Proteolytic activity, mycotoxins and andrastin A in Penicillium roqueforti strains isolated from Cabrales, Valdeón and Bejes–Tresviso local varieties of blue-veined cheeses

Prevalence and concentration of aflatoxin M1 and ochratoxin A in cheese: a global systematic review and meta-analysis and probabilistic risk assessment

Exposure to mycotoxins such as aflatoxins can endanger human health, especially infants and children. In this study, an attempt was made to retrieved studies related to the concentration of aflatoxin M1 (AFM1) and ochratoxin A (OTA). Search was performed in international databases such as Embase, PubMed, Scopus, and Web of Science for the period 1 January 2010 to 20 February 2023. Then, the pooled concentration in the defined subgroups was calculated using meta-analysis and the health risk assessment was conducted by margin of exposure (MOEs). Thirty-one scientific papers with 34 data reports (Sample size=2,277) were included in our study. The lowest and highest prevalence of AFM1 in cheese was related to El Salvador (12.18 %) and Serbia (100.00 %). The pooled prevalence of AFM1 was 49.85 %, 95 %CI (37.93-61.78 %). The lowest and highest prevalence of OTA in cheese was related to Türkiye (6.67 %) and Italy (44.21 %). The pooled prevalence of OTA was 35.64 %, 95 %CI (17.16-56.44 %). Health risk of AFM1 revealed that except Pakistan and Iran, MOE in the other countries was lower than 10,000 for adults and also except Pakistan, MOE for other countries was lower than 10,000 for children. Health risk of OTA revealed that except Greece, MOE in the other countries was higher than 10,000 for adults and also except Germany and Greece, MOE for other countries was higher than 10,000 for children. Therefore, it is recommended to conduct control plans to reduce the concentration of mycotoxins in cheese, especially AFM1.

Analysis of Mycotoxin and Secondary Metabolites in Commercial and Traditional Slovak Cheese Samples

Cheese represents a dairy product extremely inclined to fungal growth and mycotoxin production. The growth of fungi belonging to Aspergillus, Penicillium, Fusarium, Claviceps, Alternaria, and Trichoderma genera in or on cheese leads to undesirable changes able to affect the quality of the final products. In the present investigation, a total of 68 types of commercial and traditional Slovak cheeses were analyzed to investigate the occurrence of fungal metabolites. Altogether, 13 fungal metabolites were identified and quantified. Aflatoxin M1, the only mycotoxin regulated in milk and dairy products, was not detected in any case. However, the presence of metabolites that have never been reported in cheeses, such as tryptophol at a maximum concentration level from 13.4 to 7930 µg/kg (average: 490 µg/kg), was recorded. Out of all detected metabolites, enniatin B represents the most frequently detected mycotoxin (0.06–0.71 µg/kg) in the analyzed samples. Attention is drawn to the lack of data on mycotoxins’ origin from Slovak cheeses; in fact, this is the first reported investigation. Our results indicate the presence of fungal mycotoxin contamination for which maximum permissible levels are not established, highlighting the importance of monitoring the source and producers of contamination in order to protect consumers’ health.

Cheese ripening in nonconventional conditions: A multiparameter study applied to Protected Geographical Indication Canestrato di Moliterno cheese

A multiparameter study was performed to evaluate the effect of fondaco, a traditional ripening cellar without any artificial temperature and relative humidity control, on the chemical, microbiological, and sensory characteristics of Protected Geographical Indication Canestrato di Moliterno cheese. Ripening in such a nonconventional environment was associated with lower counts of lactococci, lactobacilli, and total viable bacteria, and higher presence of enterococci, in comparison with ripening in a controlled maturation room. Moreover, fondaco cheese underwent accelerated maturation, as demonstrated by faster casein degradation, greater accumulation of free AA, and higher formation of volatile organic compounds. Secondary proteolysis, as assessed by liquid chromatography-mass spectrometry of free AA and low molecular weight peptides, did not show any qualitative difference among cheeses, but fondaco samples evidenced an advanced level of peptidolysis. On the other hand, significant qualitative differences were observed in the free fatty acid profiles and in the sensory characteristics. Principal component analysis showed a clear separation of the fondaco and control cheeses, indicating that ripening in the natural room conferred unique sensory features to the product.

Sensory analysis for stuffed cheese with Penicillium nalgiovense superficial growth

Sensory analysis for stuffed cheese with Penicillium nalgiovense superficial growth using a descriptive analysis was performed. Cheeses were manufactured in a pilot plant. Penicillium nalgiovense was superficially inoculated and the cheeses were ripened at 12 °C and 90% relative humidity until packaged using a microperforated polyethylene film on day 14. The ripening process continued at either 5 °C or 12 °C for 21 days. Results showed that P. nalgiovense not only confers the external desirable appearance but also has a protective effect against dehydration process. Inoculated cheeses showed descriptors of odour and flavour associated with moulds. Ammonia notes were perceived only for inoculated cheeses on day 35 being more pronounced at 12 °C than 5 °C. The high fat content of the cheeses and the transparent and microperforated packaging might affect the oxidative stability of cheeses at the end of the ripening.

