Pub Date : 2025-10-04DOI: 10.1016/j.fm.2025.104946
Mengjiao Yuan , Tong Lu , Hongxia Zhang , Jiali Wang , Meilin Cui , Wei Zhao , Yanfang Wu , Xiaozhuang Ren , Pengbo Yao , Xiuhong Zhang
Thermoascus aurantiacus is a dominant microorganism in diverse high-temperature Daqu samples, and even in low-temperature Daqu. However, its role in producing ester-based aromatic compounds remains incompletely understood. This study employed multi-omics approaches to characterize the esters-producing capacity of T. aurantiacus QH-1 derived from low-temperature Daqu used for light-flavor Baijiu brewing. Genome sequencing uncovered 58 genes encoding enzymes involved in esters metabolism, while only 23 ester-metabolizing enzymes were identified with proteomics analysis. When the fungal cultures of T. aurantiacus QH-1 at 40 °C, 45 °C, and 50 °C were analyzed by metabolomics approach, respectively, a total of 56 kinds of volatile esters flavor compounds were detected, including 24 ethyl esters which are key contributors to Baijiu flavor. Ethyl acetate, the most important aroma ingredient in light-flavor Baijiu, was the most abundant ester across all temperature conditions. Enzymatic properties of the crude esterase from T. aurantiacus QH-1 revealed the optimal condition was at 50 °C and pH 5, with acetic acid significantly enhanced enzymatic activity. These results indicated that T. aurantiacus QH-1 could produce lots of esters flavor compounds, established it as a primary functional microorganism responsible for imparting aromatic compounds for Daqu.
{"title":"Verification of the esters-producing properties of Thermoascus aurantiacus QH-1 derived from low-temperature Daqu by multiomics","authors":"Mengjiao Yuan , Tong Lu , Hongxia Zhang , Jiali Wang , Meilin Cui , Wei Zhao , Yanfang Wu , Xiaozhuang Ren , Pengbo Yao , Xiuhong Zhang","doi":"10.1016/j.fm.2025.104946","DOIUrl":"10.1016/j.fm.2025.104946","url":null,"abstract":"<div><div><em>Thermoascus aurantiacus</em> is a dominant microorganism in diverse high-temperature Daqu samples, and even in low-temperature Daqu. However, its role in producing ester-based aromatic compounds remains incompletely understood. This study employed multi-omics approaches to characterize the esters-producing capacity of <em>T</em>. <em>aurantiacus</em> QH-1 derived from low-temperature Daqu used for light-flavor Baijiu brewing. Genome sequencing uncovered 58 genes encoding enzymes involved in esters metabolism, while only 23 ester-metabolizing enzymes were identified with proteomics analysis. When the fungal cultures of <em>T</em>. <em>aurantiacus</em> QH-1 at 40 °C, 45 °C, and 50 °C were analyzed by metabolomics approach, respectively, a total of 56 kinds of volatile esters flavor compounds were detected, including 24 ethyl esters which are key contributors to Baijiu flavor. Ethyl acetate, the most important aroma ingredient in light-flavor Baijiu, was the most abundant ester across all temperature conditions. Enzymatic properties of the crude esterase from <em>T. aurantiacus</em> QH-1 revealed the optimal condition was at 50 °C and pH 5, with acetic acid significantly enhanced enzymatic activity. These results indicated that <em>T</em>. <em>aurantiacus</em> QH-1 could produce lots of esters flavor compounds, established it as a primary functional microorganism responsible for imparting aromatic compounds for Daqu.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"134 ","pages":"Article 104946"},"PeriodicalIF":4.6,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145265614","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 : 2025-10-01DOI: 10.1016/j.fm.2025.104941
Linyun Chen , María Isabel Almeida , Lotta Kuuliala , Christophe Walgraeve , Kristof Demeestere , Frank Devlieghere
Pork is highly susceptible to microbial spoilage. The growth and metabolism of spoilage bacteria cause the formation of malodorous volatile organic compounds (VOCs), leading to sensory decline. Even though the atmosphere is a well-known extrinsic factor affecting microbial growth, the fundamental impact of bulk gas ratios on VOC production still needs to be further elaborated. The present research focuses on Pseudomonas fragi, one of the most dominant spoilage microbes in packaged meat, by studying its behavior as influenced by atmospheres. Solid pork simulation media inoculated with a pure meat-derived P. fragi strain were stored under four conditions with different bulk gas ratios (v/v% : air, 0/0/100, 20/20/60, 20/40/40). For each atmosphere, characteristic microbial VOCs were identified by combining online and offline chemical analytical tools, namely selected-ion flow-tube mass spectrometry (SIFT-MS) and thermal-desorption gas chromatography mass spectrometry (TD-GC-MS). In total, fourteen compounds were linked to the investigated P. fragi strain, including methyl acetate, ethyl acetate, methyl mercaptan, and dimethyl sulfide. Despite slower microbial growth under 0/0/100 and 20/20/60 when compared to air, anaerobic metabolites including sulfur-containing compounds and ethyl acetate were produced in high quantities at a lower microbial level. On the contrary, 40% largely limited bacterial counts and VOCs. Overall, comprehensive volatolome analysis provides informative insights into the P. fragi metabolism and its relation with the atmosphere, thus improving the understanding of meat spoilage mechanisms.
