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Abstract Kombucha, historically an Asian tea-based fermented drink, has recently become trendy in Western countries. Producers claim it bears health-enhancing properties that may come from the tea or metabolites produced by its microbiome. Despite its long history of production, microbial richness and dynamics have not been fully unraveled, especially at an industrial scale. Moreover, the impact of tea type (green or black) on microbial ecology was not studied. Here, we compared microbial communities from industrial-scale black and green tea fermentations, still traditionally carried out by a microbial biofilm, using culture-dependent and metabarcoding approaches. Dominant bacterial species belonged to Acetobacteraceae and to a lesser extent Lactobacteriaceae, while the main identified yeasts corresponded to Dekkera, Hanseniaspora and Zygosaccharomyces during all fermentations. Species richness decreased over the 8-day fermentation. Among acetic acid bacteria, Gluconacetobacter europaeus, Gluconobacter oxydans, G. saccharivorans and Acetobacter peroxydans emerged as dominant species. The main lactic acid bacteria, Oenococcus oeni, was strongly associated with green tea fermentations. Tea type did not influence yeast community, with Dekkera bruxellensis, D. anomala, Zygosaccharomyces bailii and Hanseniaspora valbyensis as most dominant. This study unraveled a distinctive core microbial community which is essential for fermentation control and could lead to Kombucha quality standardization. Microbial ecology of industrial Kombucha fermentations.

Food spoilage is a major issue for the food industry, leading to food waste, substantial economic losses for manufacturers and consumers, and a negative impact on brand names. Among causes, fungal contamination can be encountered at various stages of the food chain (e.g., post-harvest, during processing or storage). Fungal development leads to food sensory defects varying from visual deterioration to noticeable odor, flavor, or texture changes but can also have negative health impacts via mycotoxin production by some molds. In order to avoid microbial spoilage and thus extend product shelf life, different treatments—including fungicides and chemical preservatives—are used. In parallel, public authorities encourage the food industry to limit the use of these chemical compounds and develop natural methods for food preservation. This is accompanied by a strong societal demand for ‘clean label’ food products, as consumers are looking for more natural, less severely processed and safer products. In this context, microbial agents corresponding to bioprotective cultures, fermentates, culture-free supernatant or purified molecules, exhibiting antifungal activities represent a growing interest as an alternative to chemical preservation. This review presents the main fungal spoilers encountered in food products, the antifungal microorganisms tested for food bioprotection, and their mechanisms of action. A focus is made in particular on the recent in situ studies and the constraints associated with the use of antifungal microbial agents for food biopreservation.

Food fraud, corresponding to any intentional action to deceive purchasers and gain an undue economical advantage, is estimated to result in a 10 to 65 billion US dollars/year economical cost worldwide. Dairy products, such as cheese, in particular cheeses with protected land- and tradition-related labels, have been listed as among the most impacted as consumers are ready to pay a premium price for traditional and typical products. In this context, efficient food authentication methods are needed to counteract current and emerging frauds. This review reports the available authentication methods, either chemical, physical, or DNA-based methods, currently used for origin authentication, highlighting their principle, reported application to cheese geographical origin authentication, performance, and respective advantages and limits. Isotope and elemental fingerprinting showed consistent accuracy in origin authentication. Other chemical and physical methods, such as near-infrared spectroscopy and nuclear magnetic resonance, require more studies and larger sampling to assess their discriminative power. Emerging DNA-based methods, such as metabarcoding, showed good potential for origin authentication. However, metagenomics, providing a more in-depth view of the cheese microbiota (up to the strain level), but also the combination of methods relying on different targets, can be of interest for this field.

Mycotoxins, produced by fungi, frequently occur at different stages in the food supply chain between pre- and postharvest. Globally produced cereal crops are known to be highly susceptible to contamination, thus constituting a major public health concern. Among the encountered mycotoxigenic fungi in cereals, Fusarium spp. are the most frequent and produce both regulated (i.e., T-2 toxin, deoxynivalenol -DON-, zearalenone -ZEA-) and emerging (i.e., enniatins -ENNs-, beauvericin -BEA-) mycotoxins. In this study, we investigated the in vitro cytotoxic effects of regulated and emerging fusariotoxins on HepaRG cells in 2D and 3D models using undifferentiated and differentiated cells. We also studied the impact of ENN B1 and ENN B exposure on gene expression of HepaRG spheroids. Gene expression profiling pinpointed the differentially expressed genes (DEGs) and overall similar pathways were involved in responses to mycotoxin exposure. Complement cascades, metabolism, steroid hormones, bile secretion, and cholesterol pathways were all negatively impacted by both ENNs. For cholesterol biosynthesis, 23/27 genes were significantly down-regulated and could be correlated to a 30% reduction in cholesterol levels. Our results show the impact of ENNs on the cholesterol biosynthesis pathway for the first time. This finding suggests a potential negative effect on human health due to the essential role this pathway plays.

