We have collaborated on the following publications
2020
9.
Böhmer, M; Ozdín, D; Račko, M; Lichvár, M; Budiš, J; Szemes, T
Identification of bacterial and fungal communities in the roots of orchids and surrounding soil in heavy metal contaminated area of mining heaps Journal Article
In: Applied Sciences (Switzerland), 10 (20), pp. 1-18, 2020, ISSN: 20763417.
Abstract | Links | BibTeX | Tags: Bacteria, Environmental microbiome, Metagenomics, Plants
@article{Böhmer20201,
title = {Identification of bacterial and fungal communities in the roots of orchids and surrounding soil in heavy metal contaminated area of mining heaps},
author = {M Böhmer and D Ozdín and M Račko and M Lichvár and J Budiš and T Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85093967272&doi=10.3390%2fapp10207367&partnerID=40&md5=a65386928d7c2f6f118d18ce7a0e4bb3},
doi = {10.3390/app10207367},
issn = {20763417},
year = {2020},
date = {2020-01-01},
journal = {Applied Sciences (Switzerland)},
volume = {10},
number = {20},
pages = {1-18},
publisher = {MDPI AG},
abstract = {Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},
keywords = {Bacteria, Environmental microbiome, Metagenomics, Plants},
pubstate = {published},
tppubtype = {article}
}
Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
8.
Böhmer, M; Smoľak, D; Ženišová, K; Čaplová, Z; Pangallo, D; Puškárová, A; Bučková, M; Cabicarová, T; Budiš, J; Šoltýs, K; Rusňáková, D; Kuchta, T; Szemes, T
Comparison of microbial diversity during two different wine fermentation processes Journal Article
In: FEMS microbiology letters, 367 (18), 2020, ISSN: 15746968.
Abstract | Links | BibTeX | Tags: Bacteria, Food microbiome, Fungi, Metagenomics, Plants
@article{Böhmer2020b,
title = {Comparison of microbial diversity during two different wine fermentation processes},
author = {M Böhmer and D Smoľak and K Ženišová and Z Čaplová and D Pangallo and A Puškárová and M Bučková and T Cabicarová and J Budiš and K Šoltýs and D Rusňáková and T Kuchta and T Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85091808679&doi=10.1093%2ffemsle%2ffnaa150&partnerID=40&md5=bc04ad6a27036f5f7562c73abecb183f},
doi = {10.1093/femsle/fnaa150},
issn = {15746968},
year = {2020},
date = {2020-01-01},
journal = {FEMS microbiology letters},
volume = {367},
number = {18},
publisher = {NLM (Medline)},
abstract = {Wine production is a complex procedure in which an important role is played by many microorganisms, particularly yeasts and bacteria. In modern wineries, alcoholic fermentation is usually carried out by adding microbial starter cultures of Saccharomyces cerevisiae strains for precisely controlled production. Nowadays, in the Slovak Republic, autochthonous vinification is getting more popular. The present article deals with the comparison of two vinification approaches, namely spontaneous fermentation and fermentation controlled by a standard commercial S. cerevisiae starter, from the point of view of microbiota dynamics and the chemical characteristics of the wines produced. The dynamics of microbial populations were determined during the fermentation process by a 16S and 28S rRNA next-generation sequencing approach. A profile of the volatile compounds during these fermentation processes was identified by solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS). In summary, the microbial diversity in the m1 phase (initial must) was higher, despite the presence of the starter culture. In the m3 phase (young wine), the microbiome profiles of both batches were very similar. It seems that the crucial phase in order to study the relationship of the microbiome and the resulting product should be based on the m2 phase (fermented must), where the differences between the autochthonous and inoculated batches were more evident. © The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.},
keywords = {Bacteria, Food microbiome, Fungi, Metagenomics, Plants},
pubstate = {published},
tppubtype = {article}
}
Wine production is a complex procedure in which an important role is played by many microorganisms, particularly yeasts and bacteria. In modern wineries, alcoholic fermentation is usually carried out by adding microbial starter cultures of Saccharomyces cerevisiae strains for precisely controlled production. Nowadays, in the Slovak Republic, autochthonous vinification is getting more popular. The present article deals with the comparison of two vinification approaches, namely spontaneous fermentation and fermentation controlled by a standard commercial S. cerevisiae starter, from the point of view of microbiota dynamics and the chemical characteristics of the wines produced. The dynamics of microbial populations were determined during the fermentation process by a 16S and 28S rRNA next-generation sequencing approach. A profile of the volatile compounds during these fermentation processes was identified by solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS). In summary, the microbial diversity in the m1 phase (initial must) was higher, despite the presence of the starter culture. In the m3 phase (young wine), the microbiome profiles of both batches were very similar. It seems that the crucial phase in order to study the relationship of the microbiome and the resulting product should be based on the m2 phase (fermented must), where the differences between the autochthonous and inoculated batches were more evident. © The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.
