Pub Date : 2026-01-29DOI: 10.1016/j.micres.2026.128459
Xinyan Xu , Xuefang Huang , Luokai Wang , Jingxian Yang , Munazza Ijaz , Jianping Chen , Kotaro Kiga , Bin Li
Phage therapy is being used to combat pathogenic bacterial infections that threaten plant, animal, and human health. However, its application remains limited by high host specificity and the emergence of bacterial resistance. In this study, we addressed the key issues in phage therapy using rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) strain N1 and its lytic phage NP1. Strain N1 acquired resistance to the phage NP1 through mutations and downregulation of lipopolysaccharide (LPS) biosynthesis genes. A directed evolution assay using phage NP1 and the resistant strain N1R resulted in the development of phage E12–2, which overcame bacterial resistance, expanded its host range and improved bacterial suppression by targeting alternative LPS binding sites. Moreover, genome analysis identified two amino acid substitutions (V303L and G317V) in its tail fiber protein. Additionally, phage E12–2 improved disease control efficiency by 51 % compared to the wild-type phage NP1 and induced plant immunity in a plant disease model. These findings enhance our understanding of how bacteria-phage evolution shapes the dynamics of phage therapy in plants.
{"title":"Evolution of phage tail fiber proteins to counter bacterial resistance and improve biocontrol efficacy in plant disease models","authors":"Xinyan Xu , Xuefang Huang , Luokai Wang , Jingxian Yang , Munazza Ijaz , Jianping Chen , Kotaro Kiga , Bin Li","doi":"10.1016/j.micres.2026.128459","DOIUrl":"10.1016/j.micres.2026.128459","url":null,"abstract":"<div><div>Phage therapy is being used to combat pathogenic bacterial infections that threaten plant, animal, and human health. However, its application remains limited by high host specificity and the emergence of bacterial resistance. In this study, we addressed the key issues in phage therapy using rice bacterial blight pathogen <em>Xanthomonas oryzae</em> pv<em>. oryzae</em> (<em>Xoo</em>) strain N1 and its lytic phage NP1. Strain N1 acquired resistance to the phage NP1 through mutations and downregulation of lipopolysaccharide (LPS) biosynthesis genes. A directed evolution assay using phage NP1 and the resistant strain N1R resulted in the development of phage E12–2, which overcame bacterial resistance, expanded its host range and improved bacterial suppression by targeting alternative LPS binding sites. Moreover, genome analysis identified two amino acid substitutions (V303L and G317V) in its tail fiber protein. Additionally, phage E12–2 improved disease control efficiency by 51 % compared to the wild-type phage NP1 and induced plant immunity in a plant disease model. These findings enhance our understanding of how bacteria-phage evolution shapes the dynamics of phage therapy in plants.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128459"},"PeriodicalIF":6.9,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146100403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-24DOI: 10.1016/j.micres.2026.128458
Nikolaj L. Kindtler , Sanea Sheikh , Rujia He , Rute R.da Fonseca , Kristian H. Laursen , Flemming Ekelund
Soil microbial diversity is crucial for plant nutrition and health, yet how its loss affects plant performance remains unclear. We used a dilution-to-extinction approach to test how declining rhizo-microbiome diversity influences two barley cultivars: the modern RGT Planet and the older Babushka. Plants were grown in sterilized systems amended with mineral or organic nitrogen and inoculated with microbiome treatments (10-¹, 10-³, 10-⁵, and 10-⁷ dilutions), plus a no-inoculum treatment. We used amplicon sequencing (16S, ITS, 18S) to profile rhizosphere communities, and quantified plant biomass, shoot nitrogen, and chitin mineralization. Protists and fungi were present in 10-¹ and 10-³ but absent in all others. Microbiome inoculum and nitrogen source explained most variation in rhizo-microbiome composition, with cultivar having a smaller effect. Under organic nitrogen, Babushka showed a marked decline in biomass with decreasing diversity, whereas RGT was largely unaffected, indicating that the older cultivar relied more on a diverse microbiome to maintain growth. At intermediate diversity, when protists and fungi were lost, both cultivars showed improved growth and shoot nitrogen, coinciding with shifts in bacterial composition and loss of potential pathogens. Hence, reduced diversity did not always impair growth, suggesting functional compensation. Under mineral nitrogen, both cultivars were less sensitive to diversity loss. Overall, nitrogen source and cultivar identity modulated plant responses to microbial diversity loss. Diverse microbiomes promoted efficient use of organic nitrogen, particularly for the older cultivar, while the modern cultivar maintained growth at lower diversity. Our results demonstrate that the consequences of diversity loss are context-dependent and cultivar-specific.