{"title":"Volatolomics reveals the influence of O2/CO2 on the growth of Pseudomonas fragi and its volatile metabolites on meat substrates","authors":"Linyun Chen , María Isabel Almeida , Lotta Kuuliala , Christophe Walgraeve , Kristof Demeestere , Frank Devlieghere","doi":"10.1016/j.fm.2025.104941","DOIUrl":"10.1016/j.fm.2025.104941","url":null,"abstract":"<div><div>Pork is highly susceptible to microbial spoilage. The growth and metabolism of spoilage bacteria cause the formation of malodorous volatile organic compounds (VOCs), leading to sensory decline. Even though the atmosphere is a well-known extrinsic factor affecting microbial growth, the fundamental impact of bulk gas ratios on VOC production still needs to be further elaborated. The present research focuses on <em>Pseudomonas fragi</em>, one of the most dominant spoilage microbes in packaged meat, by studying its behavior as influenced by atmospheres. Solid pork simulation media inoculated with a pure meat-derived <em>P. fragi</em> strain were stored under four conditions with different bulk gas ratios (v/v% <span><math><mrow><msub><mrow><mi>O</mi></mrow><mrow><mn>2</mn></mrow></msub><mo>/</mo><msub><mrow><mi>CO</mi></mrow><mrow><mn>2</mn></mrow></msub><mo>/</mo><msub><mrow><mi>N</mi></mrow><mrow><mn>2</mn></mrow></msub></mrow></math></span>: air, 0/0/100, 20/20/60, 20/40/40). For each atmosphere, characteristic microbial VOCs were identified by combining online and offline chemical analytical tools, namely selected-ion flow-tube mass spectrometry (SIFT-MS) and thermal-desorption gas chromatography mass spectrometry (TD-GC-MS). In total, fourteen compounds were linked to the investigated <em>P. fragi</em> strain, including methyl acetate, ethyl acetate, methyl mercaptan, and dimethyl sulfide. Despite slower microbial growth under 0/0/100 and 20/20/60 when compared to air, anaerobic metabolites including sulfur-containing compounds and ethyl acetate were produced in high quantities at a lower microbial level. On the contrary, 40% <span><math><msub><mrow><mi>CO</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span> largely limited bacterial counts and VOCs. Overall, comprehensive volatolome analysis provides informative insights into the <em>P. fragi</em> metabolism and its relation with the atmosphere, thus improving the understanding of meat spoilage mechanisms.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"134 ","pages":"Article 104941"},"PeriodicalIF":4.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145216580","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 : 2025-09-27DOI: 10.1016/j.fm.2025.104943
Qili Liu , Xiaobin Xu , Yangyang Yang , Xiao Li , Pengfei Sun , Pengdong Xie , Yuanyuan Zong , Huali Xue , Yang Bi
Trichothecium roseum, the causative agent of core rot of apple fruit, is one of the most important postharvest pathogenic fungi. In addition to quality degradation and economic influence, apple fruits infected by T. roseum can metabolize trichothecene that pose a potential threat to human health. VeA is a pivotal regulator of growth, development, pathogenicity and secondary metabolism for fungi. However, the function and regulatory mechanism of TrveA in T. roseum infecting apple are still unclear. In this study, the TrveA mutant was constructed by Split-marker PCR technology, and the effects of TrveA on the pathogenicity and toxin accumulation of T. roseum infecting apple and tomato were analyzed. The regulation of spore formation, oxidative stress tolerance, reactive oxygen species (ROS) metabolism and T-2 toxin biosynthesis was explored to elucidate the potential mechanism of TrveA regulating the pathogenicity of T. roseum. The results suggested that the deletion of TrveA inhibited the growth and development of the mutant, down-regulated the expression of key regulatory genes fluG, flbA, abaA and wetA in the sporulation pathway, and interfered with trehalose biosynthesis, resulting in a decrease in sporulation. TrveA deletion reduced the level of ROS accumulation and weakened the capacity of ROS scavenging, which cut down its tolerance to oxidative stress. At the same time, the expression of key genes tri6, tri5 and tri4 involved in the T-2 toxin biosynthesis pathway was down-regulated to inhibit the biosynthesis of T-2 toxin, which eventually led to the decrease of pathogenicity to apple and tomato. This study reveals the important role of TrveA in T. roseum infecting apple fruits, which is conductive to better elucidate the regulatory mechanism of TrveA. These results will provide potential precise targets for curbing apple postharvest diseases caused by T. roseum.