Preservation stress resistance of melanin deficient conidia from Paecilomyces variotii and Penicillium roqueforti mutants generated via CRISPR/Cas9 genome editing

Background

The filamentous fungi Paecilomyces variotii and Penicillium roqueforti are prevalent food spoilers and are of interest as potential future cell factories. A functional CRISPR/Cas9 genome editing system would be beneficial for biotechnological advances as well as future (genetic) research in P. variotii and P. roqueforti.

Results

Here we describe the successful implementation of an efficient AMA1-based CRISPR/Cas9 genome editing system developed for Aspergillus niger in P. variotii and P. roqueforti in order to create melanin deficient strains. Additionally, kusA⁻ mutant strains with a disrupted non-homologous end-joining repair mechanism were created to further optimize and facilitate efficient genome editing in these species. The effect of melanin on the resistance of conidia against the food preservation stressors heat and UV-C radiation was assessed by comparing wild-type and melanin deficient mutant conidia.

Conclusions

Our findings show the successful use of CRISPR/Cas9 genome editing and its high efficiency in P. variotii and P. roqueforti in both wild-type strains as well as kusA⁻ mutant background strains. Additionally, we observed that melanin deficient conidia of three food spoiling fungi were not altered in their heat resistance. However, melanin deficient conidia had increased sensitivity towards UV-C radiation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40694-021-00111-w.

Biological control of mites by xerophile Eurotium species isolated from the surface of dry cured ham and dry beef cecina

Some meat dry products, including dry cured ham and dry beef cecina, are cured in cellars at moderately cold temperature allowing the growth of a lawn of fungi on their surface. During the curing process, frequently these products became contaminated with fungivore mites of the Acaridae family that feed on fungal mycelium and spores.

AIMS

The aim of this article is to study the possible biological control of mites by fungi that form part of the normal microbiota of these meat products.

METHODS AND RESULTS

Some yellow/orange pigmented fungi growing on the ham surface decreased the proliferation of mites; therefore, we isolated from ham and cecina xerophilic yellow/orange coloured fungal strains that were identified as members of the genus Eurotium (recently reclassified as Aspergillus section Aspergillus). Using molecular genetic tools, we have identified 158 strains as Eurotium rubrum (Aspergillus ruber), Eurotium repens (Aspergillus pseudoglaucus) and Eurotium chevalieri (Aspergillus chevalieri). Two strains, E. rubrum C47 and E. rubrum C49, showed strong miticidal activity. The toxic compound(s) are associated with the formation of cleistothecia. In synchronized mite development experiments, we observed that all stages of the mite lifecycle were inhibited by the E. rubrum C47 strain. In addition, we searched for miticidal activity in 13 culture collection Eurotium strains isolated from different habitats, and found that only one, Eurotium cristatum NRRL 4222 (Aspergillus cristatus) has a strong miticidal activity.

CONCLUSIONS

These fungal strains have proliferated on the surface of ham and cecina for decades, and possibly have acquired miticidal activity as a resistance mechanism against fungivores.

SIGNIFICANCE AND IMPACT OF THE STUDY

Biological control of infecting mites by favouring growth of E. rubrun C47, in place of the normal mixed population of Aspergillus and Penicillium, is an attractive approach to control mite infestations.

Fermented dairy foods rich in probiotics and cardiometabolic risk factors: a narrative review from prospective cohort studies

Probiotic foods, including fermented dairy (FD) products such as yogurt and cheese, naturally contain live microorganisms, but the relationship between the consumption of probiotic foods and health is unclear. The aim of the present narrative review is to integrate the available information on the relationship between the most studied FD products, which are yogurt and cheese, and cardiometabolic risk factors obtained from meta-analysis, systematic reviews of prospective cohort studies (PCSs) and PCSs published up to 2 November 2019. Additionally, the effects identified by randomized controlled trials of less-studied FD products, such as kefir and kimchi, on cardiometabolic risk factors are provided. PCSs have shown that the consumption of cheese, despite its high saturated fat content, is not associated with expected hypercholesterolemia and an increased cardiovascular risk. PCSs have revealed that the total consumption of FD appears to be associated with a lower risk of developing stroke and cardiovascular disease. The consumption of yogurt seems to be associated with a lower risk of developing type 2 diabetes. There is a lack of sufficient evidence of a protective relationship between FD or cheese consumption and metabolic syndrome. Moreover, the association of FD, cheese and yogurt with hypertension needs further evidence. In conclusion, the intake of fermented foods containing probiotics, particularly yogurt and cheese (of an undetermined type), opens up new opportunities for the management of cardiometabolic risk factors.