{"title":"Microbial diversity loss affects old and modern barley cultivars differently under varying nitrogen sources","authors":"Nikolaj L. Kindtler , Sanea Sheikh , Rujia He , Rute R.da Fonseca , Kristian H. Laursen , Flemming Ekelund","doi":"10.1016/j.micres.2026.128458","DOIUrl":"10.1016/j.micres.2026.128458","url":null,"abstract":"<div><div>Soil microbial diversity is crucial for plant nutrition and health, yet how its loss affects plant performance remains unclear. We used a dilution-to-extinction approach to test how declining rhizo-microbiome diversity influences two barley cultivars: the modern RGT Planet and the older Babushka. Plants were grown in sterilized systems amended with mineral or organic nitrogen and inoculated with microbiome treatments (10<sup>-</sup>¹, 10<sup>-</sup>³, 10<sup>-</sup>⁵, and 10<sup>-</sup>⁷ dilutions), plus a no-inoculum treatment. We used amplicon sequencing (16S, ITS, 18S) to profile rhizosphere communities, and quantified plant biomass, shoot nitrogen, and chitin mineralization. Protists and fungi were present in 10<sup>-</sup>¹ and 10<sup>-</sup>³ but absent in all others. Microbiome inoculum and nitrogen source explained most variation in rhizo-microbiome composition, with cultivar having a smaller effect. Under organic nitrogen, Babushka showed a marked decline in biomass with decreasing diversity, whereas RGT was largely unaffected, indicating that the older cultivar relied more on a diverse microbiome to maintain growth. At intermediate diversity, when protists and fungi were lost, both cultivars showed improved growth and shoot nitrogen, coinciding with shifts in bacterial composition and loss of potential pathogens. Hence, reduced diversity did not always impair growth, suggesting functional compensation. Under mineral nitrogen, both cultivars were less sensitive to diversity loss. Overall, nitrogen source and cultivar identity modulated plant responses to microbial diversity loss. Diverse microbiomes promoted efficient use of organic nitrogen, particularly for the older cultivar, while the modern cultivar maintained growth at lower diversity. Our results demonstrate that the consequences of diversity loss are context-dependent and cultivar-specific.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128458"},"PeriodicalIF":6.9,"publicationDate":"2026-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146078984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-23DOI: 10.1016/j.micres.2026.128452
Sen Zhang , Xiaoyu Wang , Dan Zhang , Ruichi Hua, Yijin Yan, Juan Yang, Jinhu Ma, Jie Wang, Xiaohuan Yang
Verticillium wilt can be caused by the soil-borne fungal pathogen Verticillium dahliae (V. dahliae). It is a destructive vascular pathogen that infects more than 200 plant species, including economically important crops such as cotton. The disease induces severe symptoms such as wilting, chlorosis, and necrosis, ultimately resulting in substantial yield losses. Conventional management strategies, including chemical fungicides and crop rotation, have exhibited limited effectiveness against V. dahliae, emphasizing the urgent need to elucidate innate plant resistance mechanisms for breeding Verticillium-resistant varieties. In this study, the defense mechanisms of root border cells (RBCs) against V. dahliae were investigated. Fluorescence microscopy and cryo-scanning electron microscopy demonstrated that RBCs were viable and free cells, exhibiting round, intermediate, and elongated morphologies. In vitro co-culture assays revealed that viable RBCs isolated from cotton or corn markedly suppressed the growth of V. dahliae, whereas heat-inactivated RBCs lost this antifungal capacity, confirming that the defense mechanism was viability-dependent. Further analysis indicated that under V. dahliae stress, RBCs secreted a thickened mucilage layer enriched in pectin and extracellular DNA (exDNA), which encapsulated fungal hyphae and formed a physical barrier. Metabolomic profiling of RBC secretions from both cotton and corn identified a conserved set of metabolites, including compounds involved in flavone and flavonol biosynthesis, valine, leucine, and isoleucine metabolism, and phenylpropanoid biosynthesis, which could contribute to chemical defense against pathogens. These findings demonstrate the cellular and molecular mechanisms underlying RBC-mediated inhibition of V. dahliae infection and provide insights for developing Verticillium wilt resistance breeding strategies in cotton.