{"title":"TrveA affects the pathogenicity to apples by regulating the sporulation, reactive oxygen species and trichothecenes metabolic pathways in Trichothecium roseum","authors":"Qili Liu , Xiaobin Xu , Yangyang Yang , Xiao Li , Pengfei Sun , Pengdong Xie , Yuanyuan Zong , Huali Xue , Yang Bi","doi":"10.1016/j.fm.2025.104943","DOIUrl":"10.1016/j.fm.2025.104943","url":null,"abstract":"<div><div><em>Trichothecium roseum</em>, the causative agent of core rot of apple fruit, is one of the most important postharvest pathogenic fungi. In addition to quality degradation and economic influence, apple fruits infected by <em>T</em>. <em>roseum</em> can metabolize trichothecene that pose a potential threat to human health. <em>VeA</em> is a pivotal regulator of growth, development, pathogenicity and secondary metabolism for fungi. However, the function and regulatory mechanism of <em>TrveA</em> in <em>T. roseum</em> infecting apple are still unclear. In this study, the <em>TrveA</em> mutant was constructed by Split-marker PCR technology, and the effects of <em>TrveA</em> on the pathogenicity and toxin accumulation of <em>T. roseum</em> infecting apple and tomato were analyzed. The regulation of spore formation, oxidative stress tolerance, reactive oxygen species (ROS) metabolism and T-2 toxin biosynthesis was explored to elucidate the potential mechanism of <em>TrveA</em> regulating the pathogenicity of <em>T. roseum</em>. The results suggested that the deletion of <em>TrveA</em> inhibited the growth and development of the mutant, down-regulated the expression of key regulatory genes <em>fluG</em>, <em>flbA</em>, <em>abaA</em> and <em>wetA</em> in the sporulation pathway, and interfered with trehalose biosynthesis, resulting in a decrease in sporulation. <em>TrveA</em> deletion reduced the level of ROS accumulation and weakened the capacity of ROS scavenging, which cut down its tolerance to oxidative stress. At the same time, the expression of key genes <em>tri6</em>, <em>tri5</em> and <em>tri4</em> involved in the T-2 toxin biosynthesis pathway was down-regulated to inhibit the biosynthesis of T-2 toxin, which eventually led to the decrease of pathogenicity to apple and tomato. This study reveals the important role of <em>TrveA</em> in <em>T. roseum</em> infecting apple fruits, which is conductive to better elucidate the regulatory mechanism of <em>TrveA</em>. These results will provide potential precise targets for curbing apple postharvest diseases caused by <em>T. roseum</em>.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"134 ","pages":"Article 104943"},"PeriodicalIF":4.6,"publicationDate":"2025-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145216579","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 : 2025-09-26DOI: 10.1016/j.fm.2025.104944
Han Wang , Bo Zou , Yana Liu , Yingying Sun , Yan Zhao , Yi Liu , Xingmin Li , Ruitong Dai
Ohmic heating (OH), a novel food processing technology, has been shown to effectively inactivate Staphylococcus aureus (S. aureus). However, the molecular repair mechanisms of OH-induced sublethal injury in S. aureus remain unclear. In this study, four experimental groups were established: intact cells (UT), OH-injured cells without repair (R0), and injured cells repaired in NB medium for either 15 min (R1, early repair stage) or 2 h (R2, mid-repair stage). Atomic force microscopy revealed that cell morphology was disrupted by OH treatment (R0) but progressively restored during repair (R0–R2). Integrated proteomic and lipidomic analyses demonstrated that OH treatment suppressed proteins and lipids involved in membrane integrity, energy metabolism, and amino acid metabolism, reflecting an adaptive stress response. During the early repair stage, upregulation of these molecules indicated activation of recovery pathways, whereas their downregulation in the mid-repair stage suggested stabilization of cellular functions. Intracellular ion concentrations and enzyme activities were consistent with proteomic trends, while lipidomics highlighted dynamic remodeling of key membrane lipids such as phosphatidylglycerol and cardiolipin. In conclusion, this study provides new insights into the molecular mechanisms underlying OH-induced injury and repair in S. aureus, advancing the understanding of bacterial stress adaptation and offering guidance for optimizing OH technology in food safety applications.