Penicillium commune affects textural properties and water distribution of hard and extra-hard cheeses

We analyzed the effects of growth of Penicillium commune, one of the most frequent fungal species associated with cheese, on the water diffusion and texture of hard and extra-hard cheeses. A total of 36 hard cheese blocks and 36 extra-hard cheese blocks were manufactured, salted at different levels (0.5, 1.25 and 2% w/w), and assigned to different treatments (control and inoculated). Cheese texture was analyzed using a penetration needle probe at 2 and 5 weeks after ripening. Firmness, defined as the maximum force detected in the penetration probe, was higher in both hard and extra-hard inoculated cheese blocks compared with the control. In addition, the presence of fungal growth on cheese rind increased the total work of penetration (a measure of resistance to probe penetration), but only in extra-hard cheeses, suggesting that the moisture of cheese might be affecting the growth capacities and performance of P. commune. The change in textural properties of cheeses was linked to desiccation of the upper 0.5-cm rind layer mediated by P. commune.

Tyrosine Induced Metabolome Alterations of Penicillium roqueforti and Quantitation of Secondary Key Metabolites in Blue-Mold Cheese

To map qualitative and quantitative metabolome alterations when Penicillium roqueforti is grown in an environment where l-tyrosine levels are perturbed, the recently established differential off-line LC-NMR (DOLC-NMR) approach was successfully applied in connection with an absolute metabolite quantitation using a quantitative ¹H NMR protocol following the ERETIC 2 (Electronic REference To access In vivo Concentrations) methodology. Among the 23 influenced metabolites, amino acid degradation products like 2-(4-hydroxyphenyl)acetic acid and 2-(3,4-dihydroxyphenyl)acetic acid underwent a tremendous upregulation in the amino acid perturbed approach. Moreover, the output of secondary metabolites like andrastin A, eremofortin B, and the tetrapeptide d-Phe-l-Val-d-Val-l-Tyr was affected in the case of the presence or absence of the added aromatic amino acid. Furthermore, the isolated secondary metabolites of P. roqueforti have been quantified for the first time in five divergent Penicillium isolates by means of a validated LC-ECHO-MS/MS method. This technique is used to compensate the effect of co-extracted matrix compounds during the analysis and to utilize quasi-internal standards to quantify all metabolites of interest accurately. This screening outlined the great variety between the different fungi of the same species. The metabolite spectra of wild-type fungi included more toxic intermediates compared to a selected fungi used as a starter culture for blue-mold cheese production. In addition, these secondary metabolites were quantified in commercially available white- and blue-mold cheese samples. The main differences between the analyte profiles of white and blue cheeses were linked to the impact of the used starter culture. Specific metabolites detected from P. roqueforti like andrastin A and B or roquefortine C could not be detected in white cheese. Among the blue cheese samples, different metabolite pattern could be observed regarding various P. roqueforti starter cultures.

French and Mediterranean-style diets: Contradictions, misconceptions and scientific facts-A review

The determination of appropriate dietary strategies for the prevention of chronic degenerative diseases, cancer, diabetes, and cardiovascular diseases remains a challenging and highly relevant issue worldwide. Epidemiological dietary interventions have been studied for decades with contrasting impacts on human health. Moreover, research scientists and physicians have long debated diets encouraging alcohol intake, such as the Mediterranean and French-style diets, with regard to their impact on human health. Understanding the effects of these diets may help to improve in the treatment and prevention of diseases. However, further studies are warranted to determine which individual food components, or combinations thereof, have a beneficial impact on different diseases, since a large number of different compounds may occur in a single food, and their fate in vivo is difficult to measure. Most explanations for the positive effects of Mediterranean-style diet, and of the French paradox, have focused largely on the beneficial properties of antioxidants, among other compounds/metabolites, in foods and red wine. Wine is a traditional alcoholic beverage that has been associated with both healthy and harmful effects. Not withstanding some doubts, there is reasonable unanimity among researchers as to the beneficial effects of moderate wine consumption on cardiovascular disease, diabetes, osteoporosis, and longevity, which have been ascribed to polyphenolic compounds present in wine. Despite this, conflicting findings regarding the impact of alcohol consumption on human health, and contradictory findings concerning the effects of non-alcoholic wine components such as resveratrol, have led to confusion among consumers. In addition to these contradictions and misconceptions, there is a paucity of human research studies confirming known positive effects of polyphenols in vivo. Furthermore, studies balancing both known and unknown prognostic factors have mostly been conducted in vitro or using animal models. Moreover, current studies have shifted focus from red wine to dairy products, such as cheese, to explain the French paradox. The aim of this review is to highlight the contradictions, misconceptions, and scientific facts about wines and diets, giving special focus to the Mediterranean and French diets in disease prevention and human health improvement. To answer the multiplicity of questions regarding the effects of diet and specific diet components on health, and to relieve consumer uncertainty and promote health, comprehensive cross-demographic studies using the latest technologies, which include foodomics and integrated omics approaches, are warranted.