{"title":"The contribution of root border cells as a defense barrier against soil-borne pathogen Verticillium dahliae: Insights from the host cotton and the non-host corn","authors":"Sen Zhang , Xiaoyu Wang , Dan Zhang , Ruichi Hua, Yijin Yan, Juan Yang, Jinhu Ma, Jie Wang, Xiaohuan Yang","doi":"10.1016/j.micres.2026.128452","DOIUrl":"10.1016/j.micres.2026.128452","url":null,"abstract":"<div><div>Verticillium wilt can be caused by the soil-borne fungal pathogen <em>Verticillium dahliae</em> (<em>V. dahliae)</em>. It is a destructive vascular pathogen that infects more than 200 plant species, including economically important crops such as cotton. The disease induces severe symptoms such as wilting, chlorosis, and necrosis, ultimately resulting in substantial yield losses. Conventional management strategies, including chemical fungicides and crop rotation, have exhibited limited effectiveness against <em>V. dahliae</em>, emphasizing the urgent need to elucidate innate plant resistance mechanisms for breeding Verticillium-resistant varieties. In this study, the defense mechanisms of root border cells (RBCs) against <em>V. dahliae</em> were investigated. Fluorescence microscopy and cryo-scanning electron microscopy demonstrated that RBCs were viable and free cells, exhibiting round, intermediate, and elongated morphologies. <em>In vitro</em> co-culture assays revealed that viable RBCs isolated from cotton or corn markedly suppressed the growth of <em>V. dahliae</em>, whereas heat-inactivated RBCs lost this antifungal capacity, confirming that the defense mechanism was viability-dependent. Further analysis indicated that under <em>V. dahliae</em> stress, RBCs secreted a thickened mucilage layer enriched in pectin and extracellular DNA (exDNA), which encapsulated fungal hyphae and formed a physical barrier. Metabolomic profiling of RBC secretions from both cotton and corn identified a conserved set of metabolites, including compounds involved in flavone and flavonol biosynthesis, valine, leucine, and isoleucine metabolism, and phenylpropanoid biosynthesis, which could contribute to chemical defense against pathogens. These findings demonstrate the cellular and molecular mechanisms underlying RBC-mediated inhibition of <em>V. dahliae</em> infection and provide insights for developing Verticillium wilt resistance breeding strategies in cotton.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128452"},"PeriodicalIF":6.9,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146078914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-20DOI: 10.1016/j.micres.2026.128456
Pieter van Dillewijn , Lydia M. Bernabéu-Roda , Virginia Cuéllar , Rafael Núñez , Otto Geiger , Isabel M. López-Lara , María J. Soto
Bacterial volatile compounds play important roles in intra- and interkingdom interactions but little is known about their effects on soil and plant microbiomes. The legume symbiont Sinorhizobium meliloti (Sm) releases volatile methylketones (MKs), one of which acts as an infochemical among bacteria and hampers plant-bacteria interactions. Inactivation of the fatty acyl-CoA ligase FadD in Sm moderately enhances MK production. To further explore the ecological role of MKs on soil and plant bacterial communities, we aimed at obtaining an MK-overproducing Sm strain by deleting the 3-oxoacyl-CoA thiolase-encoding fadA gene. Analyses of the Sm wild-type (WT) and fad mutant volatilomes identified seventeen compounds, primarily consisting of MKs and fatty acid methyl esters (FAMEs). The fadA mutant released more MKs than the fadD mutant, and substantially more than the WT, whereas FAME emission was increased in the fadD mutant. Exposure of natural soil and the Medicago truncatula rhizosphere to WT and fadA volatilomes or synthetic volatile MKs did not significantly alter bacterial alpha or beta diversity but certain genera responded differentially to each condition. Interestingly, Sm volatilomes significantly affected root endosphere Ensifer/Sinorhizobium populations by maintaining their abundance over time, in contrast to control conditions or exposure to synthetic volatile MKs. This study provides new insights on the synthesis of rhizobial volatile compounds and represents the first exploration of the effects of rhizobial volatilomes on soil and plant bacterial communities, contributing to a deeper understanding of the complex molecular bases underlying plant-bacteria interactions.
