Identification of Bacillus spp., Escherichia coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. with 16S ribosomal DNA-based oligonucleotide array hybridization

Chiang, Yu-Cheng; Yang, Chi-Yea; Li, Chin; Ho, Yi Cheng; Lin, Chi-Ying; Tsen, Hau‐Yang

doi:10.1016/j.ijfoodmicro.2005.04.028

Cited by 65 publications

(33 citation statements)

References 27 publications

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“…The products were separated in 1.5% agarose gel using SYBR Gold dye. AOB-amoA F: 5'-GGGGTTTCTACTGGTGGT R: 5'-CCCCTCkGsAAAGCCTTCTTC [18] archaeal 16S rRNA F: 5'-ACkGCTCAGTAACACGT R: 5'-yCCGGCGTTGAmTCCAATT [19,20] bacterial 16S rRNA F: 5'-CCTACGGGAGGCAGCAGT R: 5'-CGTTTACGGCGTGGACTA [21] …”

Section: Methodsmentioning

confidence: 99%

The use of Archaea in the bioaugmentation of activated sludge as a method for the biological removal of nitrogen compounds

Polus

Anielak

2017

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The use of Archaea in the bioaugmentation of activated sludge as a method for the biological removal of nitrogen compounds Wykorzystanie archaea w bioaugmentacji osadu czynnego jako metody biologicznego usuwania związków azotu Abstract This paper examines the effect of Archaea on wastewater treatment in sequencing biological reactors (SBR).The research was carried out in two SBR reactors: a reactor with activated sludge bioaugmented with Archaea (microorganisms which constitute a third domain besides Bacteria and Eukaryotes); a reactor with conventional activated sludge was used as a control. Archaea were incubated in laboratory conditions as recommended by Archaea Solutions Inc. The research revealed that the time period required for the acclimation of the activated sludge in the presence of Archaea was twice as long as in the case of regular nitrifying activated sludge. The observed nitrogen and phosphorous removal from wastewater was achieved to a higher extent in sludge with Archaea and the sludge itself settled faster. The required concentration of oxygen in the reactor with Archaea was lower than in the classic set-up -this resulted in lowering the operating costs of the treatment plant. Furthermore, the denitrification process was significantly shorter and did not require nitrate nitrogen (V).

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Section: Methodsmentioning

confidence: 99%

The use of Archaea in the bioaugmentation of activated sludge as a method for the biological removal of nitrogen compounds

Polus

Anielak

2017

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“…The development of identiication techniques for a clinical rapid diagnosis is necessary. The PCR is a rapid, sensitive, and less time-consuming than the conventional bacteriological identiication methods [40] and is extensively used to identify bacteria isolated from diferent kind of samples, including foods [41], soil [42], and infected human tissue [43].…”

Section: Molecular Methodsmentioning

confidence: 99%

“…Into the sequence of 16Sr RNA gene are indicated variable regions; Chakravorty et al [45] in his study describe nine regions with suicient diversity that are suitable for taxonomic analysis; their investigation determined that V1 hypervariable region best diferentiated among S. aureus and coagulasenegative Staphylococcus sp. Linked to the PCR technique, the use of the 16S rRNA DNA fragment, ampliied by using speciic oligonucleotides, has been proposed; this gene is widely used for the preparation of phylogenetic trees and useful in inding the evolutionary relationships between two or more individuals [40,46]. For S. aureus, the sequence of 16S ribosomal RNA is reported in the NCBI (National Center for Biotechnology Information) with just over 1.4 kb and access to the GenBank (KP728240.1) was reported by Nazari [47].…”

Section: Identiication Based On 16s Ribosomal Rna Genementioning

confidence: 99%

PCR Assay for Detection of Staphylococcus aureus in Fresh Lettuce (Lactuca sativa)

