delbrueckii subsp. indicus subsp. nov. is proposed. The type strain is NCC725T (=LMG 22083T=DSM 15996T).

scholarly journals Analysis of Vibrio vulnificus from Market Oysters and Septicemia Cases for Virulence Markers

2003 ◽  
Vol 69 (7) ◽  
pp. 4006-4011 ◽  
Author(s):  
Angelo DePaola ◽  
Jessica L. Nordstrom ◽  
Anders Dalsgaard ◽  
Anita Forslund ◽  
James Oliver ◽  
...  
Keyword(s):  
Vibrio Vulnificus ◽  
Iron Dextran ◽  
Randomly Amplified Polymorphic Dna ◽  
Environmental Isolates ◽  
Genetic Tests ◽  
Plasmid Content ◽  
Virulence Markers ◽  
Specific Pcr ◽  
Virulent Strains ◽  
Dna Pcr

ABSTRACT Representative encapsulated strains of Vibrio vulnificus from market oysters and oyster-associated primary septicemia cases (25 isolates each) were tested in a blinded fashion for potential virulence markers that may distinguish strains from these two sources. These isolates were analyzed for plasmid content, for the presence of a 460-bp amplicon by randomly amplified polymorphic DNA PCR, and for virulence in subcutaneously (s.c.) inoculated, iron-dextran-treated mice. Similar percentages of market oyster and clinical isolates possessed detectable plasmids (24 and 36%, respectively), produced the 460-bp amplicon (45 and 50%, respectively), and were judged to be virulent in the mouse s.c. inoculation-iron-dextran model (88% for each). Therefore, it appears that nearly all V. vulnificus strains in oysters are virulent and that genetic tests for plasmids and specific PCR size amplicons cannot distinguish between fully virulent and less virulent strains or between clinical and environmental isolates. The inability of these methods to distinguish food and clinical V. vulnificus isolates demonstrates the need for alternative subtyping approaches and virulence assays.

ANALYSIS OF GENETIC DIVERSITY OF 26 CASSAVA VARIETIES (Manihot esculenta CRANTZ) WITH DIFFERENT RESPONSES TO WATERLOGGING CONDITIONS BY USING RAPD MARKERS

2021 ◽  
Vol 66 (3) ◽  
pp. 170-179
Author(s):  
Sengsoulichan Dethvongsa ◽  
Vu Nguyen Anh ◽  
Van Tran Khanh
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Manihot Esculenta ◽  
Rapd Markers ◽  
Flood Tolerance ◽  
Randomly Amplified Polymorphic Dna ◽  
Manihot Esculenta Crantz ◽  
Rapd Pcr ◽  
Cassava Production ◽  
Cassava Varieties

RAPD (Randomly Amplified Polymorphic DNA) is an indicator for high and stable polymorphism, widely used in the study of the diversity of cassava. In this paper, the results of using 20 polymorphic primers OPK combined with the establishment of the phylogenetic tree to analyze the genetic diversity of 26 cassava varieties with different responses to waterlogging conditions by using the RAPD-PCR technique were presented. The purpose of this experiment was to show the genetic relevance of the studied cassava varieties. The results showed that the flood tolerance of cassava was not related to the polymorphism and branching characteristics of the stem. This information may be use as a basis for selecting flood-tolerant cassava varieties for cassava production, as well as the basis for selecting genetically different parents for breeding.

scholarly journals Molecular typing of bacteria of the genus Asaia in malaria vector Anopheles arabiensis Patton, 1905

2012 ◽  
Vol 44 (2) ◽  
pp. 7 ◽  
Author(s):  
S. Epis ◽  
M. Montagna ◽  
F. Comandatore ◽  
C. Damiani ◽  
A. Diabaté ◽  
...  
Keyword(s):  
Molecular Typing ◽  
Internal Transcribed Spacer ◽  
Anopheles Arabiensis ◽  
Acetic Acid Bacterium ◽  
Sub Saharan Africa ◽  
Randomly Amplified Polymorphic Dna ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Sub Saharan ◽  
Dna Pcr

The acetic acid bacterium <em>Asaia</em> spp. was successfully detected in <em>Anopheles arabiensis</em> Patton, 1905, one of the major vector of human malaria in Sub-Saharan Africa. A collection of 45 <em>Asaia</em> isolates in cellfree media was established from 20 individuals collected from the field in Burkina Faso. 16S rRNA universal polymerase chain reaction (PCR) and specific qPCR, for the detection of <em>Asaia</em> spp. were performed in order to reveal the presence of different bacterial taxa associated with this insect. The isolates were typed by internal transcribed spacer-PCR, BOX-PCR, and randomly amplified polymorphic DNA-PCR, proved the presence of different <em>Asaia</em> in <em>A. arabiensis</em>.

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