Berries are frequently implicated in outbreaks of foodborne illness due to viruses, particularly norovirus and hepatitis A virus. Compounds naturally present in berries can compromise the reliability of RT-qPCR methods, such as ISO 15216–1:2017, for detecting and quantifying viruses in foods. The aim of this study was to evaluate the inhibitory impact of seven phenolic compounds (ellagic acid, hydroxybenzoic acid, caffeic acid, coumaric acid, ferulic acid, quercetin, and cyanidine-3-glucoside) found naturally in raspberries as well as batch effects due to different concentrations of inhibitors (e.g., associated with ripeness) when using RT-qPCR to detect HAV in raspberries, blackberries, strawberries, blueberries, cranberries, and mixed berries. To assess the impact of dilution on RT-qPCR inhibition, samples were diluted at four levels (1/2, 1/5, 1/10, 1/100). Spiking the RT-qPCR reaction mixture with each phenolic compound at its natural concentration in raspberries showed that ellagic acid, hydroxybenzoic acid, caffeic acid and cyanidin-3-glucoside inhibited amplification, but only ellagic acid remained inhibitory in the ISO method. HAV recovery from frozen strawberries was undetectable (0 %) without additional treatment but reached 39 % with the OneStep PCR Inhibitor Removal Kit. For frozen blueberries, MobiSpin S-400 performed better, yielding about 52 % recovery compared to 23 % with OneStep. Sample dilution further enhanced HAV detection across most berry types.
{"title":"Impacts of phenolic compounds on RT-qPCR detection of hepatitis A virus in berries","authors":"Marie-Ève Collard , Éric Jubinville , Valérie Goulet-Beaulieu , Julie Jean","doi":"10.1016/j.fm.2025.105005","DOIUrl":"10.1016/j.fm.2025.105005","url":null,"abstract":"<div><div>Berries are frequently implicated in outbreaks of foodborne illness due to viruses, particularly norovirus and hepatitis A virus. Compounds naturally present in berries can compromise the reliability of RT-qPCR methods, such as ISO 15216–1:2017, for detecting and quantifying viruses in foods. The aim of this study was to evaluate the inhibitory impact of seven phenolic compounds (ellagic acid, hydroxybenzoic acid, caffeic acid, coumaric acid, ferulic acid, quercetin, and cyanidine-3-glucoside) found naturally in raspberries as well as batch effects due to different concentrations of inhibitors (e.g., associated with ripeness) when using RT-qPCR to detect HAV in raspberries, blackberries, strawberries, blueberries, cranberries, and mixed berries. To assess the impact of dilution on RT-qPCR inhibition, samples were diluted at four levels (1/2, 1/5, 1/10, 1/100). Spiking the RT-qPCR reaction mixture with each phenolic compound at its natural concentration in raspberries showed that ellagic acid, hydroxybenzoic acid, caffeic acid and cyanidin-3-glucoside inhibited amplification, but only ellagic acid remained inhibitory in the ISO method. HAV recovery from frozen strawberries was undetectable (0 %) without additional treatment but reached 39 % with the OneStep PCR Inhibitor Removal Kit. For frozen blueberries, MobiSpin S-400 performed better, yielding about 52 % recovery compared to 23 % with OneStep. Sample dilution further enhanced HAV detection across most berry types.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"136 ","pages":"Article 105005"},"PeriodicalIF":4.6,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145734845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-04DOI: 10.1016/j.fm.2025.105001
Yaling Wang , Linan He , Xing Hu , Yuhan Guan , Xiangnan Chen , Jiahui Du , Jiayan Chen , Chensheng Ma , Lianwei Ye
Bivalves are important aquaculture products whose safety is shaped by their microbiomes. Here, we present the first comprehensive characterization of Manila clam (Ruditapes philippinarum) microbiomes using both shotgun metagenomics (6 clams) and culture-based genomics (169 isolates, 40 draft genomes), integrating community, functional, and antimicrobial resistance profiling. Communities were dominated by Proteobacteria (99.3–99.9 %), with Pseudoalteromonas and Vibrio collectively accounting for 74.9–99.7 % and showing strong inverse correlations, defining Pseudoalteromonas-dominated, Vibrio-dominated, and mixed states. Species richness ranged from 22 to 180 per sample. Recognized human pathogens occurred at low abundance (<0.3 %), including Vibrio parahaemolyticus, Vibrio alginolyticus, and Photobacterium damselae, while opportunistic vibrios expanded in some clams (e.g., Vibrio cyclitrophicus 57.9 %). We reconstructed 34 high-quality MAGs, seven resolved to species (Pseudoalteromonas tetraodonis, V. cyclitrophicus, Shewanella aquimarina), alongside unclassified lineages. Metagenomes encoded 14 virulence-factor categories with 2281 subtypes, and isolate genomes added 93 further subtypes, including high-virulence loci in Escherichia coli and type III secretion genes in V. parahaemolyticus. Resistomes spanned 18 antibiotic classes with 511 subtypes; isolates contributed 22 additional antibiotic resistance genes(ARGs), including extended-spectrum β-lactamases (blaCTX-M-102) and blaNDM-1. Four carbapenemase-producing isolates (three Shewanella algae, one V. parahaemolyticus) carried blaNDM-1 on IncC plasmids, with the V. parahaemolyticus plasmid transferable to E. coli. Two P. tetraodonis MAGs encoded RiPP-like and terpene biosynthetic clusters plus phage-defense systems, consistent with Vibrio suppression. These findings demonstrate that clam microbiomes fluctuate between protective (Pseudoalteromonas) and pathogenic (Vibrio–Shewanella) states, providing a first integrated framework for assessing microbial risk, antimicrobial resistance, and food safety interventions in bivalve aquaculture.
{"title":"Metagenomic and culture-based genomics reveal virulence and resistance risks in Manila clam microbiomes","authors":"Yaling Wang , Linan He , Xing Hu , Yuhan Guan , Xiangnan Chen , Jiahui Du , Jiayan Chen , Chensheng Ma , Lianwei Ye","doi":"10.1016/j.fm.2025.105001","DOIUrl":"10.1016/j.fm.2025.105001","url":null,"abstract":"<div><div>Bivalves are important aquaculture products whose safety is shaped by their microbiomes. Here, we present the first comprehensive characterization of Manila clam (<em>Ruditapes philippinarum</em>) microbiomes using both shotgun metagenomics (6 clams) and culture-based genomics (169 isolates, 40 draft genomes), integrating community, functional, and antimicrobial resistance profiling. Communities were dominated by Proteobacteria (99.3–99.9 %), with <em>Pseudoalteromonas</em> and <em>Vibrio</em> collectively accounting for 74.9–99.7 % and showing strong inverse correlations, defining <em>Pseudoalteromonas</em>-dominated, <em>Vibrio</em>-dominated, and mixed states. Species richness ranged from 22 to 180 per sample. Recognized human pathogens occurred at low abundance (<0.3 %), including <em>Vibrio parahaemolyticus</em>, <em>Vibrio alginolyticus</em>, and <em>Photobacterium damselae</em>, while opportunistic vibrios expanded in some clams (e.g., <em>Vibrio cyclitrophicus</em> 57.9 %). We reconstructed 34 high-quality MAGs, seven resolved to species (<em>Pseudoalteromonas tetraodonis</em>, <em>V. cyclitrophicus</em>, <em>Shewanella aquimarina</em>), alongside unclassified lineages. Metagenomes encoded 14 virulence-factor categories with 2281 subtypes, and isolate genomes added 93 further subtypes, including high-virulence loci in <em>Escherichia coli</em> and type III secretion genes in <em>V. parahaemolyticus</em>. Resistomes spanned 18 antibiotic classes with 511 subtypes; isolates contributed 22 additional antibiotic resistance genes(ARGs), including extended-spectrum β-lactamases (<em>bla</em><sub>CTX-M-102</sub>) and <em>bla</em><sub>NDM-1</sub>. Four carbapenemase-producing isolates (three <em>Shewanella algae</em>, one <em>V. parahaemolyticus</em>) carried blaNDM-1 on IncC plasmids, with the <em>V. parahaemolyticus</em> plasmid transferable to <em>E. coli</em>. Two <em>P. tetraodonis</em> MAGs encoded RiPP-like and terpene biosynthetic clusters plus phage-defense systems, consistent with Vibrio suppression. These findings demonstrate that clam microbiomes fluctuate between protective (<em>Pseudoalteromonas</em>) and pathogenic (<em>Vibrio–Shewanella</em>) states, providing a first integrated framework for assessing microbial risk, antimicrobial resistance, and food safety interventions in bivalve aquaculture.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"136 ","pages":"Article 105001"},"PeriodicalIF":4.6,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145683502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-03DOI: 10.1016/j.fm.2025.105000