{"title":"The effect of Sinorhizobium meliloti volatilomes and synthetic long-chain methylketones on soil and Medicago truncatula microbiomes","authors":"Pieter van Dillewijn , Lydia M. Bernabéu-Roda , Virginia Cuéllar , Rafael Núñez , Otto Geiger , Isabel M. López-Lara , María J. Soto","doi":"10.1016/j.micres.2026.128456","DOIUrl":"10.1016/j.micres.2026.128456","url":null,"abstract":"<div><div>Bacterial volatile compounds play important roles in intra- and interkingdom interactions but little is known about their effects on soil and plant microbiomes. The legume symbiont <em>Sinorhizobium meliloti</em> (Sm) releases volatile methylketones (MKs), one of which acts as an infochemical among bacteria and hampers plant-bacteria interactions. Inactivation of the fatty acyl-CoA ligase FadD in Sm moderately enhances MK production. To further explore the ecological role of MKs on soil and plant bacterial communities, we aimed at obtaining an MK-overproducing Sm strain by deleting the 3-oxoacyl-CoA thiolase-encoding <em>fadA</em> gene. Analyses of the Sm wild-type (WT) and <em>fad</em> mutant volatilomes identified seventeen compounds, primarily consisting of MKs and fatty acid methyl esters (FAMEs). The <em>fadA</em> mutant released more MKs than the <em>fadD</em> mutant, and substantially more than the WT, whereas FAME emission was increased in the <em>fadD</em> mutant. Exposure of natural soil and the <em>Medicago truncatula</em> rhizosphere to WT and <em>fadA</em> volatilomes or synthetic volatile MKs did not significantly alter bacterial alpha or beta diversity but certain genera responded differentially to each condition. Interestingly, Sm volatilomes significantly affected root endosphere <em>Ensifer</em>/<em>Sinorhizobium</em> populations by maintaining their abundance over time, in contrast to control conditions or exposure to synthetic volatile MKs. This study provides new insights on the synthesis of rhizobial volatile compounds and represents the first exploration of the effects of rhizobial volatilomes on soil and plant bacterial communities, contributing to a deeper understanding of the complex molecular bases underlying plant-bacteria interactions.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128456"},"PeriodicalIF":6.9,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146024359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Faecalibacterium species are keystone commensals of the human gut, contributing to intestinal homeostasis, immune modulation, and epithelial health. However, their extreme sensitivity to oxygen and reactive oxygen species renders them highly vulnerable during inflammatory conditions, severely limiting their therapeutic application. Understanding the molecular mechanisms underlying their oxidative stress responses is therefore critical for harnessing these bacteria as next-generation probiotics to restore gut health. In this study, we investigated oxidative stress responses in Faecalibacterium duncaniae A2–165 using comprehensive proteomic and membrane fatty acid profiling. We demonstrated that increasing hydrogen peroxide (H₂O₂) concentrations extend the lag phase of growth and affect survival during the first hour of exposure, notably altering the redox potential. Exposure to H₂O₂ triggered a remodeling of the proteome, including detoxification systems, metal transporters, DNA repair systems, transcriptional regulators, and enzymes involved in cobalamin biosynthesis. Complementary RT-qPCR analyses revealed coordinated and time-dependent transcriptional activation of genes involved in oxidative stress response. Remarkably, cobalamin supplementation enhanced bacterial growth, mitigated H₂O₂-induced stress, and lowered superoxide levels in F. duncaniae, highlighting its direct antioxidant activity. By analyzing membrane fatty acid profiles, we showed that cobalamin preserves membrane fluidity, counteracting oxidative stress induced by H₂O₂ in F. duncaniae. These findings reveal the multifaceted strategies employed by F. duncaniae to withstand oxidative stress and provide a foundation for future efforts to optimize its production at industrial scales and its therapeutic potential as a next-generation probiotic.
