The escalating prevalence of antimicrobial resistance in food-related pathogens constitutes a critical challenge to global public health and food safety. To elucidate the mechanisms underlying the high erythromycin resistance rate observed in our previous surveillance of Staphylococcus in retail foods, we conducted a comprehensive genomic investigation of msrA-positive Staphylococcus from a nationwide retail food collection in China. We identified 102 msrA-positive isolates, all of which exhibited a multidrug-resistant (MDR) phenotype, with a significantly higher prevalence in aquatic products (13.95%), identifying this food category as a high-risk reservoir for transmitting resistant bacteria to consumers. Genomic typing revealed the dominance of the S. aureus ST15-t085 lineage (58.0%), which exhibited a specific ecological adaptation to retail aquatic products. We characterized 12 novel msrA-harboring plasmids (pMsrA-I to pMsrA-XII), with the dominant Type A plasmids carrying a coupled msrA-mphC cassette that confers synergistic high-level resistance. Structural analysis demonstrated that IS431R serves as a key driver of plasmid evolution, mediating the capture of resistance clusters. Notably, these plasmids also harbor genes conferring tolerance to heavy metals and food preservatives, physically linked to the antimicrobial resistance regions. This genetic linkage suggests that routine disinfection and environmental residues in retail food processing environments likely drive the co-selection of these multidrug-resistant plasmids. Furthermore, these isolates harbored both the plasmids and chromosomal biofilm-associated genes, as well as the neglected enterotoxin gene seh (15.7%), highlights a dual threat of environmental persistence and pathogenicity. These findings underscore the urgent need for targeted surveillance of novel resistance plasmids in the retail food market to mitigate the spread of these multidrug-resistant pathogens.
The implication of eggs as source for campylobacteriosis is not yet completely understood, since quantitative data on the contamination level are sparse. In this study 459 pooled eggshell samples derived from different production types and collected at German packaging stations and at retail were analysed by culture and culture-independent qPCR in parallel. Thermotolerant Campylobacter spp. were isolated from 1.5% of 457 samples (detection by culture). qPCR revealed presence of Campylobacter spp. in 79.9% of the samples (total DNA), with a median of 3.7 log10 (SD, ± 0.8 log10) and a maximum of 6.0 log10 genomic copies of Campylobacter spp. per 10 eggs. Visible contamination grade and production type were significantly associated with the number of genomic copies detected. A subset of the samples (n = 90) was both analysed by culture and by live/dead differentiating viable (v-)qPCR, showing that 6.6% of these samples (6/90) were culturally positive and 11.0% (10/90) contained viable Campylobacter spp. according to v-qPCR. Culturability correlated with egg age. Based on v-qPCR, positive eggs contained a median of 3.7 log10 and a maximum of 5.4 log10 viable Campylobacter per 10 eggs. Artificial contamination with a mixture of C. jejuni and C. coli strains originally isolated from eggs confirmed rapid loss of culturability most likely due to dryness and 10.3% of maximal transfer of Campylobacter spp. from the eggshells by wet contact. In conclusion, although eggs were very frequently contaminated with Campylobacter spp. (around 80% positive samples), most of the bacteria (84% of positives of the analysed subset) were dead probably due to dryness. In a few cases, a fraction of the remaining viable bacteria may be transferred from the eggshell to raw egg dishes during wet contact (opening of the shell) at maximum levels of 3.4 log10 per egg. However, the infectious potential of viable but not culturable bacteria is likely lower than that of culturable Campylobacter. This should be investigated further in order to improve risk assessment.