Biopreservation using lactic acid bacteria has gained a growing interest as an alternative to chemical preservatives and/or as a complementary tool to prevent fungal spoilage in dairy products. Among the action mechanisms of antifungal LAB, competitionexclusion for trace elements has recently been highlighted. To further investigate this mechanism, two antifungal LAB strains, Lactiplantibacillus plantarum L244 and Lactobacillus rhamnosus CIRM-BIA1759, were studied in a yogurt model. Firstly, the antifungal activity of these strains against four main dairy spoilage fungi (Penicillium biforme, Mucor racemosus, Galactomyces geotrichum and Yarrowia lipolytica) was evaluated with or without trace element (6 metals and 12 vitamins) supplementation. Only manganese supplementation led to a suppression of the antifungal activity of both L. plantarum L244 and L. rhamnosus CIRM-BIA1759 against P. biforme and/or Y. lipolytica. The scavenging of trace elements was then measured using HR-ICP-MS in both cell-free yogurt whey and fungal biomass. HR-ICP-MS results showed a significant scavenging of Mn in L. plantarum L244 and L. rhamnosus CIRM-BIA1759 whey, as well as Cu for L. rhamnosus CIRM-BIA1759. Moreover, element uptake profiles, including metal and non-metal elements, for each of the target fungi were affected by the use of antifungal cultures. Finally, the role of competitionexclusion for manganese in the inhibition of 25 fungal spoilers was evaluated via oCelloScope growth follow-up. Growth inhibition by antifungal LAB strains was suppressed after Mn supplementation in cell-free whey for the 16 (out of 25) fungi initially inhibited without Mn supplementation. The nine other fungi were not inhibited or were poorly inhibited in the different tested conditions. This study confirmed the role of competitionexclusion for Mn in the antifungal activity of L. plantarum L244 and L. rhamnosus CIRM-BIA1759 strains but also revealed that this mechanism is not generic among fungal species, as the growth behavior of several tested species was not impacted by Mn scavenging.

Environmental pollution resulting from the accumulation of plastic waste poses a major ecological challenge. Biodegradation of these polymers relies on microorganisms capable of decomposing them, generally through the biodeterioration, biofragmentation, assimilation, and mineralization stages. This study evaluates the contribution and efficacy of indigenous soil yeasts isolated from a northeastern Algerian landfill in degrading low-density polyethylene (LDPE) plastic bag films. Candida tropicalis SLNEA04 and Rhodotorula mucilaginosa SLNEA05 were identified through internal transcribed spacer (ITS) and large subunit ribosomal RNA gene sequencing. These isolates were then tested for their ability to biodegrade LDPE films and utilized as the sole carbon source in vitro in a mineral salt medium (MSM). The biodegradation effect was examined using scanning electron microscopy (SEM), attenuated total reflectance–Fourier transform infrared (ATR-FTIR) spectroscopy, and X-ray diffraction (XRD). After 30 days of incubation at 25 °C, a significant weight loss was observed compared to the control for both cultures: 7.60% and 5.53% for C. tropicalis and R. mucilaginosa, respectively. SEM analysis revealed morphological alterations, including cracks and holes, ATR-FTIR detected new functional groups (alcohols, alkynes, aldehydes, alkenes and ketones), while XRD identified changes in the polymer crystallinity and phase composition. These findings underscore the potential of the two yeast isolates in LDPE biodegradation, offering promising insights for future environmental applications.

Abstract Domestication is an excellent case study for understanding adaptation and multiple fungal lineages have been domesticated for fermenting food products. Studying domestication in fungi has thus both fundamental and applied interest. Genomic studies have revealed the existence of four populations within the blue‐cheese‐making fungus Penicillium roqueforti . The two cheese populations show footprints of domestication, but the adaptation of the two non‐cheese populations to their ecological niches (i.e., silage/spoiled food and lumber/spoiled food) has not been investigated yet. Here, we reveal the existence of a new P. roqueforti population, specific to French Termignon cheeses, produced using small‐scale traditional practices, with spontaneous blue mould colonisation. This Termignon population is genetically differentiated from the four previously identified populations, providing a novel source of genetic diversity for cheese making. The Termignon population indeed displayed substantial genetic diversity, both mating types, horizontally transferred regions previously detected in the non‐Roquefort population, and intermediate phenotypes between cheese and non‐cheese populations. Phenotypically, the non‐Roquefort cheese population was the most differentiated, with specific traits beneficial for cheese making, in particular higher tolerance to salt, to acidic pH and to lactic acid. Our results support the view that this clonal population, used for many cheese types in multiple countries, is a domesticated lineage on which humans exerted strong selection. The lumber/spoiled food and silage/spoiled food populations were not more tolerant to crop fungicides but showed faster growth in various carbon sources (e.g., dextrose, pectin, sucrose, xylose and/or lactose), which can be beneficial in their ecological niches. Such contrasted phenotypes between P. roqueforti populations, with beneficial traits for cheese‐making in the cheese populations and enhanced ability to metabolise sugars in the lumber/spoiled food population, support the inference of domestication in cheese fungi and more generally of adaptation to anthropized environments.