Qiya Yang , Xi Zhang , Duole Yin , Solairaj Dhanasekaran , Chenggong Liu , Xuewen Li , Hongyin Zhang
Red grapes are vulnerable to postharvest infections caused by Aspergillus niger and Botrytis cinerea due to their delicate skin and rich nutrient content. This study examined the effectiveness of A. pullulans S2 in managing postharvest black mold and gray mold on red grapes. Results demonstrated that A. pullulans S2 significantly reduced both the incidence and severity of disease while enhancing the activity of enzymes related to defense and the accumulation of antioxidant compounds. Additionally, 2-Phenylethanol generated by A. pullulans S2 exhibited strong antifungal properties by disrupting the cell membrane integrity and promoting reactive oxygen species accumulation in pathogens. Furthermore, a lyophilized formulation of A. pullulans S2 was developed using an optimized protective agent combination via response surface methodology. This resulted in a high post-lyophilization survival rate of 85.2 % and significant biocontrol efficacy after 90 days of storage. These results underscore the potential of A. pullulans S2 as a potent biocontrol agent for postharvest grape diseases.
{"title":"Mechanisms and formulation of Aureobasidium pullulans S2 for effective management of black and gray mold in red grapes","authors":"Qiya Yang , Xi Zhang , Duole Yin , Solairaj Dhanasekaran , Chenggong Liu , Xuewen Li , Hongyin Zhang","doi":"10.1016/j.fm.2025.105000","DOIUrl":"10.1016/j.fm.2025.105000","url":null,"abstract":"<div><div>Red grapes are vulnerable to postharvest infections caused by <em>Aspergillus niger</em> and <em>Botrytis cinerea</em> due to their delicate skin and rich nutrient content. This study examined the effectiveness of <em>A. pullulans</em> S2 in managing postharvest black mold and gray mold on red grapes. Results demonstrated that <em>A. pullulans</em> S2 significantly reduced both the incidence and severity of disease while enhancing the activity of enzymes related to defense and the accumulation of antioxidant compounds. Additionally, 2-Phenylethanol generated by <em>A. pullulans</em> S2 exhibited strong antifungal properties by disrupting the cell membrane integrity and promoting reactive oxygen species accumulation in pathogens. Furthermore, a lyophilized formulation of <em>A. pullulans</em> S2 was developed using an optimized protective agent combination via response surface methodology. This resulted in a high post-lyophilization survival rate of 85.2 % and significant biocontrol efficacy after 90 days of storage. These results underscore the potential of <em>A. pullulans</em> S2 as a potent biocontrol agent for postharvest grape diseases.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"136 ","pages":"Article 105000"},"PeriodicalIF":4.6,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145659057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-03DOI: 10.1016/j.fm.2025.104989
Hui Zhang , Meiyue Han , Zemin Pang , Weiwei Li , Xiuting Li , Baoguo Sun
Lactic acid stress is common in traditional fermented foods. Pichia kudriavzevii owes its industrial prevalence to its superior acid tolerance, making deciphering its response mechanism imperative for sustainable fermentation processes. This work explored the remarkable acid tolerance of P. kudriavzevii, which can tolerate 80 g/L lactic acid. The key lactic acid tolerance gene lldD of P. kudriavzevii was determined through transcriptomic analysis. Importantly, this work knocked out the key gene lldD related to lactic acid tolerance for the first time by using the CRISPR-Cas9 technology. Meanwhile, the lldD knockout strain (pk-ΔlldD) was successfully constructed. There were significant differences between pk-ΔlldD and P. kudriavzevii in terms of tolerance to lactic acid, metabolism of lactic acid, utilization of glucose and ethanol production. In addition, the deletion of the gene lldD has a significant impact on the ABC transporter and metabolites of the amino acid metabolic pathway in P. kudriavzevii. In conclusion, this work provides a theoretical basis for engineering high acid-tolerant industrial yeast strains through targeted genetic modification. It helps enhance the stability of fermentation processes under lactic acid stress and ultimately lays a foundation for promoting efficient and low-loss production in the fermentation industry.