Pseudomonas fluorescens is a major psychrotrophic spoilage bacterium in refrigerated foods, where its persistence is closely associated with biofilm formation under low-temperature conditions. To elucidate the mechanisms underlying cold-induced biofilm adaptation, the biofilm characteristics and transcriptomic profiles of Pseudomonas fluorescens PF07 at 10 °C and 30 °C were compared. Based on these analyses, key biofilm matrix components and regulatory factors were identified, and the resistance of the corresponding mutants under cold conditions was further evaluated. Transcriptomic analyses revealed that genes involved in Psl polysaccharide biosynthesis and c-di-GMP-associated diguanylate cyclases were markedly upregulated, whereas the transcriptional regulator AmrZ was significantly downregulated at 10 °C. Deletion of amrZ resulted in a pronounced shift in biofilm architecture, characterized by reduced surface-attached biofilms but enhanced pellicle formation accompanied by elevated exopolysaccharide production. Proteomic and genetic analyses demonstrated that AmrZ negatively regulates Psl polysaccharide synthesis and intracellular c-di-GMP levels, thereby modulating the transition between distinct biofilm states. Disruption of pslB abolished pellicle formation and significantly weakened biofilm structural integrity, even in the ΔamrZ background, highlighting the essential role of Psl polysaccharide as a key matrix component. Importantly, the ΔamrZ mutant exhibited increased resistance to sodium hypochlorite and heat treatments at low temperature, which was associated with enhanced biofilm formation and Psl overproduction. In contrast, deletion of pslB markedly increased biofilm removability, indicating that Psl was a vital protective matrix component. Collectively, these findings demonstrated that low temperature promotes the formation of highly stable and stress-resistant biofilms in P. fluorescens PF07 through AmrZ-mediated regulation of Psl polysaccharide and c-di-GMP signaling. This study provided mechanistic insights into biofilm persistence under cold-chain conditions and identified potential molecular targets for improving sanitation strategies in refrigerated food systems.
Spoilage microorganisms and pathogenic bacteria can negatively impact food safety and stability, leading to potential health risks and economic losses. Predictive microbiology is a crucial tool for forecasting microbial behavior in food matrices, and supervised machine learning stands out as an effective solution for handling complex datasets (e.g., multiple variables and non-linear relationships). This work aims to develop a growth prediction model for Listeria monocytogenes, Listeria innocua and aerobic spoilage bacteria in food and culture media using artificial neural networks. The model development involved the implementation of the Multilayer Perceptron algorithm applied to datasets obtained from the ComBase platform. We evaluated different models to understand the impact of dataset size, additional input variables, food matrix data, and microorganism data on model performance. Experimental data were also used for model validation. Results demonstrate favorable statistical metrics for all models (R2 = [0.847-0.929], RMSE = [0.55-0.852], Bf = [1.002-1.011] and Af = [1.071-1.108]), indicating the efficacy of the proposed approach for the intended application. Furthermore, validation of the model using experimental data on the growth of total aerobic spoilage bacteria in beef demonstrated its ability to accurately describe the kinetics of microbial growth. These findings underscore the potential of Multilayer Perceptron models to predict microbial growth in various food matrices and culture media, exhibiting robust performance and generalization capability.
In the production of plant-based meat alternatives, texturized vegetable proteins (TVP) are a popular choice as base ingredients. However, these can have undesired off-flavors, which negatively affects consumer experience. Examples are distinctive green, and beany notes as well as a lack of desired meat flavor. This can be counteracted by using microbial fermentation as a processing step, with the potential to reduce off-flavors and create new odor-active compounds. Therefore, pea protein texturates produced via high-moisture (HMPT) and low-moisture (LMPT) extrusion cooking were fermented for 4 weeks at 15 °C, using Staphylococcus carnosus and Kluyveromyces marxianus in otherwise sterile microaerophile conditions. Microbial and metabolic activity were assessed, aroma profiles were determined by headspace solid-phase microextraction-gas chromatography-mass spectrometry-olfactometry (HS-SPME-GC-MS-O), key odor-active compounds were identified and relative peak areas of these compounds compared. High viable cell counts (cfu/g) were documented over the course of 4 weeks. Assessment of metabolic activity revealed increased tyrosine levels in LMPT compared to HMPT samples. Similarly, 53 (LMPT) and 41 (HMPT) perceivable odor-active compounds were identified prior to fermentation in the TVP samples. Of these, 17 compounds were identified as commonly known key off-odors in pea proteins which were significantly reduced throughout the fermentation. S. carnosus led to more characteristic final odor profiles, with desirable and undesirable flavors depending on the raw material. K. marxianus led to reduction beyond perceivability of several odor-active compounds, causing less intense odor profiles.