PR Toxin - Biosynthesis, Genetic Regulation, Toxicological Potential, Prevention and Control Measures: Overview and Challenges

Out of the various mycotoxigenic food and feed contaminant, the fungal species belonging to Penicillium genera, particularly Penicillium roqueforti is of great economic importance, and well known for its crucial role in the manufacturing of Roquefort and Gorgonzola cheese. The mycotoxicosis effect of this mold is due to secretion of several metabolites, of which PR toxin is of considerable importance, with regard to food quality and safety challenges issues. The food products and silages enriched with PR toxin could lead into damage to vital internal organs, gastrointestinal perturbations, carcinogenicity, immunotoxicity, necrosis, and enzyme inhibition. Moreover, it also has the significant mutagenic potential to disrupt/alter the crucial processes like DNA replication, transcription, and translation at the molecular level. The high genetic diversities in between the various strains of P. roqueforti persuaded their nominations with Protected Geographical Indication (PGI), accordingly to the cheese type, they have been employed. Recently, the biosynthetic mechanism and toxicogenetic studies unraveled the role of ari1 and prx gene clusters that cross-talk with the synthesis of other metabolites or involve other cross-regulatory pathways to negatively regulate/inhibit the other biosynthetic route targeted for production of a strain-specific metabolites. Interestingly, the chemical conversion that imparts toxic properties to PR toxin is the substitution/oxidation of functional hydroxyl group (-OH) to aldehyde group (-CHO). The rapid conversion of PR toxin to the other derivatives such as PR imine, PR amide, and PR acid, based on conditions available reflects their unstability and degradative aspects. Since the PR toxin-induced toxicity could not be eliminated safely, the assessment of dose-response and other pharmacological aspects for its safe consumption is indispensable. The present review describes the natural occurrences, diversity, biosynthesis, genetics, toxicological aspects, control and prevention strategies, and other management aspects of PR toxin with paying special attention on economic impacts with intended legislations for avoiding PR toxin contamination with respect to food security and other biosafety purposes.

Role of sfk1 Gene in the Filamentous Fungus Penicillium roqueforti

The sfk1 (suppressor of four kinase) gene has been mainly studied in Saccharomyces cerevisiae, where it was shown to be involved in growth and thermal stress resistance. This gene is widely conserved within the phylum Ascomycota. Despite this, to date sfk1 has not been studied in any filamentous fungus. Previously, we found that the orthologous of sfk1 was differentially expressed in a strain of Penicillium roqueforti with an altered phenotype. In this work, we have performed a functional characterization of this gene by using RNAi-silencing technology. The silencing of sfk1 in P. roqueforti resulted in decreased apical growth and the promotion of conidial germination, but interesting, it had no effect on conidiation. In addition, the attenuation of the sfk1 expression sensitized the fungus to osmotic stress, but not to thermal stress. RNA-mediated gene-silencing of sfk1 also affected cell wall integrity in the fungus. Finally, the silencing of sfk1 depleted the production of the main secondary metabolites of P. roqueforti, namely roquefortine C, andrastin A, and mycophenolic acid. To the best of our knowledge this is the first study of the sfk1 gene in filamentous fungi.

Methods for genetic transformation of filamentous fungi

Filamentous fungi have been of great interest because of their excellent ability as cell factories to manufacture useful products for human beings. The development of genetic transformation techniques is a precondition that enables scientists to target and modify genes efficiently and may reveal the function of target genes. The method to deliver foreign nucleic acid into cells is the sticking point for fungal genome modification. Up to date, there are some general methods of genetic transformation for fungi, including protoplast-mediated transformation, Agrobacterium-mediated transformation, electroporation, biolistic method and shock-wave-mediated transformation. This article reviews basic protocols and principles of these transformation methods, as well as their advantages and disadvantages.