欧姆加热（OH）是一种新型的食品加工技术，已被证明可以有效地灭活金黄色葡萄球菌（S. aureus）。然而，oh诱导的金黄色葡萄球菌亚致死损伤的分子修复机制尚不清楚。本研究建立了四个实验组：完整细胞（UT）、oh损伤未修复细胞（R0）和损伤细胞在NB培养基中修复15 min （R1，修复早期）或2 h （R2，修复中期）。原子力显微镜显示，OH处理（R0）破坏了细胞形态，但在修复过程中逐渐恢复（R0 - r2）。综合蛋白质组学和脂质组学分析表明，OH处理抑制了参与膜完整性、能量代谢和氨基酸代谢的蛋白质和脂质，反映了适应性应激反应。在早期修复阶段，这些分子的上调表明恢复途径的激活，而在修复中期，它们的下调表明细胞功能的稳定。细胞内离子浓度和酶活性与蛋白质组学趋势一致，而脂质组学强调关键膜脂如磷脂酰甘油和心磷脂的动态重塑。总之，本研究对OH诱导金黄色葡萄球菌损伤和修复的分子机制提供了新的见解，促进了对细菌应激适应的认识，并为OH技术在食品安全中的优化应用提供了指导。
{"title":"Probing the repair mechanism of ohmic heating-induced sublethal injury in Staphylococcus aureus: Multi-omics analysis uncovers the remodeling patterns of proteins and lipids and applications in simulated food systems","authors":"Han Wang , Bo Zou , Yana Liu , Yingying Sun , Yan Zhao , Yi Liu , Xingmin Li , Ruitong Dai","doi":"10.1016/j.fm.2025.104944","DOIUrl":"10.1016/j.fm.2025.104944","url":null,"abstract":"<div><div>Ohmic heating (OH), a novel food processing technology, has been shown to effectively inactivate <em>Staphylococcus aureus</em> (<em>S. aureus</em>). However, the molecular repair mechanisms of OH-induced sublethal injury in <em>S. aureus</em> remain unclear. In this study, four experimental groups were established: intact cells (UT), OH-injured cells without repair (R0), and injured cells repaired in NB medium for either 15 min (R1, early repair stage) or 2 h (R2, mid-repair stage). Atomic force microscopy revealed that cell morphology was disrupted by OH treatment (R0) but progressively restored during repair (R0–R2). Integrated proteomic and lipidomic analyses demonstrated that OH treatment suppressed proteins and lipids involved in membrane integrity, energy metabolism, and amino acid metabolism, reflecting an adaptive stress response. During the early repair stage, upregulation of these molecules indicated activation of recovery pathways, whereas their downregulation in the mid-repair stage suggested stabilization of cellular functions. Intracellular ion concentrations and enzyme activities were consistent with proteomic trends, while lipidomics highlighted dynamic remodeling of key membrane lipids such as phosphatidylglycerol and cardiolipin. In conclusion, this study provides new insights into the molecular mechanisms underlying OH-induced injury and repair in <em>S. aureus</em>, advancing the understanding of bacterial stress adaptation and offering guidance for optimizing OH technology in food safety applications.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"134 ","pages":"Article 104944"},"PeriodicalIF":4.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145216581","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 : 2025-09-26DOI: 10.1016/j.fm.2025.104933
Mingjian Zhang , Yujie He , Luyi Liang , Solairaj Dhanasekaran , Yize Hu , Xiaoyun Zhang , Jun Li , Lina Zhao , Hongyin Zhang
{"title":"Corrigendum to “Study on the biocontrol efficacy of Meyerozyma caribbica against blue mold of pears and the mechanisms involved” [Food Microbiol. Volume 134, March 2026, 104917]","authors":"Mingjian Zhang , Yujie He , Luyi Liang , Solairaj Dhanasekaran , Yize Hu , Xiaoyun Zhang , Jun Li , Lina Zhao , Hongyin Zhang","doi":"10.1016/j.fm.2025.104933","DOIUrl":"10.1016/j.fm.2025.104933","url":null,"abstract":"","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"134 ","pages":"Article 104933"},"PeriodicalIF":4.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358110","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 : 2025-09-26DOI: 10.1016/j.fm.2025.104942
Ling Sun , Shiyi Chen , Yazhen Wang , Lei Sun , Zejian Wang , Yong Zhou , Ali Mohsin , Suyang Li , Luning Zhao , Afira Nayab , Wenjing Sun
Gellan gum demonstrates superior gelation properties and has been widely applied. However, the biosynthesis mechanism of gellan gum remains poorly understood, hampering efforts to increase its production. Therefore, this study comprehensively analyzed the phenotypes of a high-yield gellan gum mutant strain ATCC31461-M519 induced by ARTP treatment, its gellan gum characteristics and potential molecular mechanisms of gellan gum biosynthesis. Compared to the original strain ATCC31461, the mutant strain ATCC31461-M519 demonstrated a 59.0 % increase in gellan gum yield (5-L fermenter) along with enhanced sugar-to-gel conversion efficiency, enlarged cell size (1.72-fold length), and elevated cell permeability. Notably, its functional group composition, monosaccharide profile (glucose: rhamnose: glucuronic acid = 2.45 : 1: 0.81), and molecular weight (1.137 × 106 g/mol) remained unaltered. Whole-genome re-sequencing identified 245 SNPs and 35 InDels in the genome of the mutant strain, while RNA-seq revealed 390 differentially expressed genes (DEGs: 107 up-regulated, 283 down-regulated). Integrative multi-omics analysis revealed that the two-component system (TCS) pathway was significantly enriched in the mutant strain with 4 InDel mutated genes and 45 DEGs. Moreover, qRT-PCR analysis confirmed the expression of gelS, gelC, gelE, gelG (gellan gum synthase) in the mutant strain significantly increased by approximately 8.4, 8.6, 6.2, 5.5 fold change, respectively, and its lyase (gelR) expression decreased by 84.7 %. Therefore, the mutated genes and DEGs in the TCS pathway, up-regulated expression of synthetase, and enhanced cell membrance permeability and surface area jointly improved the production of gellan gum, which provides molecular basis to increase gellan gum production by using metabolic engineering.