7.
Bielik, V; Hric, I; BaláŽ, V; Penesová, A; Vávrová, S; Grones, J; Bokor, B; Budiš, J; Bohmer, M; Minárik, G; Augustovičová, D; Šoltys, K
Gut microbiota diversity in lean athletes is associated with positive energy balance Journal Article
In: Annals of Nutrition and Metabolism, 2020, ISSN: 02506807.
Abstract | Links | BibTeX | Tags: Bacteria, Gut microbiome, Metagenomics
@article{Bielik2020,
title = {Gut microbiota diversity in lean athletes is associated with positive energy balance},
author = {V Bielik and I Hric and V BalᎠand A Penesová and S Vávrová and J Grones and B Bokor and J Budiš and M Bohmer and G Minárik and D Augustovičová and K Šoltys},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85091307627&doi=10.1159%2f000509833&partnerID=40&md5=4461653fb07e53dc12411cda7d4cb566},
doi = {10.1159/000509833},
issn = {02506807},
year = {2020},
date = {2020-01-01},
journal = {Annals of Nutrition and Metabolism},
publisher = {S. Karger AG},
abstract = {Introduction: In contrast to obesity, little is known about the human lean phenotype associated with gut microbiota composition. Objective: We aimed to investigate whether the bacterial composition of lean athletes with a positive energy balance differs from the equal-calorie food group. Methods: Twenty-four male participants were included in this cross-sectional study: lean athletes with a positive energy balance (LA, n 12) and control group athletes (CTRLs, n 12). Nutritional data, resting and total energy expenditure, and body composition were determined. DNA was extracted from stool samples and subjected to 16S rRNA gene analysis. Results: We found 7 differentially abundant bacterial taxa between the LA and CTRL groups. Of those, 5 were significantly less abundant and 2 were enriched in the LA group. The following categories significantly associated with the community structure were identified: body fat parameters, BMI, energy intake and expenditure, oxygen consumption, and respiratory exchange ratio. Conclusions: Although we are far from a detailed interpretation of lean human body maintenance, the primary findings of our study suggest that gut microbial composition may be a factor influencing the regulation of weight gain in lean athletes with a positive energy balance. © 2020 Cambridge University Press. All rights reserved.},
keywords = {Bacteria, Gut microbiome, Metagenomics},
pubstate = {published},
tppubtype = {article}
}
Introduction: In contrast to obesity, little is known about the human lean phenotype associated with gut microbiota composition. Objective: We aimed to investigate whether the bacterial composition of lean athletes with a positive energy balance differs from the equal-calorie food group. Methods: Twenty-four male participants were included in this cross-sectional study: lean athletes with a positive energy balance (LA, n 12) and control group athletes (CTRLs, n 12). Nutritional data, resting and total energy expenditure, and body composition were determined. DNA was extracted from stool samples and subjected to 16S rRNA gene analysis. Results: We found 7 differentially abundant bacterial taxa between the LA and CTRL groups. Of those, 5 were significantly less abundant and 2 were enriched in the LA group. The following categories significantly associated with the community structure were identified: body fat parameters, BMI, energy intake and expenditure, oxygen consumption, and respiratory exchange ratio. Conclusions: Although we are far from a detailed interpretation of lean human body maintenance, the primary findings of our study suggest that gut microbial composition may be a factor influencing the regulation of weight gain in lean athletes with a positive energy balance. © 2020 Cambridge University Press. All rights reserved.