Microflora of processed cheese and the factors affecting it

The basic raw materials for the production of processed cheese are natural cheese which is treated by heat with the addition of emulsifying salts. From a point of view of the melting temperatures used (and the pH-value of the product), the course of processed cheese production can be considered "pasteurisation of cheese." During the melting process, the majority of vegetative forms of microorganisms, including bacteria of the family Enterobacteriaceae, are inactivated. The melting temperatures are not sufficient to kill the endospores, which survive the process but are often weakened. From a microbiological point of view, the biggest contamination problem of processed cheese is caused by gram-positive spore-forming rod-shaped bacteria of the genera Bacillus, Geobacillus, and Clostridium. Other factors affecting the shelf-life and quality of processed cheese are mainly the microbiological quality of the raw materials used, strict hygienic conditions during the manufacturing process as well as the type of packaging materials and storage conditions. The quality of processed cheese is not only dependent on the ingredients used but also on other parameters such as the value of water activity of the processed cheese, its pH-value, the presence of salts and emulsifying salts and the amount of fat in the product.

Experimental mould growth and mycotoxin diffusion in different food items

Isolates of Penicillium commune, Penicillium crustosum, Penicillium expansum, Penicillium roqueforti and Aspergillus versicolor, were inoculated on different food items (hard cheese, crème fraiche, tomato purée, apple and blueberry jam) and incubated at 15 °C for 14 days at 50% relative humidity (RH). After incubation the food samples were divided into 3 subsamples; A was 0-2 cm from the surface and including the fungal colony, subsample B was 2-4 cm and subsample C was the rest from >4 cm from the surface. The subsamples were analysed with a multianalyte method capable of identifying more than several hundreds of fungal metabolites. The outcome showed that mouldy food can contain a cocktail of bioactive secondary metabolites including mycotoxins and sometimes at high concentrations. Measurements of the diffusion of fungal metabolites from the colony on the surface (layer A) into the food (layer B and C) showed that the fungal metabolites do not diffuse more than 2 cm into the inner core of the hard cheese. On the other hand in more liquid foods, such as crème fraiche, fruit jams and tomato purée, the toxins diffused quite readily throughout the entire food sample. The levels of patulin found in the apple jam indicate that the tolerable daily intake for patulin may easily be exceeded even if the mouldy layer A is removed. This limited study calls for more similar studies to be performed to give risk managers a sound basis for advice to consumers.

The Biosynthetic Gene Cluster for Andrastin A in Penicillium roqueforti

Penicillium roqueforti is a filamentous fungus involved in the ripening of several kinds of blue cheeses. In addition, this fungus produces several secondary metabolites, including the meroterpenoid compound andrastin A, a promising antitumoral compound. However, to date the genomic cluster responsible for the biosynthesis of this compound in P. roqueforti has not been described. In this work, we have sequenced and annotated a genomic region of approximately 29.4 kbp (named the adr gene cluster) that is involved in the biosynthesis of andrastin A in P. roqueforti. This region contains ten genes, named adrA, adrC, adrD, adrE, adrF, adrG, adrH, adrI, adrJ and adrK. Interestingly, the adrB gene previously found in the adr cluster from P. chrysogenum, was found as a residual pseudogene in the adr cluster from P. roqueforti. RNA-mediated gene silencing of each of the ten genes resulted in significant reductions in andrastin A production, confirming that all of them are involved in the biosynthesis of this compound. Of particular interest was the adrC gene, encoding for a major facilitator superfamily transporter. According to our results, this gene is required for the production of andrastin A but does not have any role in its secretion to the extracellular medium. The identification of the adr cluster in P. roqueforti will be important to understand the molecular basis of the production of andrastin A, and for the obtainment of strains of P. roqueforti overproducing andrastin A that might be of interest for the cheese industry.

Modeling Growth and Toxin Production of Toxigenic Fungi Signaled in Cheese under Different Temperature and Water Activity Regimes

The aim of this study was to investigate in vitro and model the effect of temperature (T) and water activity (aw) conditions on growth and toxin production by some toxigenic fungi signaled in cheese. Aspergillus versicolor, Penicillium camemberti, P. citrinum, P. crustosum, P. nalgiovense, P. nordicum, P. roqueforti, P. verrucosum were considered they were grown under different T (0-40 °C) and aw (0.78-0.99) regimes. The highest relative growth occurred around 25 °C; all the fungi were very susceptible to aw and 0.99 was optimal for almost all species (except for A. versicolor, awopt = 0.96). The highest toxin production occurred between 15 and 25 °C and 0.96-0.99 aw. Therefore, during grana cheese ripening, managed between 15 and 22 °C, ochratoxin A (OTA), penitrem A (PA), roquefortine-C (ROQ-C) and mycophenolic acid (MPA) are apparently at the highest production risk. Bete and logistic function described fungal growth under different T and aw regimes well, respectively. Bete function described also STC, PA, ROQ-C and OTA production as well as function of T. These models would be very useful as starting point to develop a mechanistic model to predict fungal growth and toxin production during cheese ripening and to help advising the most proper setting of environmental factors to minimize the contamination risk.