Whole genome sequencing (WGS) has revolutionised surveillance and outbreak investigation of pathogenic bacteria in food, but cross-laboratory comparability remains challenging. An Inter-laboratory Comparison Test (ILCT) on the application of whole genome sequencing (WGS) for typing and characterisation of foodborne Staphylococcus aureus isolates was organised by the European Reference Laboratory for Coagulase-Positive Staphylococci (EURL for CPS) from 2023 to 2025. The test involved 12 National Reference Laboratories (NRLs) and evaluated variability in sequencing output, genome assembly metrics, MLST/cgMLST allele calling, and Staphylococcal enterotoxin gene detection introduced at three critical stages of the WGS workflow - DNA extraction, sequencing, and bioinformatics. While DNA extraction protocols showed minimal effects on sequencing quality, major differences arose from bioinformatics pipelines, particularly in contamination detection, reference database use, and assembly tools. Independent sequencing revealed that genome complexity, rather than sequencing depth or assembly metrics alone, most influenced cgMLST concordance. This ILCT provided a comprehensive overview of the capabilities and inconsistencies in WGS workflows at that time and highlights the need for harmonised analytical pipelines, curated reference databases, and quality thresholds.
Antimicrobial resistance exacerbates food safety risks, highlighting the need for novel, matrix-tolerant control and detection tools. Phage-derived endolysins and receptor-binding proteins (RBPs) offer high specificity, yet their performance is often reduced in complex food environments compared with buffer assays. In this review, we summarize engineering principles and food-system evidence that govern efficacy, including matrix-driven attenuation (e.g., viscosity, protein/fat adsorption, ionic strength, and proteolysis) and developability constraints linked to manufacturing and formulation. We also summarize practical endpoints for food applications spanning sanitation of food-contact surfaces, biocontrol on raw commodities, and culture-free pathogen detection. On this basis, we propose ISELI-CL (In Silico-Experiment-Learning-Iterative Closed Loop), a structured framework that combines computational design and active learning with high-throughput validation to balance activity, manufacturability, and food matrix compatibility. By treating buffer-to-food translation as a quantifiable domain shift, ISELI-CL is intended to guide candidate prioritization and matrix-aware validation of mechanism-informed phage proteins in food microbiology.
The development of high-throughput, sensitive and portable strategies for detecting foodborne pathogens is urgently needed in food safety, especially during an outbreak. Herein, an ultrasensitive suspension array was constructed by designing photonic crystal microsphere (PCM)-assisted loop-mediated isothermal amplification (LAMP) for Staphylococcus aureus detection. The PCM-LAMP suspension array integrated the optical signal enhancement capability of the biomimetic microporous three-dimensional PCM surface with the thousand-fold signal amplification of LAMP. The biomimetic PCMs displayed a periodic dielectric nanostructure and enhanced the fluorescence intensity of the LAMP reaction, leading to high sensitivity. The PCM-LAMP suspension array allowed sensitive detection of the target DNA of S. aureus without long-term culture. Under optimal conditions, the limit of detection for S. aureus genomic DNA reached as low as 0.18 fM, and the assay exhibited excellent specificity against other bacteria. Furthermore, trace target DNA in food samples was accurately quantified, demonstrating its potential for practical applications. Therefore, the developed PCM-LAMP suspension array holds great promise for ultrasensitive and rapid detection of foodborne pathogens.
Lager beers are traditionally brewed using Saccharomyces pastorianus, a natural hybrid between S. cerevisiae and S. eubayanus that combines robust fermentation with cold tolerance. However, commercial lager yeasts originate from a narrow genetic pool, limiting strain diversity and aromatic complexity. To meet growing demand for new lager beer profiles, the development of novel non-GMO strains is increasingly important. Many wild yeasts from non-brewing environments can ferment wort but produce phenolic off-flavor (POF+) by converting ferulic acid (FA) into 4-vinyl guaiacol (4-VG), restricting their industrial applicability. In this study, a de novo POF+ lager-like hybrid (FM1) generated by spore-to-spore mating between a monosporic culture of the sourdough strain S. cerevisiae Y15 and S. eubayanus x S. uvarum NBRC1948, was submitted to UV mutagenesis to reduce POF formation. Screening on FA-supplemented medium identified a POF-reduced mutant, FM1.45, showing lower ferulic acid conversion and higher cinnamic acid sensitivity than FM1. Wort microfermentation trials demonstrated that FM1 and FM1.45 both outperformed the parental strains in fermentation kinetics and produced similar aroma profiles, with FM1.45 generating substantially less 4-VG than FM1. Sanger sequencing results were consistent with a loss of the S. eubayanus PAD1-FDC1 gene cluster and a frameshift mutation in the S. cerevisiae FDC1 gene, leading to a non-functional ferulic acid decarboxylase. Flow cytometry supported a ploidy increase from 3n to 4n in FM1.45, which likely accounts for the restored spore viability observed in this mutant compared with the sterile FM1. Overall, this work demonstrates that combining interspecific hybridization with UV mutagenesis represents an effective GMO-free strategy for generating novel lager yeast strains with robust fermentation performance and reduced POF production.