{"title":"Cobalamin-mediated protection of Faecalibacterium duncaniae against oxidative stress: Insights from proteomic and membrane fatty acid profiles","authors":"Maria Alejandra de Angel Fontalvo , Simon Ménard , Rime Chebbo , Jasmina Vidic , Alban Amoros , Christine Péchoux , Lydie Oliveira Correia , Sébastien Dupont , Florence Dubois-Brissonnet , Laurent Beney , Bonastre Oliete , Jean-Marc Chatel , Sandrine Auger","doi":"10.1016/j.micres.2026.128455","DOIUrl":"10.1016/j.micres.2026.128455","url":null,"abstract":"<div><div><em>Faecalibacterium</em> species are keystone commensals of the human gut, contributing to intestinal homeostasis, immune modulation, and epithelial health. However, their extreme sensitivity to oxygen and reactive oxygen species renders them highly vulnerable during inflammatory conditions, severely limiting their therapeutic application. Understanding the molecular mechanisms underlying their oxidative stress responses is therefore critical for harnessing these bacteria as next-generation probiotics to restore gut health. In this study, we investigated oxidative stress responses in <em>Faecalibacterium duncaniae</em> A2–165 using comprehensive proteomic and membrane fatty acid profiling. We demonstrated that increasing hydrogen peroxide (H₂O₂) concentrations extend the lag phase of growth and affect survival during the first hour of exposure, notably altering the redox potential. Exposure to H₂O₂ triggered a remodeling of the proteome, including detoxification systems, metal transporters, DNA repair systems, transcriptional regulators, and enzymes involved in cobalamin biosynthesis. Complementary RT-qPCR analyses revealed coordinated and time-dependent transcriptional activation of genes involved in oxidative stress response. Remarkably, cobalamin supplementation enhanced bacterial growth, mitigated H₂O₂-induced stress, and lowered superoxide levels in <em>F. duncaniae,</em> highlighting its direct antioxidant activity. By analyzing membrane fatty acid profiles, we showed that cobalamin preserves membrane fluidity, counteracting oxidative stress induced by H₂O₂ in <em>F. duncaniae.</em> These findings reveal the multifaceted strategies employed by <em>F. duncaniae</em> to withstand oxidative stress and provide a foundation for future efforts to optimize its production at industrial scales and its therapeutic potential as a next-generation probiotic.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128455"},"PeriodicalIF":6.9,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146024357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-19DOI: 10.1016/j.micres.2026.128453
Xiao Fei , Jennifer Moussa , Priscila Regina Guerra , Sajid Nisar , Yibing Ma , Weizhe Wang , Mauro M.S. Saraiva , Heng Li , Zhemin Zhou , John Elmerdahl Olsen
Salmonella enterica subspecies enterica serovar Gallinarum biovar Gallinarum (SGa) and Pullorum (SPu) are avian-specific pathogens causing systemic disease, while S. Enteritidis (SEnt) is a broad host range serovar causing gastroenteritis. The genomic mechanisms underlying this difference in host range and pathogenicity remain incompletely understood. Here, we performed a large-scale pan-genome analysis of 5440 poultry-derived genomes (4927 SEnt, 106 SGa, 407 SPu) integrated with functional chicken and macrophage experiments. Compared with SEnt, avian-specific SGa and SPu exhibited extensive pseudogenization and shared 87 genes absent in SEnt, organized into four major genomic clusters (PG_1–PG_4) enriched in type VI secretion system genes and prophage-derived elements. Conserved SNPs distinguishing SGa/SPu from SEnt were enriched in carbohydrate and nitrogen metabolism pathways, suggesting potential metabolic divergences during infection. Infection experiments in chickens using deletion mutants revealed that deletions of genes in SPI-2 (ssaE, ssaT) and fimbrial genes (stfA, safA) were important for systemic infection of chicken with both SGa and SEnt, despite pseudogenization of fimbrial operons in SGa. Mutants in SPI-13 and SPI-14 were only significantly attenuated in SGa. The specific prophage region PG_3 was important for systemic infection in SGa, while a distinct prophage element (ENT_2) enhanced infection in SEnt. Together, these findings bridge comparative genomics with experimental validation, identifying genomic degradation, prophage acquisition, and serovar-specific pathogenicity islands as putative mechanisms underlying avian host specificity and systemic pathogenesis in Salmonella.