Biosynthetic gene clusters for relevant secondary metabolites produced by Penicillium roqueforti in blue cheeses

Ripening of blue-veined cheeses, such as the French Bleu and Roquefort, the Italian Gorgonzola, the English Stilton, the Danish Danablu or the Spanish Cabrales, Picón Bejes-Tresviso, and Valdeón, requires the growth and enzymatic activity of the mold Penicillium roqueforti, which is responsible for the characteristic texture, blue-green spots, and aroma of these types of cheeses. This filamentous fungus is able to synthesize different secondary metabolites, including andrastins, mycophenolic acid, and several mycotoxins, such as roquefortines C and D, PR-toxin and eremofortins, isofumigaclavines A and B, and festuclavine. This review provides a detailed description of the main secondary metabolites produced by P. roqueforti in blue cheese, giving a special emphasis to roquefortine, PR-toxin and mycophenolic acid, and their biosynthetic gene clusters and pathways. The knowledge of these clusters and secondary metabolism pathways, together with the ability of P. roqueforti to produce beneficial secondary metabolites, is of interest for commercial purposes.

Protease and lipase activities of fungal and bacterial strains derived from an artisanal raw ewe's milk cheese

We previously identified the microbiota present during cheese ripening and observed high protease and lipase activity in Divle Cave cheese. To determine the contribution of individual isolates to enzyme activities, we investigated a range of species representing this microbiota for their proteolytic and lipolytic ability. In total, 17 fungal, 5 yeast and 18 bacterial strains, previously isolated from Divle Cave cheese, were assessed. Qualitative protease and lipase activities were performed on skim-milk agar and spirit-blue lipase agar, respectively, and resulted in a selection of strains for quantitative assays. For the quantitative assays, the strains were grown on minimal medium containing irradiated Divle Cave cheese, obtained from the first day of ripening. Out of 16 selected filamentous fungi, Penicillium brevicompactum, Penicillium cavernicola and Penicillium olsonii showed the highest protease activity, while Mucor racemosus was the best lipase producer. Yarrowia lipolytica was the best performing yeast with respect to protease and lipase activity. From the 18 bacterial strains, 14 and 11 strains, respectively showed protease and lipase activity in agar plates. Micrococcus luteus, Bacillus stratosphericus, Brevibacterium antiquum, Psychrobacter glacincola and Pseudomonas proteolytica displayed the highest protease and lipase activity. The proteases of yeast and filamentous fungi were identified as mainly aspartic protease by specific inhibition with Pepstatin A, whereas inhibition by PMSF (phenylmethylsulfonyl fluoride) indicated that most bacterial enzymes belong to serine type protease. Our results demonstrate that aspartic proteases, which usually have high milk clotting activity, are predominantly derived from fungal strains, and therefore fungal enzymes appear to be more suitable for use in the cheese industry. Microbial enzymes studied in this research might be alternatives for rennin (chymosin) from animal source because of their low cost and stable availability. Future studies will aim to purify these enzymes to test their suitability for use in similar artisanal cheeses or in large scale commercial cheeses.

Metabolomic and Transcriptomic Comparison of Solid-State and Submerged Fermentation of Penicillium expansum KACC 40815

Penicillium spp. are known to harbor a wide array of secondary metabolites with cryptic bioactivities. However, the metabolomics of these species is not well-understood in terms of different fermentation models and conditions. The present study involved metabolomics profiling and transcriptomic analysis of Penicillium expansum 40815 under solid-state fermentation (SSF) and submerged fermentation (SmF). Metabolite profiling was carried out using ultra-performance liquid chromatography quadruple time-of-flight mass spectrometry with multivariate analysis, followed by transcriptomic analyses of differentially expressed genes. In principal component analysis, the metabolite profiling data was studied under different experimental sets, including SSF and SmF. The significantly different metabolites such as polyketide metabolites (agonodepside B, rotiorin, verrucosidin, and ochrephilone) and corresponding gene transcripts (polyketide synthase, aromatic prenyltransferase, and terpenoid synthase) were primarily detected under SmF conditions. In contrast, the meroterpenoid compounds (andrastin A and C) and their genes transcripts were exclusively detected under SSF conditions. We demonstrated that the metabolite production and its corresponding gene expression levels in P. expansum 40815 were significantly influenced by the varying growth parameters and the immediate environment. This study further provides a foundation to produce specific metabolites by regulating fermentation conditions.