{"title":"The lldD lactate dehydrogenase is a determinant of lactic acid tolerance in Pichia kudriavzevii by pyruvate metabolism pathway","authors":"Hui Zhang , Meiyue Han , Zemin Pang , Weiwei Li , Xiuting Li , Baoguo Sun","doi":"10.1016/j.fm.2025.104989","DOIUrl":"10.1016/j.fm.2025.104989","url":null,"abstract":"<div><div>Lactic acid stress is common in traditional fermented foods. <em>Pichia kudriavzevii</em> owes its industrial prevalence to its superior acid tolerance, making deciphering its response mechanism imperative for sustainable fermentation processes. This work explored the remarkable acid tolerance of <em>P. kudriavzevii</em>, which can tolerate 80 g/L lactic acid. The key lactic acid tolerance gene <em>lldD</em> of <em>P. kudriavzevii</em> was determined through transcriptomic analysis. Importantly, this work knocked out the key gene <em>lldD</em> related to lactic acid tolerance for the first time by using the CRISPR-Cas9 technology. Meanwhile, the <em>lldD</em> knockout strain (pk-Δ<em>lldD</em>) was successfully constructed. There were significant differences between pk-Δ<em>lldD</em> and <em>P. kudriavzevii</em> in terms of tolerance to lactic acid, metabolism of lactic acid, utilization of glucose and ethanol production. In addition, the deletion of the gene <em>lldD</em> has a significant impact on the ABC transporter and metabolites of the amino acid metabolic pathway in <em>P. kudriavzevii</em>. In conclusion, this work provides a theoretical basis for engineering high acid-tolerant industrial yeast strains through targeted genetic modification. It helps enhance the stability of fermentation processes under lactic acid stress and ultimately lays a foundation for promoting efficient and low-loss production in the fermentation industry.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"136 ","pages":"Article 104989"},"PeriodicalIF":4.6,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145683501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
With rising interest in legume-based fermented products, traditional legume fermentation practices are gaining renewed attention. One such example is Kaak, a traditional Lebanese baked product made using naturally fermented chickpea-soaked water. This study presents the first comprehensive analysis of Kaak production and microbial species diversity. Despite practices variations among bakers, five key steps were consistently identified: chickpea-soaked water fermentation, preparation of two starters, dough preparation and baking. Fungal species diversity, analyzed using Illumina Miseq ITS1 sequencing, revealed high variation in fungal species composition of chickpea-soaked water (W) between bakeries, with dominance of Saccharomyces cerevisiae in some samples. In contrast, the fermented starters (F1 and F2) and the dough (D) consistently included Alternaria species and S. cerevisiae. Bacterial species analysis, using 16S rDNA V3-V4 sequencing, revealed a dominance of Weissella species in some dough samples while Clostridium perfringens was consistently the most abundant bacterial species in chickpea-soaked water and throughout the process. This species seems to have a major contribution to the organoleptic properties of traditional Kaak made with chickpea-soaked water as evidenced by descriptive quantitative sensory analysis that revealed unique distinctive features of traditional Kaak, pertaining to aroma, taste and texture in comparison to Kaak made with commercial S. cerevisiae strains without chickpea-soaked water. Altogether, these findings reveal, for the first time, the unique sensorial profile of traditional Kaak associated with its specific microbial diversity and traditional production. These findings contribute to a deeper understanding of traditional legume-based fermentation and highlight the value of preserving artisanal practices.
