Development of species-specific primers for rapid identification of Debaryomyces hansenii

Wrent, Petra; Rivas, Eva-María; Prado, Elena Gil de; Peinado, J.; Silóniz, Marı́a-Isabel de

doi:10.1016/j.ijfoodmicro.2014.10.011

Cited by 9 publications

(8 citation statements)

References 26 publications

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“…Outstanding bacteria identification methods include species-specific polymerase chain reaction (PCR), amplified ribosomal DNA restriction analysis (16S-ARDRA), sequencing of 16S ribosomal RNA gene (16S rRNA PCR), tRNAAla-23S rDNA-restriction fragment length polymorphism (tRNA Ala–23S rDNA-RFLP), sequencing of the gene encoding for phenylalanyl-tRNA synthase alpha-subunit (pheS), and multiplex real-time PCR (mRealT-PCR) using the pheS as a molecular target, while DNA fingerprinting techniques include RFLP of protein-coding genes involved in primary metabolism, restriction enzyme analysis pulsed-field gel electrophoresis (REA-PFGE), randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and repetitive extragenic palindromic-PCR (REP-PCR) [ 74 , 76 ]. Similar methods are used for the identification of fungi spanning the internal transcribed spacers (ITSs) and targeting the 5.8S, 18S, 26S, or 28S region of the nuclear ribosomal RNA gene [ 80 , 81 , 82 , 83 , 84 , 85 ].…”

Section: Exploring the Cheese Microbiomementioning

confidence: 99%

Omics Approaches to Assess Flavor Development in Cheese

Anastasiou

Κάζου

Georgalaki

et al. 2022

Foods

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Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.

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Section: Exploring the Cheese Microbiomementioning

confidence: 99%

Omics Approaches to Assess Flavor Development in Cheese

Anastasiou

Κάζου

Georgalaki

et al. 2022

Foods

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“…The different restriction patterns produced by PCR-RFlP might suggest that they represent other species of the genus that also had a high percentage of similarity in sequence. Wrent et al (2015) observed that the species D. hansenii, D. fabryiand D. subglobosus produced the same restriction patterns after digestion with HinfI, HaeIII, and CfoI endonucleases. Thus, it is not possible to determine whether the different restriction patterns obtained in this study represent polymorphisms between species of Debaryomyces genus.…”

Section: Discussionmentioning

confidence: 81%

“…Martorell et al (2005) observed that the D. castellii, D. coudertii, D. hansenii, D. nepalensis, D. polymorphus, D. pseudopolymorphus, D. robertsiae, D. udenii and D. vanrijia species presented sequences of the ITS region with similarity above 99% with one or more species of the genus. Therefore, several alternative molecular markers have been proposed for identification of species of this genus, such as the use of the intron sequences of ACT1 genes (Martorell et al 2005), RPl33 (Jacques et al 2009) and the putative PAD1 homologous gene (Wrent et al 2015).…”

Section: Discussionmentioning

confidence: 99%

Antifungal susceptibility of yeasts isolated from anthropogenic watershed

Milanezi

Witusk

Sand

2019

An. Acad. Bras. Ciênc.

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Yeasts are unicellular fungi widespread in the environment, and studies suggest that there is a positive correlation between yeast and polluted aquatic environments. The aim of this study was to analyze the diversity and resistance of yeasts isolated from water samples collected along the Arroio Dilúvio in Porto Alegre to antifungals. Yeast isolates from the Arroio Dilúvio were subjected to susceptibility assays against antifungals using the minimum inhibitory concentration (MIC) test, and amplification of the ITS1-5.8S-IT2 region; in addition, the ITS-5.8S region was sequenced for some of the isolates. The amplification product was subjected to PCR-RFLP, and the restriction profile allowed the construction of a dendrogram. Susceptibility tests showed a high prevalence of resistance to azole antifungals, where 16.8% of the isolates had a resistance profile to amphotericin B. The sequence analysis allowed the identification of Candida species, including potentially pathogenic species, and species of the Debaryomyces spp. The resistance to antifungals in yeasts isolated from Arroio Dilúvio reinforces the importance of studies of environmental microbiota, and indicates that environmental degradation influences the phenotype displayed.

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“…Randomly selected strains looking similar to the type strain were chosen for further experiments. All of them were identified as D. hansenii by colony PCR with a species-specific pair of primers—DhPADF and DhPADR developed by Wrent et al [ 50 ], giving the product of 402 bp. In each case, a band of approximately 400 bp was obtained ( Figure S2 ).…”

Section: Resultsmentioning

confidence: 99%

“…As we wanted to analyze only D. hansenii strains, new yeast isolates were initially examined by colony PCR with D. hansenii species-specific pair of primers DhPadF/DhPadR developed by Wrent et al [ 50 ] under their conditions except for the initial denaturation step, which was prolonged from 5 to 10 min. The reaction was performed with a small portion of 24 hour-old biomass taken from a plate with a 10 µL tip and mixed with 10 µL of 2 × Taq Nova Red Master Mix (Blirt-DNA-Gdansk, Gdansk, Poland), 0.4 µL of 10 µM each primer, and 9.2 µL of distilled water.…”

Section: Methodsmentioning

confidence: 99%

New Cytoplasmic Virus-Like Elements (VLEs) in the Yeast Debaryomyces hansenii

Połomska

Neuvéglise

Zyzak

et al. 2021

Toxins

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Yeasts can have additional genetic information in the form of cytoplasmic linear dsDNA molecules called virus-like elements (VLEs). Some of them encode killer toxins. The aim of this work was to investigate the prevalence of such elements in D. hansenii killer yeast deposited in culture collections as well as in strains freshly isolated from blue cheeses. Possible benefits to the host from harboring such VLEs were analyzed. VLEs occurred frequently among fresh D. hansenii isolates (15/60 strains), as opposed to strains obtained from culture collections (0/75 strains). Eight new different systems were identified: four composed of two elements and four of three elements. Full sequences of three new VLE systems obtained by NGS revealed extremely high conservation among the largest molecules in these systems except for one ORF, probably encoding a protein resembling immunity determinant to killer toxins of VLE origin in other yeast species. ORFs that could be potentially involved in killer activity due to similarity to genes encoding proteins with domains of chitin-binding/digesting and deoxyribonuclease NucA/NucB activity, could be distinguished in smaller molecules. However, the discovered VLEs were not involved in the biocontrol of Yarrowia lipolytica and Penicillium roqueforti present in blue cheeses.

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Development of species-specific primers for rapid identification of Debaryomyces hansenii

Cited by 9 publications

References 26 publications

Omics Approaches to Assess Flavor Development in Cheese

Omics Approaches to Assess Flavor Development in Cheese

Antifungal susceptibility of yeasts isolated from anthropogenic watershed

New Cytoplasmic Virus-Like Elements (VLEs) in the Yeast Debaryomyces hansenii

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