2019
6.
Pangallo, D; Kraková, L; Puškárová, A; Šoltys, K; Bučková, M; Koreňová, J; Budiš, J; Kuchta, T
Transcription activity of lactic acid bacterial proteolysis-related genes during cheese maturation Journal Article
In: Food Microbiology, 82 , pp. 416-425, 2019, ISSN: 07400020.
Abstract | Links | BibTeX | Tags: Bacteria, Food microbiome, Metagenomics, Transcriptomics
@article{Pangallo2019416,
title = {Transcription activity of lactic acid bacterial proteolysis-related genes during cheese maturation},
author = {D Pangallo and L Kraková and A Puškárová and K Šoltys and M Bučková and J Koreňová and J Budiš and T Kuchta},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85063597246&doi=10.1016%2fj.fm.2019.03.015&partnerID=40&md5=ebfc8c9f9e3d1955df5b867600b581a5},
doi = {10.1016/j.fm.2019.03.015},
issn = {07400020},
year = {2019},
date = {2019-01-01},
journal = {Food Microbiology},
volume = {82},
pages = {416-425},
publisher = {Academic Press},
abstract = {The catabolism of milk protein in cheese is one way how the microorganisms influence the sensorial characteristics of the final product. In this investigation, we paid attention to four genes [prtP (cell-envelope proteinase gene), pepX (X-prolyl dipeptidyl aminopeptidase gene), pepN (aminopeptidase gene) and bcaT (branched chain aminotransferase gene)] responsible for the production of volatile aroma-active compounds from milk proteins by lactic acid bacteria (LAB). We studied the dynamics of these genes and their corresponding LAB host, during the maturation of a raw ewes’ milk-based cheese, using metagenomics and metatranscriptomics approaches. The transcriptome-oriented experiments included the analysis of total RNA (at three stages of cheese maturation) and also the construction of specific cDNA sub-libraries of the abovementioned genes. The proteolytic transcriptome analysis was supported by following the transcription activity of 16S rRNA gene and by metagenomic investigation. The combination of the described methods permitted to screen the dynamics of targeted genes throughout the cheese production. Lactococci were the major players in the LAB group, but the analysis provided also information on the role and properties of members of the genus Lactobacillus, such as Lb. rhamnosus, Lb. helveticus, Lb. pentosus, Lb. curvatus, Lb. parabuchneri, Lb. plantarum, Lb. brevis, Lb. delbrueckii, Lb. paracasei, Lb. fermentum and Lb. heilongjiangensis, proteolysis-related genes of which were active during cheese ripening. © 2019 Elsevier Ltd},
keywords = {Bacteria, Food microbiome, Metagenomics, Transcriptomics},
pubstate = {published},
tppubtype = {article}
}
The catabolism of milk protein in cheese is one way how the microorganisms influence the sensorial characteristics of the final product. In this investigation, we paid attention to four genes [prtP (cell-envelope proteinase gene), pepX (X-prolyl dipeptidyl aminopeptidase gene), pepN (aminopeptidase gene) and bcaT (branched chain aminotransferase gene)] responsible for the production of volatile aroma-active compounds from milk proteins by lactic acid bacteria (LAB). We studied the dynamics of these genes and their corresponding LAB host, during the maturation of a raw ewes’ milk-based cheese, using metagenomics and metatranscriptomics approaches. The transcriptome-oriented experiments included the analysis of total RNA (at three stages of cheese maturation) and also the construction of specific cDNA sub-libraries of the abovementioned genes. The proteolytic transcriptome analysis was supported by following the transcription activity of 16S rRNA gene and by metagenomic investigation. The combination of the described methods permitted to screen the dynamics of targeted genes throughout the cheese production. Lactococci were the major players in the LAB group, but the analysis provided also information on the role and properties of members of the genus Lactobacillus, such as Lb. rhamnosus, Lb. helveticus, Lb. pentosus, Lb. curvatus, Lb. parabuchneri, Lb. plantarum, Lb. brevis, Lb. delbrueckii, Lb. paracasei, Lb. fermentum and Lb. heilongjiangensis, proteolysis-related genes of which were active during cheese ripening. © 2019 Elsevier Ltd
5.