{"title":"Integrated multi-omics and physiological analyses reveal mechanism of enhanced gellan gum biosynthesis in an ARTP-induced Sphingomonas paucimobilis mutant","authors":"Ling Sun , Shiyi Chen , Yazhen Wang , Lei Sun , Zejian Wang , Yong Zhou , Ali Mohsin , Suyang Li , Luning Zhao , Afira Nayab , Wenjing Sun","doi":"10.1016/j.fm.2025.104942","DOIUrl":"10.1016/j.fm.2025.104942","url":null,"abstract":"<div><div>Gellan gum demonstrates superior gelation properties and has been widely applied. However, the biosynthesis mechanism of gellan gum remains poorly understood, hampering efforts to increase its production. Therefore, this study comprehensively analyzed the phenotypes of a high-yield gellan gum mutant strain ATCC31461-M519 induced by ARTP treatment, its gellan gum characteristics and potential molecular mechanisms of gellan gum biosynthesis. Compared to the original strain ATCC31461, the mutant strain ATCC31461-M519 demonstrated a 59.0 % increase in gellan gum yield (5-L fermenter) along with enhanced sugar-to-gel conversion efficiency, enlarged cell size (<em>1.72-fold length</em>), and elevated cell permeability. Notably, its functional group composition, monosaccharide profile (glucose: rhamnose: glucuronic acid = 2.45 : 1: 0.81), and molecular weight (1.137 × 10<sup>6</sup> g/mol) remained unaltered. Whole-genome re-sequencing identified 245 SNPs and 35 InDels in the genome of the mutant strain, while RNA-seq revealed 390 differentially expressed genes (DEGs: 107 up-regulated, 283 down-regulated). Integrative multi-omics analysis revealed that the two-component system (TCS) pathway was significantly enriched in the mutant strain with 4 InDel mutated genes and 45 DEGs. Moreover, qRT-PCR analysis confirmed the expression of <em>gelS</em>, <em>gelC</em>, <em>gelE</em>, <em>gelG</em> (gellan gum synthase) in the mutant strain significantly increased by approximately 8.4, 8.6, 6.2, 5.5 fold change, respectively, and its lyase (<em>gelR</em>) expression decreased by 84.7 %. Therefore, the mutated genes and DEGs in the TCS pathway, up-regulated expression of synthetase, and enhanced cell membrance permeability and surface area jointly improved the production of gellan gum, which provides molecular basis to increase gellan gum production by using metabolic engineering.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"134 ","pages":"Article 104942"},"PeriodicalIF":4.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145216582","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 : 2025-09-25DOI: 10.1016/j.fm.2025.104938
Laura Blomvall , Rauni Kivistö , Anniina Jaakkonen , Satu Olkkola , Maria Fredriksson-Ahomaa
Campylobacter is the leading cause of bacterial foodborne gastrointestinal infection in humans, and poultry is among the most important reservoirs. Turkeys have been shown to frequently carry Campylobacter, and the isolates recovered from turkeys show high antimicrobial resistance. We studied the prevalence of Campylobacter in Finnish slaughter turkeys during 2013–2023 from the monitoring data of a Finnish turkey slaughterhouse, covering 1856 turkey flocks originating from 41 farms over the monitoring period. Additionally, we used whole-genome sequencing to identify bacterial species, resistance profiles, sequence types, and core genome allelic profiles for 103 Campylobacter isolates from turkey faecal samples collected at the slaughterhouse between 2013 and 2021. In total, 9.5 % of the flocks and 82.9 % of the farms were Campylobacter positive. The prevalence varied significantly between years, months, and farms. Campylobacter jejuni (87.6 %) was the most common species followed by Campylobacter coli (4.0 %) and Campylobacter lari (1.1 %). We obtained 34 sequence types, with ST45 being the most common (20.2 % of the isolates). Genetically closely related isolates originated mostly from the same farm with a tight temporal connection. Five antimicrobial genotypic resistance profiles were identified. Most of the isolates carried only the blaOXA gene, and only one Campylobacter isolate carried several resistance genes. We showed that Campylobacter prevalence and the occurrence of antimicrobial resistance genes in the isolates is low in Finnish slaughter turkeys. Further, we demonstrated that Campylobacter spread between the flocks on the same farm, but the same STs did not persist.
