Publications by authors named "Tamas Petkovits"

7 Publications

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Anti-Biofilm Effect of Selected Essential Oils and Main Components on Mono- and Polymicrobic Bacterial Cultures.

Microorganisms 2019 Sep 12;7(9). Epub 2019 Sep 12.

Institute of Food Engineering, Faculty of Engineering, University of Szeged, H-6724 Szeged, Mars tér 7, Hungary.

Biofilms are surface-associated microbial communities resistant to sanitizers and antimicrobials. Various interactions that can contribute to increased resistance occur between the populations in biofilms. These relationships are the focus of a range of studies dealing with biofilm-associated infections and food spoilage. The present study investigated the effects of cinnamon (), marjoram (), and thyme () essential oils (EOs) and their main components, i.e., trans-cinnamaldehyde, terpinen-4-ol, and thymol, respectively, on single- and dual-species biofilms of , , and . In dual-species biofilms, was paired with each of the other three bacteria. Minimum inhibitory concentration (MIC) values for the individual bacteria ranged between 0.25 and 20 mg/mL, and trans-cinnamaldehyde and cinnamon showed the highest growth inhibitory effect. Single-species biofilms of , and were inhibited by the tested EOs and their components at sub-lethal concentrations. Scanning electron microscopy images showed that the three-dimensional structure of mature biofilms embedded in the exopolysaccharide matrix disappeared or was limited to micro-colonies with a simplified structure. In most dual-species biofilms, to eliminate living cells from the matrix, concentrations exceeding the MIC determined for individual bacteria were required.
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http://dx.doi.org/10.3390/microorganisms7090345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6780703PMC
September 2019

Anti-listerial effect of selected essential oils and thymol.

Acta Biol Hung 2016 Sep;67(3):333-43

Institute of Food Engineering, Faculty of Engineering, University of Szeged , 6722 Szeged, Mars tér 7. , Hungary.

The anti-listerial effect of marjoram, thyme essential oils (EOs) and thymol on Listeria monocytogenes inoculated chicken breast fillets was investigated. Before inoculation the fillets were pretreated by washing or not under running tap water. Inoculated samples were kept at 6 °C for 24 h to allow the growth of L. monocytogenes. After this, the fillets were put in marinating solutions containing salt (5%) and EOs or thymol in MIC/2 concentration established in vitro. Total germ count (TGC) and L. monocytogenes count was monitored on the meat surface and in the marinating solutions following 24 and 48 h storage at 6 °C. Thyme and thymol reduced significantly Listeria cell count (1-3 log CFU) in both samples. They also gave good flavour to the fried meat. The doses of EOs used were optimal for antimicrobial efficiency and had a pleasant flavour effect. Washing was not efficient in reducing total germ count.
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http://dx.doi.org/10.1556/018.67.2016.3.10DOI Listing
September 2016

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
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http://dx.doi.org/10.1093/database/bau061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075928PMC
February 2015

Re-mind the gap! Insertion - deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi.

PLoS One 2012 19;7(11):e49794. Epub 2012 Nov 19.

University of Szeged, Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary.

Rapidly evolving, indel-rich phylogenetic markers play a pivotal role in our understanding of the relationships at multiple levels of the tree of life. There is extensive evidence that indels provide conserved phylogenetic signal, however, the range of phylogenetic depths for which gaps retain tree signal has not been investigated in detail. Here we address this question using the fungal internal transcribed spacer (ITS), which is central in many phylogenetic studies, molecular ecology, detection and identification of pathogenic and non-pathogenic species. ITS is repeatedly criticized for indel-induced alignment problems and the lack of phylogenetic resolution above species level, although these have not been critically investigated. In this study, we examined whether the inclusion of gap characters in the analyses shifts the phylogenetic utility of ITS alignments towards earlier divergences. By re-analyzing 115 published fungal ITS alignments, we found that indels are slightly more conserved than nucleotide substitutions, and when included in phylogenetic analyses, improved the resolution and branch support of phylogenies across an array of taxonomic ranges and extended the resolving power of ITS towards earlier nodes of phylogenetic trees. Our results reconcile previous contradicting evidence for the effects of data exclusion: in the case of more sophisticated indel placement, the exclusion of indel-rich regions from the analyses results in a loss of tree resolution, whereas in the case of simpler alignment methods, the exclusion of gapped sites improves it. Although the empirical datasets do not provide to measure alignment accuracy objectively, our results for the ITS region are consistent with previous simulations studies alignment algorithms. We suggest that sophisticated alignment algorithms and the inclusion of indels make the ITS region and potentially other rapidly evolving indel-rich loci valuable sources of phylogenetic information, which can be exploited at multiple taxonomic levels.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049794PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501463PMC
May 2013

Homology modeling and phylogenetic relationships of catalases of an opportunistic pathogen Rhizopus oryzae.