Planý, M; Czolderová, M; Kraková, L; Puškárová, A; Bučková, M; Šoltys, K; Budiš, J; Szemes, T; Mackulak, T; Wu, J -H; Pangallo, D
Biogas production: evaluation of the influence of K2FeO4 pretreatment of maple leaves (Acer platanoides) on microbial consortia composition Journal Article
In: Bioprocess and Biosystems Engineering, 42 (7), pp. 1151-1163, 2019, ISSN: 16157591.
Abstract | Links | BibTeX | Tags: Bacteria, Biogas production, Fungi, Metagenomics, Plants
@article{Planý20191151,
title = {Biogas production: evaluation of the influence of K2FeO4 pretreatment of maple leaves (Acer platanoides) on microbial consortia composition},
author = {M Planý and M Czolderová and L Kraková and A Puškárová and M Bučková and K Šoltys and J Budiš and T Szemes and T Mackulak and J -H Wu and D Pangallo},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064487903&doi=10.1007%2fs00449-019-02112-x&partnerID=40&md5=49c72565995160169ee6d43ac9524510},
doi = {10.1007/s00449-019-02112-x},
issn = {16157591},
year = {2019},
date = {2019-01-01},
journal = {Bioprocess and Biosystems Engineering},
volume = {42},
number = {7},
pages = {1151-1163},
publisher = {Springer Verlag},
abstract = {The potential of K2FeO4 as a pretreatment agent of a lignocellulosic material was examined on leaves of Acer platanodides as the sole substrate for biogas production by anaerobic digestion carried out through modelling laboratory-scaled semi-continuous reactors differing in loading rates and substrate (pretreated and untreated leaves). The quality of bioagas produced by K2FeO4-pretreated leaves was significantly better in terms of higher methane content and lower content of H2S. K2FeO4 had no crucial influence on growth inhibition of biogas-producing bacteria, which were analysed by comprehensive culture-independent methods utilising high-throughput sequencing of specific genes [bacterial and archaeal 16S rRNA, formyltetrahydrofolate synthetase gene (fhs), methyl-coenzyme M reductase α subunit gene (mcrA) and fungal internal transcribed spacers (ITS)]. The higher amount of CH4 in biogas utilising pretreated leaves as substrate could be caused by a shift to acetoclastic methanogenesis pathway, which was indicated by the higher amount of homoacetogenic bacteria and acetotrophic methanogens detected in those reactors. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.},
keywords = {Bacteria, Biogas production, Fungi, Metagenomics, Plants},
pubstate = {published},
tppubtype = {article}
}
The potential of K2FeO4 as a pretreatment agent of a lignocellulosic material was examined on leaves of Acer platanodides as the sole substrate for biogas production by anaerobic digestion carried out through modelling laboratory-scaled semi-continuous reactors differing in loading rates and substrate (pretreated and untreated leaves). The quality of bioagas produced by K2FeO4-pretreated leaves was significantly better in terms of higher methane content and lower content of H2S. K2FeO4 had no crucial influence on growth inhibition of biogas-producing bacteria, which were analysed by comprehensive culture-independent methods utilising high-throughput sequencing of specific genes [bacterial and archaeal 16S rRNA, formyltetrahydrofolate synthetase gene (fhs), methyl-coenzyme M reductase α subunit gene (mcrA) and fungal internal transcribed spacers (ITS)]. The higher amount of CH4 in biogas utilising pretreated leaves as substrate could be caused by a shift to acetoclastic methanogenesis pathway, which was indicated by the higher amount of homoacetogenic bacteria and acetotrophic methanogens detected in those reactors. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.