{"title":"Distribution and characteristics of Campylobacter spp. in turkeys at slaughter","authors":"Laura Blomvall , Rauni Kivistö , Anniina Jaakkonen , Satu Olkkola , Maria Fredriksson-Ahomaa","doi":"10.1016/j.fm.2025.104938","DOIUrl":"10.1016/j.fm.2025.104938","url":null,"abstract":"<div><div><em>Campylobacter</em> is the leading cause of bacterial foodborne gastrointestinal infection in humans, and poultry is among the most important reservoirs. Turkeys have been shown to frequently carry <em>Campylobacter,</em> and the isolates recovered from turkeys show high antimicrobial resistance. We studied the prevalence of <em>Campylobacter</em> in Finnish slaughter turkeys during 2013–2023 from the monitoring data of a Finnish turkey slaughterhouse, covering 1856 turkey flocks originating from 41 farms over the monitoring period. Additionally, we used whole-genome sequencing to identify bacterial species, resistance profiles, sequence types, and core genome allelic profiles for 103 <em>Campylobacter</em> isolates from turkey faecal samples collected at the slaughterhouse between 2013 and 2021. In total, 9.5 % of the flocks and 82.9 % of the farms were <em>Campylobacter</em> positive. The prevalence varied significantly between years, months, and farms. <em>Campylobacter jejuni</em> (87.6 %) was the most common species followed by <em>Campylobacter coli</em> (4.0 %) and <em>Campylobacter lari</em> (1.1 %). We obtained 34 sequence types, with ST45 being the most common (20.2 % of the isolates). Genetically closely related isolates originated mostly from the same farm with a tight temporal connection. Five antimicrobial genotypic resistance profiles were identified. Most of the isolates carried only the <em>bla</em>OXA gene, and only one <em>Campylobacter</em> isolate carried several resistance genes. We showed that <em>Campylobacter</em> prevalence and the occurrence of antimicrobial resistance genes in the isolates is low in Finnish slaughter turkeys. Further, we demonstrated that <em>Campylobacter</em> spread between the flocks on the same farm, but the same STs did not persist.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"134 ","pages":"Article 104938"},"PeriodicalIF":4.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145227042","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 : 2025-09-25DOI: 10.1016/j.fm.2025.104937
Soo-Jin Jung , Md Ashrafudoulla , Jaewoo Bai , Sang-Do Ha
Bacteriophages are gaining increasing attention as targeted biological control agents against multidrug-resistant (MDR) foodborne pathogens. However, repeated exposure to bacteriophages can induce the emergence of bacteriophage-resistant mutant (BIM) strains, which may exhibit altered physiological characteristics that impair therapeutic efficacy. This study investigated the phenotypic and molecular adaptive mechanisms of multidrug-resistant Salmonella Typhimurium BIMs that acquired resistance to receptor-specific bacteriophages (STP-1 and STP-2) targeting O-antigen and flagella. Two representative BIM strains—MO-4 (O-antigen mutant) and MF-6 (flagella mutant)—were analyzed using phenotypic microarray, motility and biofilm experiments, confocal microscopy, and qRT-PCR. MO-4 exhibited extensive metabolic changes, including 10 alterations in carbon source utilization and increased resistance to 11 antibiotics, while MF-6 showed changes in sensitivity to osmotic and pH stress and increased susceptibility to 5 antibiotics. Both BIM strains exhibited reduced motility but maintained similar or enhanced biofilm formation ability on food contact surfaces. Confocal microscopy analysis revealed structurally distinct biofilms with reduced thickness and increased density. qRT-PCR analysis showed receptor-specific transcriptional changes: MO-4 lost rfaL expression, supporting O-antigen deficiency, while MF-6 showed increased fljB expression and decreased fliK expression, indicating changes in flagellar regulation. Both BIMs showed differences in the expression of tolC, rpoS, and luxS, suggesting changes in efflux, stress response, and quorum sensing. These results highlight receptor-dependent adaptation of phage-resistant Salmonella variants and emphasise the need to evaluate both genetic and phenotypic outcomes when designing effective phage-based control strategies for food safety.