Chávez‐Almanza¹,

López‐Cervantes²,

Cantú-Soto³

et al. 2017

Frontiers in Staphylococcus Aureus

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The growth in food demand and production growth of vegetables have led to the development of intensive production systems with the aim of having regular access to enough high-quality food. The aim is to determine the incidence of Staphylococcus aureus in fresh letuce by PCR in order to enhance the eiciency for detection and identiication process. The Baird-Parker method was used for isolating pathogens from 54 letuce samples. Genomic DNA extraction was performed according the Mericon DNA Bacteria Plus Kit. The detection by PCR was performed using the pair of primers: coa gene (5′-ATAGAGCTGATGGTACAGG-3′ and 5′-GCTTCCGATTGTTCGATGC-3′). The phylogenetic tree was constructed by comparing conserved sequences from the adjacent 16S gene, using the F2C 5′-AGAGTTTGATCATGGCTC-3′ and C 5′-ACGGGCGGTGTGTAC-3′ primers. To test the antimicrobial efect, we used the disk difusion method (Kirby-Bauer) using Mueller-Hinton agar and ive antibiotics with diferent concentrations. The incidence of S. aureus was 1.7%. All the isolates were situated in the ATCC 11632 clade in accordance with other reported sequences belonging to this pathogen in the NCBI database. All the isolates seemed to be resistant to penicillin (10U). The molecular techniques used in this study are suitable for the identiication of S. aureus isolated from letuce, increasing our capability of detecting this pathogen by improving the process and increasing the eiciency contributing to the safety of this vegetable.

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“…These methods targeted only small numbers of species. Only a few methods have been developed for targeting multiple species Leinberger et al, 2005;Chiang et al, 2006;Spiess et al, 2007;Cao et al, 2011 . While the methods had been reported for the identification of large numbers of microbial species and for the identification of fungi, these studies targeted medically important fungi Hsiao et al, 2005;Leinberger et al, 2005;Spiess et al, 2007;Sato et al, 2010;Sakai et al, 2014 .…”

Section: Detection Sensitivity Of the Dna Array Methods For Fungal Cellsmentioning

confidence: 99%

Development of a DNA Array for the Simple Identification of Major Filamentous Fungi in the Beverage Manufacturing Environment

Aoyama

Miyamoto

2016

Biocontrol Sci.

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Filamentous fungi were isolated from the indoor environment of a soft drink manufacturing plant and ordinary residences. The isolated strains were identified based on morphological observation and the nucleotide sequences of the region near the D2 region of the 26S rDNA. Three genera Aspergillus, Penicillium, and Cladosporium accounted for 48.1% of the fungal strains detected in the manufacturing plant and 75.3% in residences. A DNA array for identification of 15 genera and 26 species of filamentous fungi that were most frequently isolated from the manufacturing plant was developed. Genus-and species-specific probes with 13-to 20-mer were designed on the basis of the nucleotide sequences in the D2 region. The probes were affixed to a microscope slide after modifying an amino group at the 5 or 3 end. To prevent erroneous identification, 2 or 3 probes were designed for each of the target genera and species. The developed DNA array method correctly identified 9 genera Alternaria, Aureobasidium, Cladosporium, Curvularia, Exophiala, Fusarium, Penicillium, Phoma, and Trichoderma and 26 species belonging to 6 genera Aspergillus, Neosartorya, Byssochlamys, Talaromyces, Paecilomyces, and Purpureocillium in the strains isolated from the indoor environment. Identification results obtained by this DNA array method of fungi isolated from the manufacturing plant were consistent with those by the conventional method.

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Identification of Bacillus spp., Escherichia coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. with 16S ribosomal DNA-based oligonucleotide array hybridization

Cited by 65 publications

References 27 publications

The use of Archaea in the bioaugmentation of activated sludge as a method for the biological removal of nitrogen compounds

The use of Archaea in the bioaugmentation of activated sludge as a method for the biological removal of nitrogen compounds

PCR Assay for Detection of Staphylococcus aureus in Fresh Lettuce (Lactuca sativa)

Development of a DNA Array for the Simple Identification of Major Filamentous Fungi in the Beverage Manufacturing Environment

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