Molecular biodiversity of mycotoxigenic fungi that threaten food safety

Exploring Hidden Dangers: Predicting Mycotoxin-like Toxicity and Mapping Toxicological Networks in Hepatocellular Carcinoma

Mycotoxins are potent triggers of hepatocellular carcinoma (HCC) due to their intricate interplay with cellular macromolecules and signaling pathways. This study integrates machine learning and biomolecular analyses to elucidate the mechanisms underlying mycotoxin-induced hepatocarcinogenesis. Using a data set of 1767 mycotoxins and 1706 non-mycotoxin fungal metabolites, we evaluated 51 machine learning models. The KPGT model achieved optimal performance with an ROC-AUC of 0.979 and balanced accuracy of 0.930. Clustering analysis identified six distinct mycotoxin clusters with unique structural features. Network toxicology analysis revealed distinct protein-protein interaction patterns across different mycotoxin clusters, identifying key regulatory proteins including EGFR, SRC, and ESR1. GO enrichment analysis uncovered cluster-specific effects on protein complexes and macromolecular assemblies, particularly in membrane organization and vesicular transport. KEGG pathway analysis demonstrated systematic perturbation of major signaling cascades, with each mycotoxin cluster distinctly modulating protein kinase networks and receptor tyrosine kinase pathways. Molecular docking analyses validated these interactions, with binding affinities ranging from -9.6 to -4.7 kcal/mol. Notably, cluster 5 showed strong binding to SRC (-9.6 kcal/mol), EGFR (-9.5 kcal/mol), and ESR1 (-7.8 kcal/mol), providing structural insights into toxin-macromolecule recognition. These findings enhance our understanding of mycotoxin-protein interactions in HCC development and suggest potential therapeutic strategies targeting these macromolecular interfaces.

Three new species of Fusarium (Nectriaceae, Hypocreales) isolated from Eastern Cape dairy pastures in South Africa

A survey of the fungal diversity associated with mixed pastures from Eastern Cape dairy farms in South Africa led to the isolation of 155 Fusarium strains that belong to the Fusariumincarnatum-equiseti species complex (FIESC). Using single and multigene phylogenies based on partial sequences of the translation elongation factor 1-alpha (TEF), calmodulin (CaM), and the partial RNA polymerase second largest subunit (RPB2) genes, we identified 11 species. They included F.brevicaudatum, F.clavus, F.coffeatum, F.croceum, F.goeppertmayerae, and F.heslopiae, with five species that were found to be new. Based on morphological and phylogenetic data, three new species are formally described here as F.cumulatum, F.mariecurieae, and F.pascuum. We also provided a description for F.goeppertmayerae, as the authors who identified and named this species did not include one. We have chosen to not describe the remaining species, as our cultures lack proper morphological structure development. This study shows that mixed pastures harbour a diverse range of Fusarium species and highlights the need for further studies into their potential to impact animal health.

Dietary Mycotoxins: An Overview on Toxicokinetics, Toxicodynamics, Toxicity, Epidemiology, Detection, and Their Mitigation with Special Emphasis on Aflatoxicosis in Humans and Animals

Mycotoxins are secondary metabolites of filamentous fungi and ubiquitous dietary contaminants. Aflatoxins, a group of mycotoxins with high prevalence and toxicity, have raised a high level of public health concern, the most prevalent and toxic being aflatoxin B1 (AFB1). Many aspects appertaining to AFB1 poisoning are not well understood. Yet this information is necessary to devise appropriate surveillance and mitigation strategies against human and animal aflatoxicosis. This review provides an in-depth update of work carried out on mycotoxin poisoning, particularly aflatoxicosis in humans and animals, to identify gaps in knowledge. Hypotheses explaining the functional significance of mycotoxins in fungal biology and their dietary epidemiological data are presented and briefly discussed. The toxicology of aflatoxins and the challenges of their mitigation are discussed in depth. It was concluded that the identification of potential mycotoxin-hazard-prone food items and quantification of the associated risk of cancer ailments in humans is a prime priority. There is a dearth of reliable sampling methodologies for estimating AFB1 in animal feed. Data update on AFB1 in animal feed and its implication in animal production, mitigation strategies, and elucidation of risk factors to this hazard is required. To reduce the burden of aflatoxins, surveillance employing predictive technology, and biocontrol strategies seem promising approaches.

The sweating process promotes toxigenic fungi expansion and increases the risk of combined contamination of mycotoxins in Radix Dipsaci