{"title":"Receptor-specific phage resistance induced phenotypic and gene expression shifts in Salmonella Typhimurium impacting biofilm formation on food contact surfaces","authors":"Soo-Jin Jung , Md Ashrafudoulla , Jaewoo Bai , Sang-Do Ha","doi":"10.1016/j.fm.2025.104937","DOIUrl":"10.1016/j.fm.2025.104937","url":null,"abstract":"<div><div>Bacteriophages are gaining increasing attention as targeted biological control agents against multidrug-resistant (MDR) foodborne pathogens. However, repeated exposure to bacteriophages can induce the emergence of bacteriophage-resistant mutant (BIM) strains, which may exhibit altered physiological characteristics that impair therapeutic efficacy. This study investigated the phenotypic and molecular adaptive mechanisms of multidrug-resistant <em>Salmonella</em> Typhimurium BIMs that acquired resistance to receptor-specific bacteriophages (STP-1 and STP-2) targeting O-antigen and flagella. Two representative BIM strains—MO-4 (O-antigen mutant) and MF-6 (flagella mutant)—were analyzed using phenotypic microarray, motility and biofilm experiments, confocal microscopy, and qRT-PCR. MO-4 exhibited extensive metabolic changes, including 10 alterations in carbon source utilization and increased resistance to 11 antibiotics, while MF-6 showed changes in sensitivity to osmotic and pH stress and increased susceptibility to 5 antibiotics. Both BIM strains exhibited reduced motility but maintained similar or enhanced biofilm formation ability on food contact surfaces. Confocal microscopy analysis revealed structurally distinct biofilms with reduced thickness and increased density. qRT-PCR analysis showed receptor-specific transcriptional changes: MO-4 lost <em>rfaL</em> expression, supporting O-antigen deficiency, while MF-6 showed increased <em>fljB</em> expression and decreased <em>fliK</em> expression, indicating changes in flagellar regulation. Both BIMs showed differences in the expression of <em>tolC</em>, <em>rpoS</em>, and <em>luxS</em>, suggesting changes in efflux, stress response, and quorum sensing. These results highlight receptor-dependent adaptation of phage-resistant <em>Salmonella</em> variants and emphasise the need to evaluate both genetic and phenotypic outcomes when designing effective phage-based control strategies for food safety.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"134 ","pages":"Article 104937"},"PeriodicalIF":4.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145216583","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 : 2025-09-24DOI: 10.1016/j.fm.2025.104940
Qiuying Li , Chenyang Jia , Jiaxing Sun, Tong Sun, Jianrong Li, Xuepeng Li
The strong spoilage capability and cold adaptability of Shewanella putrefaciens present a serious threat to the quality and safety of fish. This study aimed to investigate the synergic antibacterial effects of six phenolic acids (Gallic acid, GA; Caffeic acid, CA; Protocatechuic acid; Ferulic acid; Chlorogenic acid; p-Coumaric acid) in pairs against S. putrefaciens, and to illustrate the antibacterial mechanisms. The fractional inhibitory concentration index (FICI) of 15 combinations of phenolic acids against S. putrefaciens ranged from 0.5 to 0.75, suggesting synergistic or partial synergistic antibacterial effects of these phenolic acids. Time-kill curves and morphologic observation demonstrated that GA and CA (GC) exhibited the strongest synergistic effect against S. putrefaciens. GC synergistically damaged the structure integrity of S. putrefaciens, leading to the leakage of intracellular substances and inhibiting the activity of Na+K+-ATPase and respiratory chain dehydrogenase. Both GA and CA could bind to DNA and cause changes in DNA content. Proteomics analysis revealed that 399 proteins were affected in the GC groups, a number significantly higher than that in the single GA and CA groups. GC inhibited dissimilatory nitrate and sulfate reduction, and enhanced fatty acid degradation and assimilatory sulfate reduction, which might cause the imbalance of energy supply and ROS accumulation. Meanwhile, the antioxidant-related enzymes, efflux systems and some two-components systems were upregulated, while chemotaxis were inhibited. GC synergistically inhibited S. putrefaciens in turbot, and retarded the spoilage process. The results revealed multi-targeted synergistic antibacterial mechanisms of GC against S. putrefaciens, suggesting GC might be a good strategy for controlling S. putrefaciens and fish spoilage.
{"title":"Synergistic antibacterial effects and mechanisms of different phenolic acids against Shewanella putrefaciens from fish, with emphasis on the combination of gallic acid and caffeic acid","authors":"Qiuying Li , Chenyang Jia , Jiaxing Sun, Tong Sun, Jianrong Li, Xuepeng Li","doi":"10.1016/j.fm.2025.104940","DOIUrl":"10.1016/j.fm.2025.104940","url":null,"abstract":"<div><div>The strong spoilage capability and cold adaptability of <em>Shewanella putrefaciens</em> present a serious threat to the quality and safety of fish. This study aimed to investigate the synergic antibacterial effects of six phenolic acids (Gallic acid, GA; Caffeic acid, CA; Protocatechuic acid; Ferulic acid; Chlorogenic acid; p-Coumaric acid) in pairs against <em>S</em>. <em>putrefaciens</em>, and to illustrate the antibacterial mechanisms. The fractional inhibitory concentration index (FICI) of 15 combinations of phenolic acids against <em>S. putrefaciens</em> ranged from 0.5 to 0.75, suggesting synergistic or partial synergistic antibacterial effects of these phenolic acids. Time-kill curves and morphologic observation demonstrated that GA and CA (GC) exhibited the strongest synergistic effect against <em>S. putrefaciens</em>. GC synergistically damaged the structure integrity of <em>S. putrefaciens</em>, leading to the leakage of intracellular substances and inhibiting the activity of Na<sup>+</sup>K<sup>+</sup>-ATPase and respiratory chain dehydrogenase. Both GA and CA could bind to DNA and cause changes in DNA content. Proteomics analysis revealed that 399 proteins were affected in the GC groups, a number significantly higher than that in the single GA and CA groups. GC inhibited dissimilatory nitrate and sulfate reduction, and enhanced fatty acid degradation and assimilatory sulfate reduction, which might cause the imbalance of energy supply and ROS accumulation. Meanwhile, the antioxidant-related enzymes, efflux systems and some two-components systems were upregulated, while chemotaxis were inhibited. GC synergistically inhibited <em>S. putrefaciens</em> in turbot, and retarded the spoilage process. The results revealed multi-targeted synergistic antibacterial mechanisms of GC against <em>S. putrefaciens</em>, suggesting GC might be a good strategy for controlling <em>S. putrefaciens</em> and fish spoilage.