4.
Sádecká, J; Čaplová, Z; Tomáška, M; Šoltys, K; Kopuncová, M; Budiš, J; Drončovský, M; Kolek, E I; Koreňová, J; Kuchta, T
Microorganisms and volatile aroma-active compounds in bryndza cheese produced and marketed in Slovakia Journal Article
In: Journal of Food and Nutrition Research, 58 (4), pp. 382-392, 2019, ISSN: 13368672.
Abstract | Links | BibTeX | Tags: Bacteria, Food microbiome, Fungi, Metagenomics
@article{Sádecká2019382,
title = {Microorganisms and volatile aroma-active compounds in bryndza cheese produced and marketed in Slovakia},
author = {J Sádecká and Z Čaplová and M Tomáška and K Šoltys and M Kopuncová and J Budiš and M Drončovský and E I Kolek and J Koreňová and T Kuchta},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85076215677&partnerID=40&md5=462a79588febfb4630b304b476f04a07},
issn = {13368672},
year = {2019},
date = {2019-01-01},
journal = {Journal of Food and Nutrition Research},
volume = {58},
number = {4},
pages = {382-392},
publisher = {Food Reseach Institute},
abstract = {Ten industrially and traditionally produced versions of bryndza, a typical Slovakian ewes’ cheese, covering the dominating offer in the market in Slovakia, were studied regarding the contents of microorganisms and key volatile aromaactive compounds. Culture-based microbiological analysis was complemented by culture-independent analysis by high throughput sequencing on Illumina MiSeq platform using 16S rDNA and internal transcribed spacer amplicons. Aroma-active compounds extracted by headspace solid-phase microextraction were analysed by gas chromatographyolfactometry supported by gas chromatography-mass spectrometry. Bacterial microflora was found to be dominated by lactic acid bacteria, mostly lactococci, followed by streptococci, lactobacilli and leuconostocs. A portion of cheeses contained Enterobacteriaceae, pseudomonads or Chryseobacterium spp. and, exceptionally, coagulase-positive staphylococci at a legally acceptable level. Eukaryotic microflora was dominated by Dipodascaceae in most samples. Certain samples contained contaminants such as Mucor spp. Key aroma-active compounds comprised butanoic acid, δ-decalactone, acetic acid, diacetyl and guaiacol. Further significant aroma-active compounds were 3-methylbutanol, 3-methylbutanoic acid, 2-phenylethanol, octanoic acid and p-cresol. The results demonstrated that geographical location, involvement of pasteurization or admixture of the cows’ milk-based component do not entirely determine the aroma profile of bryndza cheese, but it appears to be the result of a complex interplay of the production technology and microorganisms. © 2019 National Agricultural and Food Centre (Slovakia).},
keywords = {Bacteria, Food microbiome, Fungi, Metagenomics},
pubstate = {published},
tppubtype = {article}
}
Ten industrially and traditionally produced versions of bryndza, a typical Slovakian ewes’ cheese, covering the dominating offer in the market in Slovakia, were studied regarding the contents of microorganisms and key volatile aromaactive compounds. Culture-based microbiological analysis was complemented by culture-independent analysis by high throughput sequencing on Illumina MiSeq platform using 16S rDNA and internal transcribed spacer amplicons. Aroma-active compounds extracted by headspace solid-phase microextraction were analysed by gas chromatographyolfactometry supported by gas chromatography-mass spectrometry. Bacterial microflora was found to be dominated by lactic acid bacteria, mostly lactococci, followed by streptococci, lactobacilli and leuconostocs. A portion of cheeses contained Enterobacteriaceae, pseudomonads or Chryseobacterium spp. and, exceptionally, coagulase-positive staphylococci at a legally acceptable level. Eukaryotic microflora was dominated by Dipodascaceae in most samples. Certain samples contained contaminants such as Mucor spp. Key aroma-active compounds comprised butanoic acid, δ-decalactone, acetic acid, diacetyl and guaiacol. Further significant aroma-active compounds were 3-methylbutanol, 3-methylbutanoic acid, 2-phenylethanol, octanoic acid and p-cresol. The results demonstrated that geographical location, involvement of pasteurization or admixture of the cows’ milk-based component do not entirely determine the aroma profile of bryndza cheese, but it appears to be the result of a complex interplay of the production technology and microorganisms. © 2019 National Agricultural and Food Centre (Slovakia).