Sweating is one of the most important processing methods of Chinese medicinal herbs. However, the high temperature and humidity environment required for sweating Chinese medicinal herbs makes it very easy for fungi to breed, especially toxigenic fungi. The mycotoxins produced by these fungi will then contaminate the Chinese medicinal herbs. In this study, we explored the changes in mycobiota, toxigenic fungi, and mycotoxins with and without sweating in Radix Dipsaci (RD), a typical representative of traditional Chinese medicine that requires processing through sweating. We also isolated and identified the toxigenic fungi from RD, whether they were subjected to sweating treatment or not, and examined their toxigenic genes and ability. The results showed that the detection rate of mycotoxins (aflatoxins, ochratoxins, zearalenone, and T-2 toxin) in RD with sweating was 36%, which was 2.25-fold higher than that in RD without sweating. We also detected T-2 toxin in the RD with sweating, whereas it was not found in the RD without sweating. The sweating process altered the fungal composition and increased the abundance of Fusarium and Aspergillus in RD. Aspergillus and Fusarium were the most frequently contaminating fungi in the RD. Morphological and molecular identification confirmed the presence of key toxigenic fungal strains in RD samples, including A. flavus, A. westerdijkiae, F. oxysporum and F. graminearum. These four fungi, respectively, carried AflR, PKS, Tri7, and PKS14, which were key genes for the biosynthesis of aflatoxins, ochratoxins, zearalenone, and T-2 toxin. The toxigenic ability of these four fungal strains was verified in different matrices. We also found that A. flavus, A. westerdijkiae, and F. oxysporum were isolated in RD both with sweating and without sweating, but their isolation frequency was significantly higher in the RD with sweating than in the RD without sweating. F. graminearum was not isolated from RD without sweating, but it was isolated from RD with sweating. These findings suggest that the sweating process promotes the expansion of toxigenic fungi and increases the risk of combined mycotoxin contamination in RD.

Recent Advances of Food Hazard Detection Based on Artificial Nanochannel Sensors

Food quality and safety are related to the health and safety of people, and food hazards are important influencing factors affecting food safety. It is strongly necessary to develop food safety rapid detection technology to ensure food safety. As a new detection technology, artificial nanochannel-based electrochemical and other methods have the advantages of being real-time, simple, and sensitive and are widely used in the detection of food hazards. In this paper, we review artificial nanochannel sensors as a new detection technology in food safety for different types of food hazards: biological hazards (bacteria, toxins, viruses) and chemical hazards (heavy metals, organic pollutants, food additives). At the same time, we critically discuss the advantages and disadvantages of artificial nanochannel sensor detection, as well as the restrictions and solutions of detection, and finally look forward to the challenges and development prospects of food safety detection technology based on the limitations of artificial nanochannel detection. We expect to provide a theoretical basis and inspiration for the development of rapid real-time detection technology for food hazards and the production of portable detection equipment in the future.

The biodiversity of Aspergillus flavus in stored rice grain leads to a decrease in the overall aflatoxin B1 production in these species

Aspergillus flavus is a significant fungus that poses a threat to food safety by producing mycotoxins in various crops. In this study, A. flavus isolates were obtained from storage rice collected from seven provinces in southern China, and their AFB1 production, biosynthesis genes presence, and diversity were detected. Results showed that 56 out of the 81 A. flavus isolates produced detectable levels of AFB1, and 71 isolates (87.6 %) possessed aflR gene in their AF synthesis gene cluster, while only 41 isolates (50.6 %) had the ver-1 gene present. Genetic diversity analysis using inter-simple sequence repeats (ISSR) markers revealed seven main clusters among the isolates and the genetic similarity coefficients of 81 A. flavus isolates ranged from 0.53 to 1.00. Additionally, coculture assays were conducted using two toxigenic and two atoxigenic isolates from the same grain depot to investigate the effect of intraspecific inhibition on AFB1 production and to assess the AFB1 contamination risk of storage rice. The in situ results demonstrated that the atoxigenic isolates effectively inhibited the AFB1 contamination of toxigenic isolates. These findings provide insight into the genetic diversity of A. flavus isolates populations and highlight the potential food safety hazards of them in stored rice grain in China.

Toward Machine Learning-Driven Mass Spectrometric Identification of Trichothecenes in the Absence of Standard Reference Materials

While a significant body of work exists on the detection of commonly known trichothecene toxins, biological, environmental, and other transformational processes can generate many under-characterized and unknown modified trichothecenes. Lacking both analytical reference standards and associated mass spectral databases, identification of these modified compounds reflects both a challenge and a critical gap from forensic and public health perspectives. We report here the application of machine learning (ML) techniques toward identification of discriminative fragment ions from mass spectrometric data that can be exploited to detect evidence of type A and B trichothecenes. The goal of this work is to establish a new method for the identification of unknown, though structurally similar trichothecenes, by leveraging objective ML techniques. Discriminative fragments derived from a series of gradient-boosted machine learners are then used to develop ML-driven precursor ion scan (PIS) methods on a triple quadrupole mass spectrometer (QQQ) for screening of "unknown unknown" trichothecenes. Specifically, we apply the PIS method to a laboratory-synthesized trichothecene, a first step in demonstrating the power of alternative, machine learning-driven mass spectrometric methods.

Co-occurrence of mycotoxins: A review on bioanalytical methods for simultaneous analysis in human biological samples, mixture toxicity and risk assessment strategies

Mycotoxins are the toxic chemical substances that are produced by various fungal species and some of these are harmful to humans. Mycotoxins are ubiquitous in nature and humans could be exposed to multiple mycotoxins simultaneously. Unfortunately, exposure to mixed mycotoxins is not very well studied. Various studies have demonstrated the capacity of mycotoxins to show synergistic effect in the presence of other mycotoxins, thus, increasing the risk of toxicity. Hence, it is important to monitor mixed mycotoxins in human biological samples which would serve as a crucial information for risk assessment. Through this review paper, we aim to summarize the mixture toxicity of mycotoxins and the various bio-analytical techniques that are being used for the simultaneous analysis of mixed mycotoxins in human biological samples. Different sample preparation and clean-up techniques employed till date for eliminating the interferences from human biological samples without affecting the analyses of the mycotoxins are also discussed. Further, a brief introduction of risk assessment strategies that have been or could be adopted for multiple mycotoxin risk assessments is also mentioned. To the best of our knowledge, this is the first review that focuses solely on the occurrence of multiple mycotoxins in human biological samples as well as their risk assessment strategies.