Evolutionary formation of gene clusters by reorganization: the meleagrin/roquefortine paradigm in different fungi

The biosynthesis of secondary metabolites in fungi is catalyzed by enzymes encoded by genes linked in clusters that are frequently co-regulated at the transcriptional level. Formation of gene clusters may take place by de novo assembly of genes recruited from other cellular functions, but also novel gene clusters are formed by reorganization of progenitor clusters and are distributed by horizontal gene transfer. This article reviews (i) the published information on the roquefortine/meleagrin/neoxaline gene clusters of Penicillium chrysogenum (Penicillium rubens) and the short roquefortine cluster of Penicillium roqueforti, and (ii) the correlation of the genes present in those clusters with the enzymes and metabolites derived from these pathways. The P. chrysogenum roq/mel cluster consists of seven genes and includes a gene (roqT) encoding a 12-TMS transporter protein of the MFS family. Interestingly, the orthologous P. roquefortine gene cluster has only four genes and the roqT gene is present as a residual pseudogene that encodes only small peptides. Two of the genes present in the central region of the P. chrysogenum roq/mel cluster have been lost during the evolutionary formation of the short cluster and the order of the structural genes in the cluster has been rearranged. The two lost genes encode a N1 atom hydroxylase (nox) and a roquefortine scaffold-reorganizing oxygenase (sro). As a consequence P. roqueforti has lost the ability to convert the roquefortine-type carbon skeleton to the glandicoline/meleagrin-type scaffold and is unable to produce glandicoline B, meleagrin and neoxaline. The loss of this genetic information is not recent and occurred probably millions of years ago when a progenitor Penicillium strain got adapted to life in a few rich habitats such as cheese, fermented cereal grains or silage. P. roqueforti may be considered as a "domesticated" variant of a progenitor common to contemporary P. chrysogenum and related Penicillia.

Towards an Ecosystem Approach to Cheese Microbiology

Cheese is an ideal environment to serve as a model for the behavior of microbes in complex communities and at the same time allow detailed genetic analysis. Linking organisms, and their genes, to their role in the environment becomes possible in the case of cheese since cheese microbial communities have been "in culture" for thousands of years, with the knowledge of how to grow these organisms passed down by generations of cheesemakers. Recent reviews have described several emerging approaches to link molecular systems biology to ecosystem-scale processes, known as ecosystems biology. These approaches integrate massive datasets now available through high-throughput sequencing technologies with measurements of ecosystem properties. High-throughput datasets uncover the "parts list" (e.g., the species and all the genes within each species) of an ecosystem as well as the molecular basis of interactions within this parts list. Novel computational frameworks make it possible to link species and their interactions to ecosystem properties. Applying these approaches across multiple temporal and spatial scales makes it possible to understand how changes in the parts lists over space and time lead to changes in ecosystems processes. By manipulating the species present within model systems, we can test hypotheses related to the role of microbes in ecosystem function. Due to the tractability of cheese microbial communities, we have the opportunity to use an ecosystems biology approach from the scale of individual microbial cells within a cheese to replicated cheese microbial communities across continents. Using cheese as a model microbial ecosystem can provide a way to answer important questions concerning the form, function, and evolution of microbial communities.

A natural short pathway synthesizes roquefortine C but not meleagrin in three different Penicillium roqueforti strains

The production of mycotoxins and other secondary metabolites in Penicillium roqueforti is of great interest because of its long history of use in blue-veined cheese manufacture. In this article, we report the cloning and characterization of the roquefortine gene cluster in three different P. roqueforti strains isolated from blue cheese in the USA (the type strain), France, and the UK (Cheshire cheese). All three strains showed an identical roquefortine gene cluster organization and almost identical (98-99%) gene nucleotide sequences in the entire 16.6-kb cluster region. When compared with the Penicillium chrysogenum roquefortine/meleagrin seven-gene cluster, the P. roqueforti roquefortine cluster contains only four genes (rds, rdh, rpt, and gmt) encoding the roquefortine dipeptide synthetase, roquefortine D dehydrogenase, roquefortine prenyltransferase, and a methyltransferase, respectively. Silencing of the rds or rpt genes by the RNAi strategy reduced roquefortine C production by 50% confirming the involvement of these two key genes in roquefortine biosynthesis. An additional putative gene, orthologous of the MFS transporter roqT, is rearranged in all three strains as a pseudogene. The same four genes and a complete (not rearranged) roqT, encoding a MFS transporter containing 12 TMS domains, occur in the seven-gene cluster in P. chrysogenum although organized differently. Interestingly, the two "late" genes of the P. chrysogenum roquefortine/meleagrin gene cluster that convert roquefortine C to glandicoline B and meleagrin are absent in the P. roqueforti four-gene cluster. No meleagrin production was detected in P. roqueforti cultures grown in YES medium, while P. chrysogenum produces meleagrin in these conditions. No orthologous genes of the two missing meleagrin synthesizing genes were found elsewhere in the recently released P. roqueforti genome. Our data suggest that during evolution, the seven-gene cluster present in P. chrysogenum, and probably also in other glandicoline/meleagrin producing fungi, has been trimmed down to a short cluster in P. roqueforti leading to the synthesis of roquefortine C rather than meleagrin as a final product.