Background Despite a growing number of investigations on early diverging fungi, the corresponding lineages have not been as extensively characterized as Ascomycota or Basidiomycota ones. The Mucor genus, pertaining to one of these lineages is not an exception. To this date, a restricted number of Mucor annotated genomes is publicly available and mainly correspond to the reference species, Mucor circinelloides, and to medically relevant species. However, the Mucor genus is composed of a large number of ubiquitous species as well as few species that have been reported to specifically occur in certain habitats. The present study aimed to expand the range of Mucor genomes available and identify potential genomic imprints of adaptation to different environments and lifestyles in the Mucor genus. Results In this study, we report four newly sequenced genomes of Mucor isolates collected from non-clinical environments pertaining to species with contrasted lifestyles, namely Mucor fuscus and Mucor lanceolatus , two species used in cheese production (during ripening), Mucor racemosus , a recurrent cheese spoiler sometimes described as an opportunistic animal and human pathogen, and Mucor endophyticus , a plant endophyte. Comparison of these new genomes with those previously available for six Mucor and two Rhizopus (formerly identified as M. racemosus ) isolates allowed global structural and functional description such as their TE content, core and species-specific genes and specialized genes. We proposed gene candidates involved in iron metabolism; some of these genes being known to be involved in pathogenicity; and described patterns such as a reduced number of CAZymes in the species used for cheese ripening as well as in the endophytic isolate that might be related to adaptation to different environments and lifestyles within the Mucor genus. Conclusions This study extended the descriptive data set for Mucor genomes, pointed out the complexity of obtaining a robust phylogeny even with multiple genes families and allowed identifying contrasting potentially lifestyle-associated gene repertoires. The obtained data will allow investigating further the link between genetic and its biological data, especially in terms of adaptation to a given habitat.

Fungi exhibit substantial morphological and genetic diversity, often associated with cryptic species differing in ecological niches. Penicillium roqueforti is used as a starter culture for blue-veined cheeses, being responsible for their flavor and color, but is also a common spoilage organism in various foods. Different types of blue-veined cheeses are manufactured and consumed worldwide, displaying specific organoleptic properties. These features may be due to the different manufacturing methods and/or to the specific P. roqueforti strains used. Substantial morphological diversity exists within P. roqueforti and, although not taxonomically valid, several technological names have been used for strains on different cheeses (e.g., P. gorgonzolae, P. stilton). A worldwide P. roqueforti collection from 120 individual blue-veined cheeses and 21 other substrates was analyzed here to determine (i) whether P. roqueforti is a complex of cryptic species, by applying the Genealogical Concordance Phylogenetic Species Recognition criterion (GC-PSR), (ii) whether the population structure assessed using microsatellite markers correspond to blue cheese types, and (iii) whether the genetic clusters display different morphologies. GC-PSR multi-locus sequence analyses showed no evidence of cryptic species. The population structure analysis using microsatellites revealed the existence of highly differentiated populations, corresponding to blue cheese types and with contrasted morphologies. This suggests that the population structure has been shaped by different cheese-making processes or that different populations were recruited for different cheese types. Cheese-making fungi thus constitute good models for studying fungal diversification under recent selection.

This study explores tomato agri-food residues as sources of bacteria with bioprotective potential to enhance product shelf-life and safety. A total of 245 bacterial strains were isolated, comprising predominantly Pseudomonas (52%) and Bacillus (44%) spp., with lactic acid bacteria (LAB) present at lower levels (4%). The antimicrobial activity of these isolates was assessed against pathogenic and spoilage bacteria and phytopathogenic molds. Notably, the Bacillus isolate TRB1-7 exhibited moderate activity against L. monocytogenes (inhibition halo diameter: 10.64 mm), while Pseudomonas and LAB isolates showed limited or no inhibition. Antifungal assays highlighted significant antifungal potential for Bacillus isolates. Results showed that 16% and 15% of the 245 isolates inhibited F. oxysporum and C. acutatum growth, respectively. Nine of these isolates underwent acid-adaptation and were evaluated against the selected molds using Potato Dextrose Agar (PDA) at pH 4.0 to simulate tomato conditions. Only isolate BRZ3-2, identified as B. aerius, was adapted to acidic conditions and inhibited F. oxysporum by 25%. Experiments on tomato-based agar at the same pH showed no inhibition by Bacillus isolates. These results suggest that tomato microbiota harbors acid-tolerant Bacillus strains with potential for post-harvest bio-preservation. Further studies on strains TRB1-7 and BRZ3-2 are required to develop effective bioprotective applications.