Life Sci 2012 Aug 28;91(3-4):115-26. Epub 2012 Jun 28.

Institute of Pharmaceutical Analysis, Faculty of Pharmacy, University of Szeged H-6720 Szeged, Somogyi u. 4, Hungary.

Aims: A homology modeling methodology was developed and used to obtain the 3D structures for four putative catalases of Rhizopus oryzae in order to assess their functionality.

Main Methods: Homology models were built using different modeling strategies using non-protein compounds as steric constraints, a symmetry constraint to force identical chains and an additional loop modeling algorithm. Percent structural overlap values (SO) were calculated for each model-template pair to qualify the homology models.

Key Findings: Comparing the different modeling strategies by the SO values revealed that the quality of the models, i.e. the similarity to the template was greatly increased in the presence of the prosthetic groups, modeling multiple protein chains together, enforcing symmetrical chains and applying additional loop modeling. For the best homology models achieved this way, the SO values express similar evolutionary relationships between the proteins modeled and the templates that were previously established by phylogenetic analysis. In three out of the four catalases of R. oryzae the highest quality models, the active center, i.e. the heme molecule and the surrounding amino acids showed a spatial arrangement identical to that observed experimentally in other catalases. The remaining protein is missing an 11 residue long fragment and has mutated residues within the active center.

Significance: Better homology models can be obtained with templates chosen by phylogenetic relationship, although building an accurate model needs structural constraints too. Calculating the structural overlap between the models and the templates may also help to find the appropriate templates.
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http://dx.doi.org/10.1016/j.lfs.2012.06.016DOI Listing
August 2012

Data partitions, Bayesian analysis and phylogeny of the zygomycetous fungal family Mortierellaceae, inferred from nuclear ribosomal DNA sequences.

PLoS One 2011 10;6(11):e27507. Epub 2011 Nov 10.

Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.

Although the fungal order Mortierellales constitutes one of the largest classical groups of Zygomycota, its phylogeny is poorly understood and no modern taxonomic revision is currently available. In the present study, 90 type and reference strains were used to infer a comprehensive phylogeny of Mortierellales from the sequence data of the complete ITS region and the LSU and SSU genes with a special attention to the monophyly of the genus Mortierella. Out of 15 alternative partitioning strategies compared on the basis of Bayes factors, the one with the highest number of partitions was found optimal (with mixture models yielding the best likelihood and tree length values), implying a higher complexity of evolutionary patterns in the ribosomal genes than generally recognized. Modeling the ITS1, 5.8S, and ITS2, loci separately improved model fit significantly as compared to treating all as one and the same partition. Further, within-partition mixture models suggests that not only the SSU, LSU and ITS regions evolve under qualitatively and/or quantitatively different constraints, but that significant heterogeneity can be found within these loci also. The phylogenetic analysis indicated that the genus Mortierella is paraphyletic with respect to the genera Dissophora, Gamsiella and Lobosporangium and the resulting phylogeny contradict previous, morphology-based sectional classification of Mortierella. Based on tree structure and phenotypic traits, we recognize 12 major clades, for which we attempt to summarize phenotypic similarities. M. longicollis is closely related to the outgroup taxon Rhizopus oryzae, suggesting that it belongs to the Mucorales. Our results demonstrate that traits used in previous classifications of the Mortierellales are highly homoplastic and that the Mortierellales is in a need of a reclassification, where new, phylogenetically informative phenotypic traits should be identified, with molecular phylogenies playing a decisive role.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027507PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213126PMC
May 2012

Where is the unseen fungal diversity hidden? A study of Mortierella reveals a large contribution of reference collections to the identification of fungal environmental sequences.

New Phytol 2011 Aug 31;191(3):789-794. Epub 2011 Mar 31.

Faculty of Science and Informatics, Department of Microbiology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.

• Estimation of the proportion of undescribed fungal taxa is an issue that has remained unresolved for many decades. Several very different estimates have been published, and the relative contributions of traditional taxonomic and next-generation sequencing (NGS) techniques to species discovery have also been called into question recently. • Here, we addressed the question of what proportion of hitherto unidentifiable molecular operational taxonomic units (MOTUs) have already been described but not sequenced, and how many of them represent truly undescribed lineages. We accomplished this by modeling the effects of increasing type strain sequencing effort on the number of identifiable MOTUs of the widespread soil fungus Mortierella. • We found a nearly linear relationship between the number of type strains sequenced and the number of identifiable MOTUs. Using this relationship, we made predictions about the total number of Mortierella species and found that it was very close to the number of described species in Mortierella. • These results suggest that the unusually high number of unidentifiable MOTUs in environmental sequencing projects can be, at least in some fungal groups, ascribed to a lag in type strain and specimen sequencing rather than to a high number of undescribed species.
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http://dx.doi.org/10.1111/j.1469-8137.2011.03707.xDOI Listing
August 2011
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