Efficient multiplex CRISPR/Cpf1 (Cas12a) genome editing system in Aspergillus aculeatus TBRC 277

CRISPR/Cas technology is a versatile tool for genome engineering in many organisms, including filamentous fungi. Cpf1 is a multi-domain protein of class 2 (type V) RNA-guided CRISPR/Cas endonuclease, and is an alternative platform with distinct features when compared to Cas9. However, application of this technology in filamentous fungi is limited. Here, we present a single CRISPR/Cpf1 plasmid system in Aspergillus aculeatus strain TBRC 277, an industrially relevant cell factory. We first evaluated the functionality of three Cpf1 orthologs from Acidaminococcus sp. BV3L6 (AsCpf1), Francisella tularensis subsp. novicida U112 (FnCpf1), and Lachnospiraceae bacterium (LbCpf1), in RNA-guided site-specific DNA cleavage at the pksP locus. FnCpf1 showed the highest editing efficiency (93%) among the three Cpf1s. It was further investigated for its ability to delete a 1.7kb and a 0.5kb from pksP and pyrG genes, respectively, using two protospacers targeting these gene loci in a single crRNA array. Lastly, simultaneous editing of three sites within TBRC 277 genome was performed using three guide sequences targeting these two genes as well as an additional gene, kusA, which resulted in combined editing efficiency of 40%. The editing of the NHEJ pathway by targeting kusA to generate a NHEJ-deficient strain of A. aculeatus TBRC 277 improved gene targeting efficiency and yielded more precise gene-editing than that of using wild-type strain. This promising genome-editing system can be used for strain improvement in industrial applications such as production of valuable bioproducts.

Aflatoxin M1 in Brazilian goat milk and health risk assessment

Contamination of goat milk with aflatoxin M₁ (AFM₁) is a public health concern. This study investigated filamentous fungi in goat feed and quantified AFM₁ in milk samples (n = 108) from goat fed forage and concentrate. Based on the detected AFM₁ concentration, risk assessment analyses were performed concerning the Estimated Daily Intake (EDI) for one-year-old children and adults. Filamentous fungi were found in goat feed samples in a range of 3.1 ± 1.9 to 4.2 ± 0.2 log CFU/g. Five genera were identified, to cite Aspergillus, Penicillium, Fusarium, Rhizopus and Acremonium. Aspergillus species comprised A. flavus, A. niger, and A. ochraceus. All goat milk samples were contaminated with AFM₁ (5.60-48.20 ng/L; mean 21.90 ± 10.28 ng/L) in amounts below the limits imposed by regulatory agencies. However, EDI values for AFM₁ through goat milk estimated for one-year-old children were above the Tolerable Daily Intake. The calculated Hazard Index for one-year-old children indicated potential risk of liver cancer due to goat milk consumption. The Margin of Exposure values to AFM₁ in one-year-old children and adults consuming goat milk as the unique milk source indicated increased health risk. Therefore, contamination of goat milk with AFM₁ should be considered a high priority for Brazil's risk management actions.

Occurrence and diversity of waterborne fungi and associated mycotoxins in treated drinking water distribution system in South Africa: implications on water quality and public health

Despite increased public health concerns on the occurrences of potentially pathogenic/mycotoxigenic fungi in public drinking water system, dissemination of hygienically relevant fungi and their associated mycotoxins via distribution system under the dual burden of ageing infrastructure and ancillary distribution network lacking infrastructure for high-pressure water delivery systems is unknown. In this study, the diversity of fungi and occurrence of mycotoxins at 30 different points along treated piped water supply and ancillary distribution networks in Johannesburg, South Africa, were monitored for 12 months. Mycological analysis using cultural and molecular methods yielded 282 fungi belonging to phylum Ascomycota, having Aspergillus (91%), Penicillium (65%) and Trichoderma (31%) as dominant genera, with Aspergillus fumigatus, Penicillium citrinum, Purpureocillium lilacinum and Aspergillus flavus as the most prevalent species. Communal standpipe and reservoir outlets had significantly higher prevalence than other water samples. There was no strong correlation between total coliforms (r = 0.4266) and residual chlorine (r = - 0.1937), and fungal prevalence at p < 0.05. LC-MS/MS analysis detected aflatoxins B1, M1, G1 and G2 in 50, 9, 9 and 46% of water samples analysed, respectively, ranging between 0 and 3.18 ng/l. Deoxynivalenol (DON), 3-acetyl DON and 15-acetyl DON levels were between 8.4-96.1, 18.7-145.7 and 15.2-71.6 ng/l, respectively. However, the estimated average daily dose (ADD) for detected mycotoxins was below the tolerable daily intake (TDI), suggesting no toxicological risk. Presence of potentially mycotoxigenic fungi, despite the low toxicological risk, demonstrates a need for appropriate monitoring for fungi and mycotoxins in treated drinking water distribution systems for improved water quality and long-term public health assurance.