{"title":"From process to flavor: Microbial and sensory characterization of traditional Kaak and its artisanal production methods","authors":"Rachelle Alhosry , Lucie Arnould , Olivier Rué , Rosette Daoud , Pierre Abi Nakhoul , Delphine Sicard , Marie-José Ayoub","doi":"10.1016/j.fm.2025.104999","DOIUrl":"10.1016/j.fm.2025.104999","url":null,"abstract":"<div><div>With rising interest in legume-based fermented products, traditional legume fermentation practices are gaining renewed attention. One such example is Kaak, a traditional Lebanese baked product made using naturally fermented chickpea-soaked water. This study presents the first comprehensive analysis of Kaak production and microbial species diversity. Despite practices variations among bakers, five key steps were consistently identified: chickpea-soaked water fermentation, preparation of two starters, dough preparation and baking. Fungal species diversity, analyzed using Illumina Miseq ITS1 sequencing, revealed high variation in fungal species composition of chickpea-soaked water (W) between bakeries, with dominance of <em>Saccharomyces cerevisiae</em> in some samples. In contrast, the fermented starters (F1 and F2) and the dough (D) consistently included <em>Alternaria</em> species and <em>S. cerevisiae.</em> Bacterial species analysis, using 16S rDNA V3-V4 sequencing, revealed a dominance of <em>Weissella</em> species in some dough samples while <em>Clostridium perfringens</em> was consistently the most abundant bacterial species in chickpea-soaked water and throughout the process. This species seems to have a major contribution to the organoleptic properties of traditional Kaak made with chickpea-soaked water as evidenced by descriptive quantitative sensory analysis that revealed unique distinctive features of traditional Kaak, pertaining to aroma, taste and texture in comparison to Kaak made with commercial <em>S. cerevisiae</em> strains without chickpea-soaked water. Altogether, these findings reveal, for the first time, the unique sensorial profile of traditional Kaak associated with its specific microbial diversity and traditional production. These findings contribute to a deeper understanding of traditional legume-based fermentation and highlight the value of preserving artisanal practices.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"136 ","pages":"Article 104999"},"PeriodicalIF":4.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145787739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Food-borne diseases caused by pathogens are a global public health concern. The positive detection rate (%) and arithmetic mean of seven pathogens in common foods were collected by the China National Foodborne Diseases Surveillance Network from 2019 to 2023, and the number of cases and population incidence were calculated by combining the pathogen concentration and food consumption data of 10,753 people in 20 townships in Zhejiang Province using a swift quantitative risk assessment model. The estimated case number was 1,504,937, and the incidence rate was 0.03 episodes per person-year. The pathogen-food product combinations with the highest number of cases were Vibrio parahemolyticus-marine fish, Staphylococcus aureus-cooked meat products, and Vibrio parahemolyticus-marine shellfish. Marine fish, Chinese salads, and cooked meat products were the top three high-risk food types. Vibrio parahemolyticus, Staphylococcus aureus, and Bacillus cereus were the dominant pathogens. Multi-criteria decision analysis (MCDA) method presented more informative pathogen-food combinations ranking compared to the sQMRA model. Vibrio parahaemolyticusaureus-marine fishes, Vibrio parahaemolyticusaureus-fresh water products, and Vibrio parahaemolyticusaureus-marine shellfish were ranked as the top combinations. These results demonstrate that there should be a greater focus on improving the active surveillance system and quantitative risk assessment methods of related food-pathogen combinations in formulating scientific public health policy.