Cronobacter sakazakii is a relevant pathogen in low-moisture foods (LMF), especially in powdered infant formulas (PIF). The objective of this study was to evaluate five matrices as dry carriers of C. sakazakii, as well as the dry transfer and adhesion capacity onto clean and conditioned stainless steel (SS) and polypropylene (PP) coupons. Soil, PIF, wheat flour, fine corn flour and whole milk powder showed potential as dry carriers, achieving counts up to 7 log CFU/g. The inoculum viability loss was greater at 37 °C, and storage time affected the inoculum in corn flour, wheat flour and soil. On clean coupons, the inoculum showed lower viability loss at 25 °C, with no significant difference among the carriers and storage times (p > 0.05). The highest counts of transferred but non-adhered cells (NAC), culturable adhered cells (CAC) and viable adhered cells (VAC) were obtained using soil as the dry carrier (p < 0.05). For pre-conditioned coupons, the highest initial NAC count was observed in PP conditioned with wheat flour. A significant difference (p < 0.05) was observed between the surfaces, except for soil conditioning. In contrast, the initial count only had significant difference (p < 0.05) between surfaces conditioned with soil. The VBNC population showed the highest counts for wheat flour on day zero. In general, soil showed a greater capacity for dry transfer and adhere C. sakazakii on abiotic surfaces, particularly on PP. Furthermore, the presence of organic residues favored pathogen adhesion and viability, indicating a higher risk of cross-contamination.
Donkey milk (DM) is a nutritionally rich source of bioactive compounds, essential vitamins and minerals. However, its potential for developing functional fermented products remains unexplored. To address this gap, we investigated microbial dynamics during spontaneous fermentation of raw Zamorano-Leonese DM to isolate lactic acid bacteria (LAB) suitable for dairy applications. Raw milk from Zamorano-Leonese breed donkeys, raised on an organic farm in Salamanca (Spain), was spontaneously fermented at 37 °C until reaching pH 4.6. Metataxonomic analysis revealed a clear shift from environmental bacteria dominating the raw milk to an increased prevalence of LAB at the end of the fermentation process. Through culturomics, 34 bacterial strains were isolated and identified by 16S rRNA gene sequencing, including ten potential LAB candidates. Among these, five Lactococcus lactis isolates were selected to ferment pasteurized DM, which showed promising technological features and were subsequently subjected to whole-genome sequencing. L. lactis subsp. lactis CECT 31096 was selected due to its broad enzymatic repertoire linked to fermentation and the absence of antibiotic resistance or virulence-related genes. When used to ferment pasteurized DM, this strain improved both the physicochemical and nutritional profile of the resulting product. Fermentation significantly enhanced the bioaccesibility of bioactive compounds, as demonstrated by a higher inhibition of angiotensin-converting enzyme (the fermented sample showed IC50 values of 3.17 g/L compared with IC50 7.23 g/L from pasteurized milk), doubling after digestion (IC50 1.25 g/L). Additionally, fermentation with L. lactis subsp. lactis CECT 31096 significantly increased soluble free phenols and peptides, boosting the reducing power and antioxidant capacity, and thereby enhancing the functionality of the final product.