A Polyphasic Approach to Compare the Genomic Profiles of Aflatoxigenic and Non-Aflatoxigenic Isolates of Aspergillus Section Flavi

Aflatoxins (AF) are highly toxic compounds produced by Aspergillus section Flavi. They spoil food crops and present a serious global health hazard to humans and livestock. The aim of this study was to examine the phylogenetic relationships among aflatoxigenic and non-aflatoxigenic Aspergillus isolates. A polyphasic approach combining phylogenetic, sequence, and toxin analyses was applied to 40 Aspergillus section Flavi isolates collected from eight countries around the world (USA, Philippines, Egypt, India, Australia, Indonesia, China, and Uganda). This allows one to pinpoint the key genomic features that distinguish AF producing and non-producing isolates. Based on molecular identification, 32 (80%) were identified as A. flavus, three (7.5%) as A. parasiticus, three (7.5%) as A. nomius and one (2.5%) as A. tamarii. Toxin analysis showed that 22 (55%) Aspergillus isolates were aflatoxigenic. The majority of the toxic isolates (62.5%) originated from Egypt. The highest aflatoxin production potential was observed in an A. nomius isolate which is originally isolated from the Philippines. DNA-based molecular markers such as random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) were used to evaluate the genetic diversity and phylogenetic relationships among these 40 Aspergillus isolates, which were originally selected from 80 isolates. The percentage of polymorphic bands in three RAPD and three ISSR primers was 81.9% and 79.37%, respectively. Analysis of molecular variance showed significant diversity within the populations, 92% for RAPD and 85% for ISSR primers. The average of Polymorphism Information Content (PIC), Marker Index (MI), Nei's gene diversity (H) and Shannon's diversity index (I) in ISSR markers are higher than those in RAPD markers. Based on banding patterns and gene diversities values, we observed that the ISSR-PCR provides clearer data and is more successful in genetic diversity analyses than RAPD-PCR. Dendrograms generated from UPGMA (Unweighted Pair Group Method with Arithmetic Mean) cluster analyses for RAPD and ISSR markers were related to the geographic origin.

Variation in secondary metabolite production potential in the Fusarium incarnatum-equiseti species complex revealed by comparative analysis of 13 genomes

Background

The Fusarium incarnatum-equiseti species complex (FIESC) comprises 33 phylogenetically distinct species that have been recovered from diverse biological sources, but have been most often isolated from agricultural plants and soils. Collectively, members of FIESC can produce diverse mycotoxins. However, because the species diversity of FIESC has been recognized only recently, the potential of species to cause mycotoxin contamination of crop plants is unclear. In this study, therefore, we used comparative genomics to investigate the distribution of and variation in genes and gene clusters responsible for the synthesis of mycotoxins and other secondary metabolites (SMs) in FIESC.

Results

We examined genomes of 13 members of FIESC that were selected based primarily on their phylogenetic diversity and/or occurrence on crops. The presence and absence of SM biosynthetic gene clusters varied markedly among the genomes. For example, the trichothecene mycotoxin as well as the carotenoid and fusarubin pigment clusters were present in all genomes examined, whereas the enniatin, fusarin, and zearalenone mycotoxin clusters were present in only some genomes. Some clusters exhibited discontinuous patterns of distribution in that their presence and absence was not correlated with the phylogenetic relationships of species. We also found evidence that cluster loss and horizontal gene transfer have contributed to such distribution patterns. For example, a combination of multiple phylogenetic analyses suggest that five NRPS and seven PKS genes were introduced into FIESC from other Fusarium lineages.

Conclusion

Our results suggest that although the portion of the genome devoted to SM biosynthesis has remained similar during the evolutionary diversification of FIESC, the ability to produce SMs could be affected by the different distribution of related functional and complete gene clusters.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5567-7) contains supplementary material, which is available to authorized users.

Developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for plant biomass degradation

Fungal strain engineering is commonly used in many areas of biotechnology, including the production of plant biomass degrading enzymes. Its aim varies from the production of specific enzymes to overall increased enzyme production levels and modification of the composition of the enzyme set that is produced by the fungus. Strain engineering involves a diverse range of methodologies, including classical mutagenesis, genetic engineering and genome editing. In this review, the main approaches for strain engineering of filamentous fungi in the field of plant biomass degradation will be discussed, including recent and not yet implemented methods, such as CRISPR/Cas9 genome editing and adaptive evolution.

A survey of fungal microbiota in airways of healthy volunteer subjects from Puglia (Apulia), Italy

BACKGROUND

The human respiratory tract represents the major portal of entry for numerous microorganisms, primarily those occurring as airborne particles such as viral and bacterial entities, or fungal spores. Microorganism characteristics coupled with the local host immune response will determine whether they will be cleared or adhere and colonize the airways leading to acute or chronic pulmonary disease. Like bacteria, fungi can cause severe lung diseases, but their infection rates are much lower. The lung microbiota is commonly sampled using relatively invasive bronchoscopic procedures. Exhaled breath condensate (EBC) collection offers a potentially less invasive alternative for lung microbiota sampling. This study tries to determine the composition of fungal communities in a cohort of healthy adult volunteer subjects from Puglia (Apulia), Italy.

METHODS

Fungi diversity in 27 EBC samples collected from Italian adult volunteers was investigated using conventional microbiological culturing and DNA sequencing approach.