{"title":"Swift quantitative risk assessment and multi-criteria decision analysis on main food-borne pathogens in market food in Zhejiang Province, China","authors":"Yue He , Yunjiao Zhu , Hexiang Zhang , Jiang Chen , Bing Zhu , Jikai Wang , Ronghua Zhang , Lili Chen , Xiaojuan Qi , Junyan Zhang","doi":"10.1016/j.fm.2025.104988","DOIUrl":"10.1016/j.fm.2025.104988","url":null,"abstract":"<div><div>Food-borne diseases caused by pathogens are a global public health concern. The positive detection rate (%) and arithmetic mean of seven pathogens in common foods were collected by the China National Foodborne Diseases Surveillance Network from 2019 to 2023, and the number of cases and population incidence were calculated by combining the pathogen concentration and food consumption data of 10,753 people in 20 townships in Zhejiang Province using a swift quantitative risk assessment model. The estimated case number was 1,504,937, and the incidence rate was 0.03 episodes per person-year. The pathogen-food product combinations with the highest number of cases were <em>Vibrio parahemolyticus</em>-marine fish, <em>Staphylococcus aureus</em>-cooked meat products, and <em>Vibrio parahemolyticus</em>-marine shellfish. Marine fish, Chinese salads, and cooked meat products were the top three high-risk food types. <em>Vibrio parahemolyticus</em>, <em>Staphylococcus aureus</em>, and <em>Bacillus cereus</em> were the dominant pathogens. Multi-criteria decision analysis (MCDA) method presented more informative pathogen-food combinations ranking compared to the sQMRA model. <em>Vibrio parahaemolyticusaureus</em>-marine fishes, <em>Vibrio parahaemolyticusaureus</em>-fresh water products, and <em>Vibrio parahaemolyticusaureus</em>-marine shellfish were ranked as the top combinations. These results demonstrate that there should be a greater focus on improving the active surveillance system and quantitative risk assessment methods of related food-pathogen combinations in formulating scientific public health policy.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"136 ","pages":"Article 104988"},"PeriodicalIF":4.6,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145659064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-25DOI: 10.1016/j.fm.2025.104987
Yuzhu Zhao , Dingyi Wang , Kangjie Lou , Kai Hu , Ling He , Kan Shi , Shuwen Liu , Hongyu Zhao
Previous studies have demonstrated that non-Saccharomyces yeasts can enhance malolactic fermentation (MLF) efficiency during co-fermentation. However, the underlying mechanisms remain unclear. Here, we demonstrate how specific strains create favorable metabolic niches through tripartite fermentation assays involving 16 strains from 8 species co-cultured with Saccharomyces cerevisiae F5 and Oenococcus oeni SD-2a, Hanseniaspora spp. emerged as optimal partners, reducing MLF duration by 50 % (≤48 h vs. 96 h in controls) while increasing O. oeni biomass by > 10-fold. Metabolomic analysis revealed that O. oeni utilizes malate as a carbon source within an ecological niche shaped by yeast-driven sugar competition, while upregulated nicotinamide metabolism enhanced NAD+ regeneration, boosting malolactic enzyme activity. Furthermore, strain-specific peptide secretion provided targeted bacterial support: H. osmophila NX39 produced quorum-sensing peptides and fumarate to activate bacterial pathways, whereas H. uvarum HN2 synthesized nutritional peptides and arabitol to alleviate auxotrophy. Exogenous amino acids (Glu/Trp/Cys) further enhanced MLF efficiency, with glutamate specifically accelerating early O. oeni growth while maintaining S. cerevisiae viability (stable at 108 CFU/mL). These findings transform co-inoculation from a high-risk practice into a robust enological strategy by establishing triple-strain simultaneous alcoholic-malolactic fermentation systems, providing a foundation for next-generation precision enology.
{"title":"Hanseniaspora species can create a privileged niche for Oenococcus oeni during triple-strain simultaneous alcoholic-malolactic fermentation based on metabolomics analysis","authors":"Yuzhu Zhao , Dingyi Wang , Kangjie Lou , Kai Hu , Ling He , Kan Shi , Shuwen Liu , Hongyu Zhao","doi":"10.1016/j.fm.2025.104987","DOIUrl":"10.1016/j.fm.2025.104987","url":null,"abstract":"<div><div>Previous studies have demonstrated that non-<em>Saccharomyces</em> yeasts can enhance malolactic fermentation (MLF) efficiency during co-fermentation. However, the underlying mechanisms remain unclear. Here, we demonstrate how specific strains create favorable metabolic niches through tripartite fermentation