Molecular characterization of the PR-toxin gene cluster in Penicillium roqueforti and Penicillium chrysogenum: cross talk of secondary metabolite pathways

The PR-toxin is a potent mycotoxin produced by Penicillium roqueforti in moulded grains and grass silages and may contaminate blue-veined cheese. The PR-toxin derives from the 15 carbon atoms sesquiterpene aristolochene formed by the aristolochene synthase (encoded by ari1). We have cloned and sequenced a four gene cluster that includes the ari1 gene from P. roqueforti. Gene silencing of each of the four genes (named prx1 to prx4) resulted in a reduction of 65-75% in the production of PR-toxin indicating that the four genes encode enzymes involved in PR-toxin biosynthesis. Interestingly the four silenced mutants overproduce large amounts of mycophenolic acid, an antitumor compound formed by an unrelated pathway suggesting a cross-talk of PR-toxin and mycophenolic acid production. An eleven gene cluster that includes the above mentioned four prx genes and a 14-TMS drug/H(+) antiporter was found in the genome of Penicillium chrysogenum. This eleven gene cluster has been reported to be very poorly expressed in a transcriptomic study of P. chrysogenum genes under conditions of penicillin production (strongly aerated cultures). We found that this apparently silent gene cluster is able to produce PR-toxin in P. chrysogenum under static culture conditions on hydrated rice medium. Noteworthily, the production of PR-toxin was 2.6-fold higher in P. chrysogenum npe10, a strain deleted in the 56.8kb amplifiable region containing the pen gene cluster, than in the parental strain Wisconsin 54-1255 providing another example of cross-talk between secondary metabolite pathways in this fungus. A detailed PR-toxin biosynthesis pathway is proposed based on all available evidence.

Morphological, molecular, and mycotoxigenic identification of dominant filamentous fungi from moldy civil cheese

Moldy Civil is a mold-ripened variety of cheese produced mainly in eastern Turkey. This cheese is produced with Civil cheese and whey curd cheese (Lor). Civil cheese has had a geographical presence since 2009 and is manufactured with skim milk. In the production of Moldy Civil cheese, Civil cheese or a mixture of Civil and Lor cheese is pressed into goat skins or plastic bags and ripened for 3 months or longer. During the ripening period, natural contaminating molds grow on the surface of and inside the cheese. In this study, 186 mold strains were isolated from 41 samples of Moldy Civil cheese, and 165 of these strains were identified as Penicillium roqueforti. Identification and mycotoxicologic analyses were conducted using morphotypic and molecular methods. PCR amplicons of the ITS1-5.8S-ITS4 region were subjected to sequence analysis. This research is the first using molecular methods on Moldy Civil cheese. Mycotoxicologic analyses were conducted using thin-layer chromatography, and random amplified polymorphic DNA genotypes were determined using the ari1 primer. Of 165 isolates, only 28 produced no penicillic acid, P. roqueforti toxin, or roquefortine.

Atlantinone A, a Meroterpenoid Produced by Penicillium ribeum and Several Cheese Associated Penicillium Species

Atlantinone A has been isolated from the psychrotolerant fungus Penicillium ribeum. The exact structure of the compound was confirmed by mass spectrometric and 1- and 2D NMR experiments. Atlantinone A was originally only produced upon chemical epigenetic manipulation of P. hirayamae, however in this study the compound was found to be produced at standard growth conditions by the following species; P. solitum, P. discolor, P. commune, P. caseifulvum, P. palitans, P. novae-zeelandiae and P. monticola. A biosynthetic pathway to atlantinone A starting from andrastin A is proposed.

Food fermentations: microorganisms with technological beneficial use

Microbial food cultures have directly or indirectly come under various regulatory frameworks in the course of the last decades. Several of those regulatory frameworks put emphasis on "the history of use", "traditional food", or "general recognition of safety". Authoritative lists of microorganisms with a documented use in food have therefore come into high demand. One such list was published in 2002 as a result of a joint project between the International Dairy Federation (IDF) and the European Food and Feed Cultures Association (EFFCA). The "2002 IDF inventory" has become a de facto reference for food cultures in practical use. However, as the focus mainly was on commercially available dairy cultures, there was an unmet need for a list with a wider scope. We present an updated inventory of microorganisms used in food fermentations covering a wide range of food matrices (dairy, meat, fish, vegetables, legumes, cereals, beverages, and vinegar). We have also reviewed and updated the taxonomy of the microorganisms used in food fermentations in order to bring the taxonomy in agreement with the current standing in nomenclature.