RESULTS

Ten tested subjects (37,03%) turned out to present fungi in the EBC. We observed complex fungal communities, in which more than 10% of the isolated species are represented by Aspergillus sydowii (14,8%) and Cladosporium spp (11,11%). Three subjects that showed fungal presence in EBC have been diagnosed with a respiratory disease.

CONCLUSIONS

We present a survey of an important scientific field in its early stages that is fungal contamination of airways of healthy subjects in a small geographic area. Furthermore, we interpreted our results to highlight the potential role of fungi in the context of respiratory diseases.

Selection of Fusarium Trichothecene Toxin Genes for Molecular Detection Depends on TRI Gene Cluster Organization and Gene Function

Food security is a global concern. Fusarium are among the most economically important fungal pathogens because they are ubiquitous, disease management remains a challenge, they produce mycotoxins that affect food and feed safety, and trichothecene mycotoxin production can increase the pathogenicity of some Fusarium species depending on the host species. Although trichothecenes may differ in structure by their patterns of hydroxylation or acetylation, these small changes have a significant impact on toxicity and the biological activity of these compounds. Therefore, detecting and identifying which chemotype is present in a given population are important to predicting the specific toxins that may be produced and, therefore, to evaluating the risk of exposure. Due to the challenges of inducing trichothecene production by Fusarium isolates in vitro for subsequent chemical analysis, PCR assays using gene-specific primers, either singly or in combination, designed against specific genes of the trichothecene gene cluster of multiple species of Fusarium have been developed. The establishment of TRI genotypes that potentially correspond to a specific chemotype requires examination of an information and knowledge pipeline whose critical aspects in sequential order are: (i) understanding the TRI gene cluster organization which differs according to Fusarium species under study; (ii) knowledge of the re-arrangements to the core TRI gene cluster over evolutionary time, which also differs according to Fusarium species; (iii) the functions of the TRI genes in the biosynthesis of trichothecene analogs; and (iv) based on (i)⁻(iii), selection of appropriate target TRI gene(s) for primer design in PCR amplification for the Fusarium species under study. This review, therefore, explains this pipeline and its connection to utilizing TRI genotypes as a possible proxy to chemotype designation.

Identification of amino acids negatively affecting Fusarium trichothecene biosynthesis

Nitrogen sources in media have a significant impact on the onset of secondary metabolism in fungi. For transcriptional activation of many nitrogen catabolic genes, an AreA transcription factor is indispensable. This also holds true for Fusarium graminearum that produces trichothecenes, an important group of mycotoxin, in axenic culture. Despite the presence of numerous consensus AreA-binding sites in the promoters of Tri genes in the trichothecene cluster core region, the effect of medium amino acids on trichothecene biosynthesis is poorly understood. In this study, we examined the effect of certain amino acids, which were predicted to activate AreA function and increase Tri gene transcription, on trichothecene production in liquid culture. By frequent monitoring and adjustments in the pH of the culture medium, including replacement of the spent medium with fresh medium, we demonstrate the suppressive effects of the amino acids, used as the sole nitrogen source, on trichothecene biosynthesis. When the medium pH was maintained at 4.0, Gly, L-Ser, and L-Thr suppressed trichothecene production by F. graminearum. Enhanced trichothecene-inducing effects were observed when the medium pH was 3.5, with only L-Thr suppressing trichothecene synthesis.

Efficient oligo nucleotide mediated CRISPR-Cas9 gene editing in Aspergilli

CRISPR-Cas9 technologies are revolutionizing fungal gene editing. Here we show that survival of specific Cas9/sgRNA mediated DNA double strand breaks (DSBs) depends on the non-homologous end-joining, NHEJ, DNA repair pathway and we use this observation to develop a tool, TAPE, to assess protospacer efficiency in Aspergillus nidulans. Moreover, we show that in NHEJ deficient strains, highly efficient marker-free gene targeting can be performed. Indeed, we show that even single-stranded oligo nucleotides efficiently work as repair templates of specific Cas9/sgRNA induced DNA DSBs in A. nidulans, A. niger, and in A. oryzae indicating that this type of repair may be wide-spread in filamentous fungi. Importantly, we demonstrate that by using single-stranded oligo nucleotides for CRISPR-Cas9 mediated gene editing it is possible to introduce specific point mutations as well gene deletions at efficiencies approaching 100%. The efficiency of the system invites for multiplexing and we have designed a vector system with the capacity of delivering Cas9 and multiple sgRNAs based on polymerase III promoters and tRNA spacers. We show that it is possible to introduce two point mutations and one gene insertion in one transformation experiment with a very high efficiency. Our system is compatible with future high-throughput gene-editing experiments.

Microbial Inhibition of Fusarium Pathogens and Biological Modification of Trichothecenes in Cereal Grains

Fungi of the genus Fusarium infect cereal crops during the growing season and cause head blight and other diseases. Their toxic secondary metabolites (mycotoxins) contaminate grains. Several dozen toxic compounds produced by fungal pathogens have been identified to date. Type B trichothecenes—deoxynivalenol, its acetyl derivatives and nivalenol (produced mainly by F. graminearum and F. culmorum)—are most commonly detected in cereal grains. “T-2 toxin” (produced by, among others, F. sporotrichioides) belongs to type-A trichothecenes which are more toxic than other trichothecenes. Antagonistic bacteria and fungi can affect pathogens of the genus Fusarium via different modes of action: direct (mycoparasitism or hyperparasitism), mixed-path (antibiotic secretion, production of lytic enzymes) and indirect (induction of host defense responses). Microbial modification of trichothecenes involves acetylation, deacetylation, oxidation, de-epoxidation, and epimerization, and it lowers the pathogenic potential of fungi of the genus Fusarium. Other modifing mechanisms described in the paper involve the physical adsorption of mycotoxins in bacterial cells and the conjugation of mycotoxins to glucose and other compounds in plant and fungal cells. The development of several patents supports the commercialization and wider application of microorganisms biodegrading mycotoxins in grains and, consequently, in feed additives.