Wet Spirulina is a nutrient-dense food resource, but its rapid quality deterioration necessitates the adoption of effective, non-thermal processing strategies to ensure safety and stability. Fermentation-driven production of microbial volatile organic compounds (VOCs) represents a promising alternative to thermal treatments by suppressing spoilage metabolites and enhancing sensory attributes. However, the influence of oxygen availability on VOC activity and quality of wet Spirulina remains insufficiently characterized. This study systematically examined the role of oxygen dynamics, namely aerobic, anaerobic, and cascade (aerobic-to-anaerobic shift) conditions on VOC formation, bioactive compounds, and biogenic amines during fermentation. Among all tested regimes, cascade oxygen regulation yielded the most prominent improvements. It promoted microbial populations to ∼8.4 log CFU/mL and enhanced protein hydrolysis, resulting in 1.13-fold higher amino acids (1775.45 mg/L) compared to anaerobic fermentation. It also improved the availability of precursors for the production of desirable fruity and floral aromatics. This condition produced markedly higher concentrations of phenylethyl acetate (22.35 mg/L), phenylethyl alcohol (9.39 mg/L), and related esters, driving a distinct sensory transition from bitterness to sweeter umami notes for significant improvement in acceptability. Furthermore, the cascade fermentation increased phenolic activity by 41.9% and reduced key spoilage biogenic amines including putrescine, cadaverine, and spermine to below the detection limit. These outcomes demonstrate that targeted oxygen modulation can effectively steer microbial metabolism toward beneficial bioactive synthesis while enhancing safety. Overall, this work validates the efficacy of cascade oxygen regulation as a controllable and non-thermal strategy to improve the quality, functionality, and safety of wet Spirulina.
Information on childhood cancer burden is crucial for effective cancer policy planning. Unfortunately, observed paediatric cancer data are not available in every country, and previous global burden estimates have not discretely reported several common cancers of childhood. We aimed to inform efforts to address childhood cancer burden globally by analysing results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2023, which now include nine additional cancer causes compared with previous GBD analyses. GBD 2023 data sources for cancer estimation included population-based cancer registries, vital registration systems, and verbal autopsies. For childhood cancers (defined as those occurring at ages 0-19 years), mortality was estimated using cancer-specific ensemble models and incidence was estimated using mortality estimates and modelled mortality-to-incidence ratios (MIRs). Years of life lost (YLLs) were estimated by multiplying age-specific cancer deaths by the standard life expectancy at the age of death. Prevalence was estimated using survival estimates modelled from MIRs and multiplied by sequelae-specific disability weights to estimate years lived with disability (YLDs). Disability-adjusted life-years (DALYs) were estimated as the sum of YLLs and YLDs. Estimates are presented globally and by geographical and resource groupings, and all estimates are presented with 95% uncertainty intervals (UIs). Globally, in 2023, there were an estimated 377 000 incident childhood cancer cases (95% UI 288 000-489 000), 144 000 deaths (131 000-162 000), and 11·7 million (10·7-13·2) DALYs due to childhood cancer. Deaths due to childhood cancer decreased by 27·0% (15·5-36·1) globally, from 197 000 (173 000-218 000) in 1990, but increased in the WHO African region by 55·6% (25·5-92·4), from 31 500 (24 900-38 500) to 49 000 (42 600-58 200) between 1990 and 2023. In 2023, age-standardised YLLs due to childhood cancer were inversely correlated with country-level Socio-demographic Index. Childhood cancer was the eighth-leading cause of childhood deaths and the ninth-leading cause of DALYs among all cancers in 2023. The percentage of DALYs due to uncategorised childhood cancers was reduced from 26·5% (26·5-26·5) in GBD 2017 to 10·5% (8·1-13·1) with the addition of the nine new cancer causes. Target cancers for the WHO Global Initiative for Childhood Cancer (GICC) comprised 47·3% (42·2-52·0) of global childhood cancer deaths in 2023. Global childhood cancer burden remains a substantial contributor to global childhood disease and cancer burden and is disproportionately weighted towards resource-limited settings. The estimation of additional cancer types relevant in childhood provides a step towards alignment with WHO GICC targets. Efforts to decrease global childhood cancer burden should focus on addressing the inequities in burden worldwide and support comprehensive improvements along the childhood cancer diagnosis and care continuum. St Jude Children's Research Hospital, Gates Foundation, and St Baldrick's Foundation.