assays involving 16 strains from 8 species co-cultured with <em>Saccharomyces cerevisiae</em> F5 and <em>Oenococcus oeni</em> SD-2a, <em>Hanseniaspora</em> spp. emerged as optimal partners, reducing MLF duration by 50 % (≤48 h vs. 96 h in controls) while increasing <em>O. oeni</em> biomass by > 10-fold. Metabolomic analysis revealed that <em>O. oeni</em> utilizes malate as a carbon source within an ecological niche shaped by yeast-driven sugar competition, while upregulated nicotinamide metabolism enhanced NAD<sup>+</sup> regeneration, boosting malolactic enzyme activity. Furthermore, strain-specific peptide secretion provided targeted bacterial support: <em>H. osmophila</em> NX39 produced quorum-sensing peptides and fumarate to activate bacterial pathways, whereas <em>H. uvarum</em> HN2 synthesized nutritional peptides and arabitol to alleviate auxotrophy. Exogenous amino acids (Glu/Trp/Cys) further enhanced MLF efficiency, with glutamate specifically accelerating early <em>O. oeni</em> growth while maintaining <em>S. cerevisiae</em> viability (stable at 10<sup>8</sup> CFU/mL). These findings transform co-inoculation from a high-risk practice into a robust enological strategy by establishing triple-strain simultaneous alcoholic-malolactic fermentation systems, providing a foundation for next-generation precision enology.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"135 ","pages":"Article 104987"},"PeriodicalIF":4.6,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145620313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-22DOI: 10.1016/j.fm.2025.104985
Haiying Chen, Mengyao Yang, Tao Wang, Min Zhou, Lingjun Wei
This study pioneered an integrated investigation of superheated steam (SHS) sterilization by quantifying kinetics and unraveling dual-action mechanisms against foodborne pathogens (Salmonella Typhimurium, Listeria monocytogenes and Staphylococcus aureus) on pork belly surfaces. Sterilization kinetics of SHS with different treatment temperature (160–200 °C) and flow rates (20–30 kg h−1) during 60 s were modeled using Weibull and Logistic equations. Comparatively, the Logistic equation was rigorously validated as superior (R2 ≥ 0.998, RMSE ≤ 0.097, Af ≤ 1.183), enabling precise prediction of microbial inactivation dynamics. Kinetic analysis revealed a novel biphasic pattern: rapid pathogen reduction (≤20 s) followed by a distinct tailing phase (20–60 s), challenging conventional single-phase sterilization assumptions. Mechanistically, SHS induced immediate disruption of cell wall/membrane integrity, evidenced by a decline from 2.07 to 2.25 to 0.52–0.75 King units·(100 mL)−1 in AKP activity, an increase from 2.88 to 2.98 to 3.93–4.18 mS cm−1 in conductivity, and concurrent surges in nucleic acid/protein leakage within 20 s. Critically, ATPase activity plummeted 68–77 %, from 3.46 to 3.53 to 0.8–1.1 U·mg prot−1, directly linking membrane destabilization to energy metabolism collapse. These findings established SHS as a multi-modal intervention, synergizing thermal inactivation with targeted biochemical disruption of microbial homeostasis (cellular ion balance disruption, material exchange, and ATPase activity interference). By providing mechanistic insights and predictive modeling tools, this research validated SHS as a scalable, eco-friendly alternative to chemical sanitizers, reducing antimicrobial resistance risks and environmental footprint in meat processing.
{"title":"Superheated steam sterilization of foodborne pathogens on pork belly: Biphasic kinetics, dual-action mechanisms, and logistic model validation","authors":"Haiying Chen, Mengyao Yang, Tao Wang, Min Zhou, Lingjun Wei","doi":"10.1016/j.fm.2025.104985","DOIUrl":"10.1016/j.fm.2025.104985","url":null,"abstract":"<div><div>This study pioneered an integrated investigation of superheated steam (SHS) sterilization by quantifying kinetics and unraveling dual-action mechanisms against foodborne pathogens (<em>Salmonella</em> Typhimurium, <em>Listeria monocytogenes</em> and <em>Staphylococcus aureus</em>) on pork belly surfaces. Sterilization kinetics of SHS with different treatment temperature (160–200 °C) and flow rates (20–30 kg h<sup>−1</sup>) during 60 s were modeled using Weibull and Logistic equations. Comparatively, the Logistic equation was rigorously validated as superior (<em>R</em><sup><em>2</em></sup> ≥ 0.998, <em>RMSE</em> ≤ 0.097, <em>Af</em> ≤ 1.183), enabling precise prediction of microbial inactivation dynamics. Kinetic analysis revealed a novel biphasic pattern: rapid pathogen reduction (≤20 s) followed by a distinct tailing