Studies on the Presence of Mycotoxins in Biological Samples: An Overview

Mycotoxins are fungal secondary metabolites with bioaccumulation levels leading to their carry-over into animal fluids, organs, and tissues. As a consequence, mycotoxin determination in biological samples from humans and animals has been reported worldwide. Since most mycotoxins show toxic effects at low concentrations and considering the extremely low levels present in biological samples, the application of reliable detection methods is required. This review summarizes the information regarding the studies involving mycotoxin determination in biological samples over the last 10 years. Relevant data on extraction methodology, detection techniques, sample size, limits of detection, and quantitation are presented herein. Briefly, liquid-liquid extraction followed by LC-MS/MS determination was the most common technique. The most analyzed mycotoxin was ochratoxin A, followed by zearalenone and deoxynivalenol—including their metabolites, enniatins, fumonisins, aflatoxins, T-2 and HT-2 toxins. Moreover, the studies were classified by their purpose, mainly focused on the development of analytical methodologies, mycotoxin biomonitoring, and exposure assessment. The study of tissue distribution, bioaccumulation, carry-over, persistence and transference of mycotoxins, as well as, toxicokinetics and ADME (absorption, distribution, metabolism and excretion) were other proposed goals for biological sample analysis. Finally, an overview of risk assessment was discussed.

Genome editing approaches: manipulating of lovastatin and taxol synthesis of filamentous fungi by CRISPR/Cas9 system

Filamentous fungi are prolific repertoire of structurally diverse secondary metabolites of remarkable biological activities such as lovastatin and paclitaxel that have been approved by FDA as drugs for hypercholesterolemia and cancer treatment. The clusters of genes encoding lovastatin and paclitaxel are cryptic at standard laboratory cultural conditions (Kennedy et al. Science 284:1368-1372, 1999; Bergmann et al. Nature Chem Biol 3:213-217, 2007). The expression of these genes might be triggered in response to nutritional and physical conditions; nevertheless, the overall yield of these metabolites does not match the global need. Consequently, overexpression of the downstream limiting enzymes and/or blocking the competing metabolic pathways of these metabolites could be the most successful technologies to enhance their yield. This is the first review summarizing the different strategies implemented for fungal genome editing, molecular regulatory mechanisms, and prospective of clustered regulatory interspaced short palindromic repeat/Cas9 system in metabolic engineering of fungi to improve their yield of lovastatin and taxol to industrial scale. Thus, elucidating the putative metabolic pathways in fungi for overproduction of lovastatin and taxol was the ultimate objective of this review.

Forthcoming Challenges in Mycotoxins Toxicology Research for Safer Food-A Need for Multi-Omics Approach

The presence of mycotoxins in food represents a severe threat for public health and welfare, and poses relevant research challenges in the food toxicology field. Nowadays, food toxicologists have to provide answers to food-related toxicological issues, but at the same time they should provide the appropriate knowledge in background to effectively support the evidence-based decision-making in food safety. Therefore, keeping in mind that regulatory actions should be based on sound scientific findings, the present opinion addresses the main challenges in providing reliable data for supporting the risk assessment of foodborne mycotoxins.

Mycotoxins: An Underhand Food Problem

Among the food safety issues, the occurrence of fungal species able to produce toxic metabolites on the agro-food products has acquired a general attention. These compounds, the mycotoxins, generally provided of low molecular weight, are the result of the secondary metabolism of the toxigenic fungi. They may have toxic activity toward the plants, but mostly represent a serious risk for human and animal health worldwide, since they can be accumulated on many final crop products and they have a broad range of toxic biological activities. In particular, mainly cereals are the most sensitive crops to the colonization of toxigenic fungal species which accumulate in the grains the related mycotoxins both in the field, until the harvest stage, and in the storage. According to a Food and Agriculture Organization study, approximately 25 % of the global food and feed output is contaminated by mycotoxins. Therefore, since a large proportion of the world's population consumes, as a staple food, the cereals, the consumption of mycotoxin-contaminated cereals is a main issue for health risk worldwide. Furthermore, mycotoxin contamination can have a huge economic and social impact, especially when mycotoxin occurrence on the food commodities is over the regulation limits established by different national and transnational institutions, implying that contaminated products must be discarded. Finally, the climate change due to the global warming can alter stages and rates of toxigenic fungi development and modify host-resistance and host-pathogen interactions, influencing deeply also the conditions for mycotoxin production that vary for each individual pathogen. New combinations of mycotoxins/host plants/geographical areas are arising to the attention of the scientific community and require new diagnostic tools and deeper knowledge of both biology and genetics of toxigenic fungi. Moreover, to spread awareness and knowledge at international level on both the hazard that mycotoxins represent for consumers and costs for stakeholders is of key importance for developing all possible measures aimed to control such dangerous contaminants worldwide.