Improving the environmental stress tolerance of Saccharomyces cerevisiae can enhance fermentation performance and reduce beer deterioration caused by yeast autolysis. This study investigates the deletion of the NTH1 gene (encoding neutral trehalase) and the FKS3 gene (encoding 1,3-β-glucan synthase) in the S. cerevisiae WLP029 strain (Kölsch brewing yeast) to improve its stress tolerance. CRISPR/Cas9 technology was used to create three strains: S. cerevisiae WLP029Δnth1, S. cerevisiae WLP029Δfks3, and S. cerevisiae WLP029Δfks3Δnth1. The stress tolerance of these strains was evaluated through various tests, including survival and metabolic recovery after lyophilization, as well as viability and autolysis during fermentation and refrigerated storage of beer. RNA-seq analysis was conducted to examine the impact of NTH1 and FKS3 deletions on gene expression. The deletion of the NTH1 gene in S. cerevisiae WLP029Δnth1Δfks3 resulted in a significant loss of neutral trehalase activity and a greater accumulation of intracellular trehalose. The three gene deletion strains had significantly higher survival rates and metabolic activity post-lyophilization compared to the wild-type strain. Scanning electron microscopy revealed that the single gene deletion strains, particularly WLP029Δnth1, had better cell integrity after lyophilization, suggesting that NTH1 and FKS3 deletions help maintain cell wall morphology and improve metabolic recovery. During the fermentation period, the WLP029Δnth1Δfks3 strain exhibited the highest viability. Beer storage at 4 °C revealed that the WLP029Δnth1Δfks3 strain exhibited superior resistance to autolysis, with a delayed release of nucleic acids and proteins. The deletions of NTH1, FKS3, or both led to increased expression of antioxidant and stress-response proteins, suggesting enhanced environmental tolerance.
This study investigated the effect of Lactiplantibacillus pentosus R3 in reducing N-dimethylnitrosamine (NDMA) content during simulated gastrointestinal digestion of fermented sausages. The results showed that the content of NDMA in the fermented sausages increased during digestion (P < 0.05). Compared with the control, the NDMA content in the inoculated sausage was significantly lower (P < 0.05). Meanwhile, the strain was found to reduce the content of NDMA precursors (putrescine and dimethylamine) during the gastrointestinal digestion (P < 0.05). The activity and antioxidant capacity of L. pentosus were found to be significantly reduced after digestion in simulated gastric juice, which was weakly affected by simulated intestinal digestion. In the simulated gastric juice, L. pentosus demonstrated a greater capacity for reducing the level of putrescine and dimethylamine. Conversely, in the simulated intestinal juice, the strain exhibited a preference for direct reduction of NDMA. Therefore, L. pentosus can reduce the NDMA content during the gastrointestinal digestion of fermented sausages via reduction of the precursors in gastric digestion, direct reduction during intestinal digestion and inhibition of the formation reaction via its antioxidant function. It is promising to decrease NDMA during the digestion of fermented meat products by L. pentosus.
This study focuses on the characterisation of mannoprotein extracts (MPs) obtained from active dry yeast of Saccharomyces cerevisiae and non-Saccharomyces strains, including those of Torulaspora delbrueckii, Lachancea thermotolerans, and Metschnikowia pulcherrima, and their effects on wine malolactic fermentation (MLF) carried out by Oenococcus oeni. Mannoproteins are essential components of the yeast cell wall, are released during the autolysis process, and vary in size, molecular weight, and protein content depending on the extraction method. In this work, it was observed that the MPs obtained through cellular autolysis induction had a higher molecular weight, a richer sugar composition-including mannose and glucose-and a higher protein content than the MPs obtained through the alkali medium method. All the MPs extracts had beneficial effects on MLF in white and red wines. The consumption of mannoprotein by O. oeni was observed in all the fermentations, indicating the relationship between MPs and O. oeni metabolism improvement. Finally, the addition of MPs did not significantly affect colour parameters, tannins, or anthocyanins at the end of MLF in red wines, keeping these components stable and, therefore, maintaining the final stability of the wine. In conclusion, this work demonstrates the potential of MPs as effective activators of MLF in wine.
Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures.
In this study, Yarrowia lipolytica was cultured with L-Phenylalanine (L-Phe) as an inducer to investigate its effect on the biocontrol efficacy of Y. lipolytica against postharvest diseases in pears. This investigation also clarifies the physiological mechanisms by which L-Phe induces the biocontrol efficacy of Y. lipolytica. Experimental results confirmed that L-Phe could trigger and enhance the effectiveness of Y. lipolytica in controlling postharvest blue mold in pears. Furthermore, Y. lipolytica inhibited the spore germination rate and germ tube length of Penicillium expansum in a liquid medium and decreased the colony diameter of P. expansum on a solid medium. Cultivating Y. lipolytica with the inducer (L-Phe) improved its growth, reproduction, and biofilm-forming efficiency on pear surfaces. Moreover, Y. lipolytica induced by L-Phe increased the activities of defense-related enzymes in pears, promoted the accumulation of antimicrobial secondary metabolites, and upregulated the genes encoding defense-related enzymes compared to Y. lipolytica alone. These changes collectively enhance the disease resistance of pears. Therefore L-Phe can improve the biocontrol efficacy of Y. lipolytica against postharvest blue mold in pears.