3.
Tomáška, M; Čaplová, Z; Sádecká, J; Šoltys, K; Kopuncová, M; Budiš, J; Drončovský, M; Kolek, E; Koreňová, J; Kuchta, T
Microorganisms and volatile aroma-active compounds in “nite“and “vojky” cheeses Journal Article
In: Journal of Food and Nutrition Research, 58 (2), pp. 187-200, 2019, ISSN: 13368672.
Abstract | Links | BibTeX | Tags: Bacteria, Food microbiome, Fungi, Metagenomics
@article{Tomáška2019187,
title = {Microorganisms and volatile aroma-active compounds in “nite“and “vojky” cheeses},
author = {M Tomáška and Z Čaplová and J Sádecká and K Šoltys and M Kopuncová and J Budiš and M Drončovský and E Kolek and J Koreňová and T Kuchta},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85070496049&partnerID=40&md5=62737878bddf81c54e9649a0583d4e54},
issn = {13368672},
year = {2019},
date = {2019-01-01},
journal = {Journal of Food and Nutrition Research},
volume = {58},
number = {2},
pages = {187-200},
publisher = {Food Reseach Institute},
abstract = {“Nite“and “vojky“are various string-like forms of a traditional cheese in Slovakia. These products are manufactured by shaping of pasteurized or raw cows’ or ewes’ milk-based lump cheeses after melting in hot water. Unsmoked versions of these cheeses from three producers were studied regarding the contents of microorganisms and volatile aroma-active compounds in four seasons during a year. Culture-based microbiological analysis was carried out using selective media. Because eukaryotic microflora was found to be negligible, culture-independent analysis was focused to prokaryotes, using 16S rDNA amplification coupled to high throughput sequencing on Illumina MiSeq platform (Illumina, San Diego, California, USA). Aroma-active compounds were extracted by headspace solid-phase microextraction and subsequently analysed by gas chromatography-olfactometry supported by gas chromatography-mass spectrometry. Microflora was found to be dominated by Lactococcus spp. with significant levels of Streptococcus spp., Lactobacillus spp. and Enterococcus spp. Dominant aroma-active compounds comprised butanoic acid, diacetyl and 3-methylbutanoic acid, the latter being profound in “nite“produced from unpasteurized ewes’ milk. Traditionally produced cheeses contained a more diverse prokaryotic microflora and had a stronger aroma profile containing a rich complex of volatile aroma-active compounds, while “nite“produced from pasteurized cows’ milk by industrial process contained a uniform microflora and had a weaker aroma profile. © 2019, Food Reseach Institute. All rights reserved.},
keywords = {Bacteria, Food microbiome, Fungi, Metagenomics},
pubstate = {published},
tppubtype = {article}
}
“Nite“and “vojky“are various string-like forms of a traditional cheese in Slovakia. These products are manufactured by shaping of pasteurized or raw cows’ or ewes’ milk-based lump cheeses after melting in hot water. Unsmoked versions of these cheeses from three producers were studied regarding the contents of microorganisms and volatile aroma-active compounds in four seasons during a year. Culture-based microbiological analysis was carried out using selective media. Because eukaryotic microflora was found to be negligible, culture-independent analysis was focused to prokaryotes, using 16S rDNA amplification coupled to high throughput sequencing on Illumina MiSeq platform (Illumina, San Diego, California, USA). Aroma-active compounds were extracted by headspace solid-phase microextraction and subsequently analysed by gas chromatography-olfactometry supported by gas chromatography-mass spectrometry. Microflora was found to be dominated by Lactococcus spp. with significant levels of Streptococcus spp., Lactobacillus spp. and Enterococcus spp. Dominant aroma-active compounds comprised butanoic acid, diacetyl and 3-methylbutanoic acid, the latter being profound in “nite“produced from unpasteurized ewes’ milk. Traditionally produced cheeses contained a more diverse prokaryotic microflora and had a stronger aroma profile containing a rich complex of volatile aroma-active compounds, while “nite“produced from pasteurized cows’ milk by industrial process contained a uniform microflora and had a weaker aroma profile. © 2019, Food Reseach Institute. All rights reserved.