Challenges in Specialty Coffee Processing and Quality Assurance

Coffee is an important crop that assures a sustainable economy to farmers in tropical regions. A dramatic concern for coffee production is currently represented by climate change, which threatens the survival of Coffea arabica cultivation worldwide and imposes modifications of the agronomic practices to prevent this risk. The quality of coffee beans depends on optimized protocols of cultivation, ripe berries collection, and removal of the outer fruit layers by dry or wet processes and moisture reduction. Storage and shipment represent two steps where bean quality needs to be preserved by preventing fungal contamination that may impact the final product and form mycotoxins, mainly ochratoxin A. In this review, we describe the challenges faced by the coffee industry to guarantee quality from production to roasting and brewing. An overview of novel technologies, such as the application of starter cultures in fermentation and the exploitation of industrial enzymes in accelerating the process of flavour development in coffee beans, is given. Moreover, the results of studies on microbial populations on coffee and the differences found in fungi, yeasts and bacteria composition among the investigations, are summarized. In particular, this review describes new attempts to contain the development of mycotoxigenic fungi, through the application of antagonistic microorganisms such as S. cerevisiae. The new wave of specialty coffees, i.e., those with a cupping score higher than 85/100, is also presented. It is shown how, through careful coffee production methods and controlled fermentation processes, coffee producers may increase their income by assuring high standards of quality and high added value for the coffee experience sector.

Different Toxicity Mechanisms for Citrinin and Ochratoxin A Revealed by Transcriptomic Analysis in Yeast

Citrinin (CIT) and ochratoxin A (OTA) are important mycotoxins, which frequently co-contaminate foodstuff. In order to assess the toxicologic threat posed by the two mycotoxins separately or in combination, their biological effects were studied here using genomic transcription profiling and specific live cell gene expression reporters in yeast cells. Both CIT and OTA cause highly transient transcriptional activation of different stress genes, which is greatly enhanced by the disruption of the multidrug exporter Pdr5. Therefore, we performed genome-wide transcription profiling experiments with the pdr5 mutant in response to acute CIT, OTA, or combined CIT/OTA exposure. We found that CIT and OTA activate divergent and largely nonoverlapping gene sets in yeast. CIT mainly caused the rapid induction of antioxidant and drug extrusion-related gene functions, while OTA mainly deregulated developmental genes related with yeast sporulation and sexual reproduction, having only a minor effect on the antioxidant response. The simultaneous exposure to CIT and OTA gave rise to a genomic response, which combined the specific features of the separated mycotoxin treatments. The application of stress-specific mutants and reporter gene fusions further confirmed that both mycotoxins have divergent biological effects in cells. Our results indicate that CIT exposure causes a strong oxidative stress, which triggers a massive transcriptional antioxidant and drug extrusion response, while OTA mainly deregulates developmental genes and only marginally induces the antioxidant defense.

A CRISPR-Cas9 System for Genetic Engineering of Filamentous Fungi

The number of fully sequenced fungal genomes is rapidly increasing. Since genetic tools are poorly developed for most filamentous fungi, it is currently difficult to employ genetic engineering for understanding the biology of these fungi and to fully exploit them industrially. For that reason there is a demand for developing versatile methods that can be used to genetically manipulate non-model filamentous fungi. To facilitate this, we have developed a CRISPR-Cas9 based system adapted for use in filamentous fungi. The system is simple and versatile, as RNA guided mutagenesis can be achieved by transforming a target fungus with a single plasmid. The system currently contains four CRISPR-Cas9 vectors, which are equipped with commonly used fungal markers allowing for selection in a broad range of fungi. Moreover, we have developed a script that allows identification of protospacers that target gene homologs in multiple species to facilitate introduction of common mutations in different filamentous fungi. With these tools we have performed RNA-guided mutagenesis in six species of which one has not previously been genetically engineered. Moreover, for a wild-type Aspergillus aculeatus strain, we have used our CRISPR Cas9 system to generate a strain that contains an AACU_pyrG marker and demonstrated that the resulting strain can be used for iterative gene targeting.

Molecular strategies for detection and quantification of mycotoxin-producing Fusarium species: a review

Fusarium contamination is considered a major agricultural problem, which could not only significantly reduce yield and quality of agricultural products, but produce mycotoxins that are virulence factors responsible for many diseases of humans and farm animals. One strategy to identify toxigenic Fusarium species is the use of modern molecular methods, which include the analysis of DNA target regions for differentiation of the Fusarium species, particularly the mycotoxin-producing Fusarium species such as F. verticillioides and F. graminearum. Additionally, polymerase chain reaction assays are used to determine the genes involved in the biosynthesis of the toxins in order to facilitate a qualitative and quantitative detection of Fusarium-producing mycotoxins. Also, it is worth mentioning that some factors that modulate the biosynthesis of mycotoxins are not only determined by their biosynthetic gene clusters, but also by environmental conditions. Therefore, all of the aforementioned factors which may affect the molecular diagnosis of mycotoxins will be reviewed and discussed in this paper.