A controlled nitrogen atmosphere (CNA) is favorable for postharvest grain management in large-grain warehouses. Storage fungi with a high hypoxic tolerance pose a potential threat to the safe storage of grains under a CNA. In this study, CNA storage of wheat grain was simulated, and Aspergillus chevalieri was identified as the predominant storage fungus after a 30-day storage period. Under an atmosphere of 2% O2, A. chevalieri grows on agar plates with the same colony diameter as that under normoxic conditions. The dry weight of A. chevalieri mycelia grown in liquid culture under hypoxic conditions was reduced by 60.56% compared with that under normoxic conditions. Scanning electron microscopy revealed that A. chevalieri mycelia exposed to hypoxic stress were shriveled and wrinkled. The ergosterol content of A. chevalieri mycelia under hypoxic stress increased by 151.17% compared with the control group. Catalase and superoxide dismutase were significantly upregulated in A. chevalieri by hypoxic stress, whereas the levels of H2O2, superoxide anions, and ATP were considerably decreased. Transcriptomic analysis identified 1345 differentially expressed genes, primarily enriched in pathways related to longevity regulation, mitochondrial autophagy, amino acid metabolism, ubiquitination metabolism, coenzyme A biosynthesis and glycolysis. Metabolomic profiling further revealed 87 markedly altered metabolites primarily involved in starch and sucrose metabolism, arginine and proline metabolism, and lysine degradation. By integrating multi-omics data with physiological and biochemical analyses, this study systematically elucidates the hypoxia adaptation mechanism of A. chevalieri under CNA conditions, providing insights that may facilitate the prevention and control of hypoxia-tolerant storage fungi.
Meningitis remains the leading infectious cause of neurological disabilities globally, disproportionately affecting children younger than 5 years and populations in the African meningitis belt. Whereas previous global estimates focused on ten pathogen categories, this study presents the most comprehensive analysis to date, assessing the meningitis burden attributable to 17 causative pathogens based on the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2023 framework. GBD is a systematic, scientific effort aimed at quantifying the comparative magnitude of health loss caused by diseases, injuries, and risk factors across age groups, sexes, and geographical locations over time. We estimated meningitis mortality using the Cause of Death Ensemble model (CODEm) and morbidity using DisMod-MR 2.1, incorporating data from vital registration, verbal autopsy, surveillance, hospital data, and systematic reviews. Aetiology-specific estimates were generated with pathogen-linked case-fatality ratios and splined binomial regression models. Risk factor attribution was based on established risk-outcome pairs and population attributable fractions. In 2023, there were 259 000 (95% uncertainty interval 202 000-335 000) global deaths and 2·54 million (2·20-2·93) incident cases of meningitis. Children younger than 5 years accounted for more than a third of deaths (86 600 [53 300-149 000]). Streptococcus pneumoniae, Neisseria meningitidis, non-polio enteroviruses, and other viruses were the leading causes of death, while non-polio enteroviruses caused the most cases. The four WHO-defined preventable meningitis pathogens of interest (S pneumoniae, N meningitidis, Haemophilus influenzae, and Group B streptococcus) contributed to 98 700 deaths (77 000-127 000) and 594 000 cases (514 000-686 000). Low birthweight, short gestation, and household air pollution were the top risk factors for meningitis-related mortality. Although mortality and incidence have declined significantly since 1990, progress is insufficient to meet WHO 2030 targets. Despite marked progress in reducing bacterial meningitis via global vaccination campaigns, a substantial meningitis burden persists, attributable both to common pathogens such as S pneumoniae and N meningitidis and to emerging non-bacterial pathogens such as Candida spp and drug-resistant fungi. Achieving WHO goals will require sustained investment in surveillance, vaccination, maternal screening, and health-system strengthening, especially in high-burden settings. Gates Foundation, Wellcome Trust, and UK Department of Health and Social Care.