2018
2.
Kraková, L; Šoltys, K; Puškárová, A; Bučková, M; Jeszeová, L; Kucharík, M; Budiš, J; Orovčík, L; Szemes, T; Pangallo, D
The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment Journal Article
In: Environmental Microbiology, 20 (9), pp. 3294-3308, 2018, ISSN: 14622912.
Abstract | Links | BibTeX | Tags: Bacteria, Biodeterioration, Fungi, Metagenomics
@article{Kraková20183294,
title = {The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment},
author = {L Kraková and K Šoltys and A Puškárová and M Bučková and L Jeszeová and M Kucharík and J Budiš and L Orovčík and T Szemes and D Pangallo},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85053249745&doi=10.1111%2f1462-2920.14312&partnerID=40&md5=31ee6742ce17089e12cc092f5dc64938},
doi = {10.1111/1462-2920.14312},
issn = {14622912},
year = {2018},
date = {2018-01-01},
journal = {Environmental Microbiology},
volume = {20},
number = {9},
pages = {3294-3308},
publisher = {Blackwell Publishing Ltd},
abstract = {This microbiological survey was performed to determine the conservation state of a mummy in the Slovak castle of Krásna Hôrka and its surrounding environment. Culture-dependent identification was coupled with biodegradation assays on keratin, gelatin and cellulose. Next Generation Sequencing (NGS) using Illumina platform was used for a deeper microbial investigation. Three environmental samples were collected: from the glass of the sarcophagus, from the air inside it, and from the air of the chapel where the mummy is located. Seven different samples were taken from mummy's surface: from the left ear, left-hand palm, left-hand nail, left instep, right hand, abdomen and mineral crystals embedded within the skin. Three internal organ samples, from the lung, pleura and stomach, were also included in this study. Together, the culture-dependent and culture-independent analyses revealed that the bacterial communities present had fewer taxa than the fungal ones. The mycobiome showed the largest variability and included Epicoccum nigrum, Penicillium spp., Alternaria spp., Aspergillus spp., Cladosporium spp. and Aureobasidium pullulans; many other Ascomycota and Basidiomycota genera were detected by NGS. The most interesting results came from the skin mineral crystals and the internal organs. The hydrolytic assays revealed those microorganisms which might be considered dangerous ‘mummy pathogens’. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd},
keywords = {Bacteria, Biodeterioration, Fungi, Metagenomics},
pubstate = {published},
tppubtype = {article}
}
This microbiological survey was performed to determine the conservation state of a mummy in the Slovak castle of Krásna Hôrka and its surrounding environment. Culture-dependent identification was coupled with biodegradation assays on keratin, gelatin and cellulose. Next Generation Sequencing (NGS) using Illumina platform was used for a deeper microbial investigation. Three environmental samples were collected: from the glass of the sarcophagus, from the air inside it, and from the air of the chapel where the mummy is located. Seven different samples were taken from mummy's surface: from the left ear, left-hand palm, left-hand nail, left instep, right hand, abdomen and mineral crystals embedded within the skin. Three internal organ samples, from the lung, pleura and stomach, were also included in this study. Together, the culture-dependent and culture-independent analyses revealed that the bacterial communities present had fewer taxa than the fungal ones. The mycobiome showed the largest variability and included Epicoccum nigrum, Penicillium spp., Alternaria spp., Aspergillus spp., Cladosporium spp. and Aureobasidium pullulans; many other Ascomycota and Basidiomycota genera were detected by NGS. The most interesting results came from the skin mineral crystals and the internal organs. The hydrolytic assays revealed those microorganisms which might be considered dangerous ‘mummy pathogens’. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd
2016
1.