phase (20–60 s), challenging conventional single-phase sterilization assumptions. Mechanistically, SHS induced immediate disruption of cell wall/membrane integrity, evidenced by a decline from 2.07 to 2.25 to 0.52–0.75 King units·(100 mL)<sup>−1</sup> in AKP activity, an increase from 2.88 to 2.98 to 3.93–4.18 mS cm<sup>−1</sup> in conductivity, and concurrent surges in nucleic acid/protein leakage within 20 s. Critically, ATPase activity plummeted 68–77 %, from 3.46 to 3.53 to 0.8–1.1 U·mg prot<sup>−1</sup>, directly linking membrane destabilization to energy metabolism collapse. These findings established SHS as a multi-modal intervention, synergizing thermal inactivation with targeted biochemical disruption of microbial homeostasis (cellular ion balance disruption, material exchange, and ATPase activity interference). By providing mechanistic insights and predictive modeling tools, this research validated SHS as a scalable, eco-friendly alternative to chemical sanitizers, reducing antimicrobial resistance risks and environmental footprint in meat processing.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"135 ","pages":"Article 104985"},"PeriodicalIF":4.6,"publicationDate":"2025-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145620315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-11-22DOI: 10.1016/j.fm.2025.104986
Zhihua Li , Chi Zhao , Zhenyu Mao , Lingyan Zhao , Petri Penttinen , Suyi Zhang
Fermented red peppers (FRPs) provide distinct flavor and possible health benefits, but understanding of their microbial functions, viral diversity, pathogenicity, and horizontal gene transfer (HGT) patterns remains limited. Integrated multi-method analysis revealed FRP's bacterial community was dominated by Bacillus (21.52 %), Lactobacillus sensu lato (14.27 %), and Pantoea (13.60 %). Bacillus drove core fermentation with an over 40 % contribution to carbon degradation and iron reduction. The virome was dominated by Caudoviricetes phages, yet 25.5 % of the functions of viral genes remained unknown. Critically, multidrug resistance genes were the most abundant ARGs, and beneficial bacteria served as major reservoirs for ARGs, co-occurring with potential opportunistic pathogens. Despite inhibitory conditions, these last dominated key metabolic nodes hydrogen generation and acetate oxidation. Counterintuitively, ARG profiles correlated with bacterial composition but not with mobile genetic elements or detected HGT events, challenging HGT as the primary ARG driver. These findings necessitate dual strategies: leveraging key microbes for fermentation efficiency while implementing stringent monitoring to mitigate pathogen and ARG related risks.
{"title":"Metagenomics insights into bacterial community, viral diversity and community-scale functions in fermented red pepper","authors":"Zhihua Li , Chi Zhao , Zhenyu Mao , Lingyan Zhao , Petri Penttinen , Suyi Zhang","doi":"10.1016/j.fm.2025.104986","DOIUrl":"10.1016/j.fm.2025.104986","url":null,"abstract":"<div><div>Fermented red peppers (FRPs) provide distinct flavor and possible health benefits, but understanding of their microbial functions, viral diversity, pathogenicity, and horizontal gene transfer (HGT) patterns remains limited. Integrated multi-method analysis revealed FRP's bacterial community was dominated by <em>Bacillus</em> (21.52 %), <em>Lactobacillus sensu lato</em> (14.27 %), and <em>Pantoea</em> (13.60 %). <em>Bacillus</em> drove core fermentation with an over 40 % contribution to carbon degradation and iron reduction. The virome was dominated by Caudoviricetes phages, yet 25.5 % of the functions of viral genes remained unknown. Critically, multidrug resistance genes were the most abundant ARGs, and beneficial bacteria served as major reservoirs for ARGs, co-occurring with potential opportunistic pathogens. Despite inhibitory conditions, these last dominated key metabolic nodes hydrogen generation and acetate oxidation. Counterintuitively, ARG profiles correlated with bacterial composition but not with mobile genetic elements or detected HGT events, challenging HGT as the primary ARG driver. These findings necessitate dual strategies: leveraging key microbes for fermentation efficiency while implementing stringent monitoring to mitigate pathogen and ARG related risks.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"135 ","pages":"Article 104986"},"PeriodicalIF":4.6,"publicationDate":"2025-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145620314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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