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"134 ","pages":"Article 104940"},"PeriodicalIF":4.6,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145154951","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}
This study presents a genome-informed surveillance model to investigate the persistence and spread of colistin-resistant Escherichia coli in broiler chicken processing. The study targeted a high-throughput poultry facility—previously linked to retail meat contamination by colistin-resistant E. coli and Salmonella—where 200 carcasses were sampled across ten production batches to assess the prevalence and genomic characteristics of antimicrobial-resistant strains within the processing line. We analyzed one E. coli isolate per carcass to characterize antimicrobial resistance (AMR), and utilized whole-genome sequencing (WGS) to delineate phylogeny, virulence, AMR determinants, and plasmid content. Colistin-resistant E. coli isolates were detected in all production batches and were confirmed in 10.5 % (21/200) of the carcasses, with all isolates carrying the mcr-1.1 gene. Notably, 57.1 % of these isolates also harbored a PmrB Y358N putative colistin resistance mutation. Phylogenetic analysis revealed substantial diversity, with 31 sequence types detected; however, six isolates belonging to ST162 were identified as a resident strains cluster, persisting over four months and from multiple farms and flocks. All colistin-resistant E. coli isolates were phenotypically multidrug-resistant (MDR), carrying 10–25 AMR resistance genes per genome, including ESBL genes such as blaCTX-M-55 (57.1 %). Virulence profiling showed a high prevalence of iron acquisition, serum resistance, and efflux-related genes, with an average of 22.5 putative virulence factors per isolate. Plasmidome analysis (n = 20 plasmids) revealed the dominance of IncI2 (60 %) and IncHI2-type replicons, with 90 % of plasmids predicted to be conjugative. Mobile genetic elements involved in horizontal gene transfer, such as MOBP relaxases and MPF-T systems, were prevalent (70 %), indicating a high potential for plasmid-mediated dissemination of AMR genes within the sampled isolates. This work offers a scalable model for processing facility-level AMR tracking and reinforces the value of WGS for industry-led food safety risk management, particularly for high-priority AMR determinants such as colistin resistance.
{"title":"Resident or transient? Whole-genome approach to tracking colistin-resistant Escherichia coli in the broiler chicken processing chain","authors":"Ihab Habib , Mohamed-Yousif Ibrahim Mohamed , Glindya Bhagya Lakshmi , Akela Ghazawi , Mushtaq Khan","doi":"10.1016/j.fm.2025.104939","DOIUrl":"10.1016/j.fm.2025.104939","url":null,"abstract":"<div><div>This study presents a genome-informed surveillance model to investigate the persistence and spread of colistin-resistant <em>Escherichia coli</em> in broiler chicken processing. The study targeted a high-throughput poultry facility—previously linked to retail meat contamination by colistin-resistant <em>E. coli</em> and <em>Salmonella</em>—where 200 carcasses were sampled across ten production batches to assess the prevalence and genomic characteristics of antimicrobial-resistant strains within the processing line. We analyzed one <em>E. coli</em> isolate per carcass to characterize antimicrobial resistance (AMR), and utilized whole-genome sequencing (WGS) to delineate phylogeny, virulence, AMR determinants, and plasmid content. Colistin-resistant <em>E. coli</em> isolates were detected in all production batches and were confirmed in 10.5 % (21/200) of the carcasses, with all isolates carrying the <em>mcr-1.1</em> gene. Notably, 57.1 % of these isolates also harbored a PmrB Y358N putative colistin resistance mutation. Phylogenetic analysis revealed substantial diversity, with 31 sequence types detected; however, six isolates belonging to ST162 were identified as a resident strains cluster, persisting over four months and from multiple farms and flocks. All colistin-resistant <em>E. coli</em> isolates were phenotypically multidrug-resistant (MDR), carrying 10–25 AMR resistance genes per genome, including ESBL genes such as <em>bla</em><sub>CTX-M-55</sub> (57.1 %). Virulence profiling showed a high prevalence of iron acquisition, serum resistance, and efflux-related genes, with an average of 22.5 putative virulence factors per isolate. Plasmidome analysis (n = 20 plasmids) revealed the dominance of IncI2 (60 %) and IncHI2-type replicons, with 90 % of plasmids predicted to be conjugative. Mobile genetic elements involved in horizontal gene transfer, such as MOBP relaxases and MPF-T systems, were prevalent (70 %), indicating a high potential for plasmid-mediated dissemination of AMR genes within the sampled isolates. This work offers a scalable model for processing facility-level AMR tracking and reinforces the value of WGS for industry-led food safety risk management, particularly for high-priority AMR determinants such as colistin resistance.</div></div>","PeriodicalId":12399,"journal":{"name":"Food microbiology","volume":"134 ","pages":"Article 104939"},"PeriodicalIF":4.6,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145154950","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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