SnPKS19 Encodes the Polyketide Synthase for Alternariol Mycotoxin Biosynthesis in the Wheat Pathogen Parastagonospora nodorum

Alternariol (AOH) is an important mycotoxin from the Alternaria fungi. AOH was detected for the first time in the wheat pathogen Parastagonospora nodorum in a recent study. Here, we exploited reverse genetics to demonstrate that SNOG_15829 (SnPKS19), a close homolog of Penicillium aethiopicum norlichexanthone (NLX) synthase gene gsfA, is required for AOH production. We further validate that SnPKS19 is solely responsible for AOH production by heterologous expression in Aspergillus nidulans. The expression profile of SnPKS19 based on previous P. nodorum microarray data correlated with the presence of AOH in vitro and its absence in planta. Subsequent characterization of the ΔSnPKS19 mutants showed that SnPKS19 and AOH are not involved in virulence and oxidative stress tolerance. Identification and characterization of the P. nodorum SnPKS19 cast light on a possible alternative AOH synthase gene in Alternaria alternata and allowed us to survey the distribution of AOH synthase genes in other fungal genomes. We further demonstrate that phylogenetic analysis could be used to differentiate between AOH synthases and the closely related NLX synthases. This study provides the basis for studying the genetic regulation of AOH production and for development of molecular diagnostic methods for detecting AOH-producing fungi in the future.

Phytotoxic and antibacterial metabolites from Fusarium proliferatum ZS07 isolated from the gut of long-horned grasshoppers

In the proceeding of screening new bioactive natural products, the ethyl acetate extract of the fermentation broth of Fusarium proliferatum ZS07, a fungus residing in the gut of long-horned grasshoppers (Tettigonia chinensis), was found possessing selective phytotoxic activity against the radicle growth of Amaranthus retroflexus L. Bioactivity-guided fractionation lead to the isolation of six fungal metabolites 1-6, including a new polyketide derivate O-methylated SMA93 (2) and five known compounds SMA93 (1), rhodolamprometrin (3), radicinin (4), dehydroallogibberic acid (5), and 3-methyl-6,8-dihydroxyisocoumarin (6). Their structures were identified on the basis of spectroscopic analysis and by comparison of the corresponding data to those reported in the literature previously. Phytotoxic effects of the four isolated compounds 1-4 on the radicle growth of A. retroflexus L. seeds were investigated under laboratory conditions, and compounds 2 and 4 showed good phytotoxic activity in the concentration of 100 μg/mL, with the inhibition rates of 83.0 and 65.2%, respectively. Furthermore, the antibacterial activity of compounds 1-5 were evaluated against selected bacteria. Compounds 1-3 were found to possess potent antibacterial activity against Bacillus subtilis (ATCC 6633), with the minimum inhibitory concentration (MIC) values of 3.13-12.50 μg/mL, while Escherichia coli (ATCC 8739) and Salmonella typhimurium [CMCC(B) 50115] were not susceptible. These results suggest that the new polyketide derivate 2 and known compounds 1, 3, and 4 have potential to be used as biocontrol agents in agriculture.

Molecular diagnostics on the toxigenic potential of Fusarium spp. plant pathogens

AIMS

We propose and test an efficient and rapid protocol for the detection of toxigenic Fusarium isolates producing three main types of Fusarium-associated mycotoxins (fumonisins, trichothecenes and zearelanone).

METHODS AND RESULTS

The novel approach utilizes partially multiplexed markers based on genes essential for mycotoxin biosynthesis (fumonisin--fum6, fum8; trichothecenes--tri5, tri6; zearalenone, zea2) in Fusarium spp. The protocol has been verified by screening a collection of 96 isolates representing diverse species of filamentous fungi. Each Fusarium isolate was taxonomically identified through both molecular and morphological techniques. The results demonstrate a reliable detection of toxigenic potential for trichothecenes (sensitivity 100%, specificity 95%), zearalenone (sensitivity 100%, specificity 100%) and fumonisins (sensitivity 94%, specificity 88%). Both presence and identity of toxin biosynthetic genes were further confirmed by direct sequencing of amplification products.

CONCLUSIONS

The cross-species-specific PCR markers for key biosynthetic genes provide a sensitive detection of toxigenic fungal isolates, contaminating biological material derived from agricultural fields.

SIGNIFICANCE AND IMPACT OF THE STUDY

The conducted study shows that a PCR-based assay of biosynthetic genes is a reliable, cost-effective, early warning system against Fusarium contamination. Its future use as a high-throughput detection strategy complementing chemical assays enables effective targeted application of crop protection products.

Toxicity mechanisms of the food contaminant citrinin: application of a quantitative yeast model

Mycotoxins are important food contaminants and a serious threat for human nutrition. However, in many cases the mechanisms of toxicity for this diverse group of metabolites are poorly understood. Here we apply live cell gene expression reporters in yeast as a quantitative model to unravel the cellular defense mechanisms in response to the mycotoxin citrinin. We find that citrinin triggers a fast and dose dependent activation of stress responsive promoters such as GRE2 or SOD2. More specifically, oxidative stress responsive pathways via the transcription factors Yap1 and Skn7 are critically implied in the response to citrinin. Additionally, genes in various multidrug resistance transport systems are functionally involved in the resistance to citrinin. Our study identifies the antioxidant defense as a major physiological response in the case of citrinin. In general, our results show that the use of live cell gene expression reporters in yeast are a powerful tool to identify toxicity targets and detoxification mechanisms of a broad range of food contaminants relevant for human nutrition.