Kraková, L; Šoltys, K; Budiš, J; Grivalský, T; Ďuriš, F; Pangallo, D; Szemes, T
Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning Journal Article
In: Extremophiles, 20 (5), pp. 795-808, 2016, ISSN: 14310651.
Abstract | Links | BibTeX | Tags: Bacteria, Environmental microbiome, Metagenomics
@article{Kraková2016795,
title = {Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning},
author = {L Kraková and K Šoltys and J Budiš and T Grivalský and F Ďuriš and D Pangallo and T Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84976272674&doi=10.1007%2fs00792-016-0855-5&partnerID=40&md5=a73c4e305f7b0f97139840b4328bff01},
doi = {10.1007/s00792-016-0855-5},
issn = {14310651},
year = {2016},
date = {2016-01-01},
journal = {Extremophiles},
volume = {20},
number = {5},
pages = {795-808},
publisher = {Springer Tokyo},
abstract = {Different protocols based on Illumina high-throughput DNA sequencing and denaturing gradient gel electrophoresis (DGGE)-cloning were developed and applied for investigating hot spring related samples. The study was focused on three target genes: archaeal and bacterial 16S rRNA and mcrA of methanogenic microflora. Shorter read lengths of the currently most popular technology of sequencing by Illumina do not allow analysis of the complete 16S rRNA region, or of longer gene fragments, as was the case of Sanger sequencing. Here, we demonstrate that there is no need for special indexed or tailed primer sets dedicated to short variable regions of 16S rRNA since the presented approach allows the analysis of complete bacterial 16S rRNA amplicons (V1–V9) and longer archaeal 16S rRNA and mcrA sequences. Sample augmented with transposon is represented by a set of approximately 300 bp long fragments that can be easily sequenced by Illumina MiSeq. Furthermore, a low proportion of chimeric sequences was observed. DGGE-cloning based strategies were performed combining semi-nested PCR, DGGE and clone library construction. Comparing both investigation methods, a certain degree of complementarity was observed confirming that the DGGE-cloning approach is not obsolete. Novel protocols were created for several types of laboratories, utilizing the traditional DGGE technique or using the most modern Illumina sequencing. © 2016, Springer Japan.},
keywords = {Bacteria, Environmental microbiome, Metagenomics},
pubstate = {published},
tppubtype = {article}
}
Different protocols based on Illumina high-throughput DNA sequencing and denaturing gradient gel electrophoresis (DGGE)-cloning were developed and applied for investigating hot spring related samples. The study was focused on three target genes: archaeal and bacterial 16S rRNA and mcrA of methanogenic microflora. Shorter read lengths of the currently most popular technology of sequencing by Illumina do not allow analysis of the complete 16S rRNA region, or of longer gene fragments, as was the case of Sanger sequencing. Here, we demonstrate that there is no need for special indexed or tailed primer sets dedicated to short variable regions of 16S rRNA since the presented approach allows the analysis of complete bacterial 16S rRNA amplicons (V1–V9) and longer archaeal 16S rRNA and mcrA sequences. Sample augmented with transposon is represented by a set of approximately 300 bp long fragments that can be easily sequenced by Illumina MiSeq. Furthermore, a low proportion of chimeric sequences was observed. DGGE-cloning based strategies were performed combining semi-nested PCR, DGGE and clone library construction. Comparing both investigation methods, a certain degree of complementarity was observed confirming that the DGGE-cloning approach is not obsolete. Novel protocols were created for several types of laboratories, utilizing the traditional DGGE technique or using the most modern Illumina sequencing. © 2016, Springer Japan.