{"title":"Comparative pan-genomics and in vivo validation identify genetic factors important for virulence of Salmonella enterica serovar Gallinarum and serovar Enteritidis in the avian host","authors":"Xiao Fei , Jennifer Moussa , Priscila Regina Guerra , Sajid Nisar , Yibing Ma , Weizhe Wang , Mauro M.S. Saraiva , Heng Li , Zhemin Zhou , John Elmerdahl Olsen","doi":"10.1016/j.micres.2026.128453","DOIUrl":"10.1016/j.micres.2026.128453","url":null,"abstract":"<div><div><em>Salmonella enterica</em> subspecies <em>enterica</em> serovar Gallinarum biovar Gallinarum (SGa) and Pullorum (SPu) are avian-specific pathogens causing systemic disease, while <em>S</em>. Enteritidis (SEnt) is a broad host range serovar causing gastroenteritis. The genomic mechanisms underlying this difference in host range and pathogenicity remain incompletely understood. Here, we performed a large-scale pan-genome analysis of 5440 poultry-derived genomes (4927 SEnt, 106 SGa, 407 SPu) integrated with functional chicken and macrophage experiments. Compared with SEnt, avian-specific SGa and SPu exhibited extensive pseudogenization and shared 87 genes absent in SEnt, organized into four major genomic clusters (PG_1–PG_4) enriched in type VI secretion system genes and prophage-derived elements. Conserved SNPs distinguishing SGa/SPu from SEnt were enriched in carbohydrate and nitrogen metabolism pathways, suggesting potential metabolic divergences during infection. Infection experiments in chickens using deletion mutants revealed that deletions of genes in SPI-2 (<em>ssaE</em>, <em>ssaT</em>) and fimbrial genes (<em>stfA</em>, <em>safA</em>) were important for systemic infection of chicken with both SGa and SEnt, despite pseudogenization of fimbrial operons in SGa. Mutants in SPI-13 and SPI-14 were only significantly attenuated in SGa. The specific prophage region PG_3 was important for systemic infection in SGa, while a distinct prophage element (ENT_2) enhanced infection in SEnt. Together, these findings bridge comparative genomics with experimental validation, identifying genomic degradation, prophage acquisition, and serovar-specific pathogenicity islands as putative mechanisms underlying avian host specificity and systemic pathogenesis in <em>Salmonella</em>.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128453"},"PeriodicalIF":6.9,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146024358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-19DOI: 10.1016/j.micres.2026.128454
Junnan Huang , Xuejuan Xia , Jing Lu , Xuanyu Chen , Keyao Ye , Jia Yu , Zhuosi Li , Yue Ma , Xiaojie Qin , Yangtai Liu , Xiang Wang , Hai Chi , Guannan Li , Chang Liu , Qingli Dong
Listeria monocytogenes (LM) is a significant foodborne pathogen with considerable resilience in diverse environments. Following ingestion via contaminated food, LM can breach the intestinal barrier and infect target organs, causing systemic infection. This breach represents a critical step in its pathogenesis. The gut microbiota, a key component of intestinal defense, can restrict the colonization and invasion of the pathogen through mechanisms such as nutrient competition and bacteriocin production. In response, LM has evolved counterstrategies to enhance its survival and invasiveness in the gut environment. Furthermore, the efficacy of the gut microbiota in resisting LM is influenced by multiple factors, such as population differences and dietary habits, leading to variations in susceptibility to infection among individuals. Currently, antibiotic therapy for listeriosis faces limitations, highlighting the need for alternative control and therapeutic strategies. This review systematically summarizes the mechanisms by which the gut microbiota resists LM, the adaptive strategies of the pathogen, and the factors influencing this interaction. It also discusses current microbiota-based preventive and therapeutic approaches, aiming to provide a theoretical foundation for future research.
{"title":"Protective role of the gut microbiota against Listeria monocytogenes: From colonization resistance to therapeutic approaches","authors":"Junnan Huang , Xuejuan Xia , Jing Lu , Xuanyu Chen , Keyao Ye , Jia Yu , Zhuosi Li , Yue Ma , Xiaojie Qin , Yangtai Liu , Xiang Wang , Hai Chi , Guannan Li , Chang Liu , Qingli Dong","doi":"10.1016/j.micres.2026.128454","DOIUrl":"10.1016/j.micres.2026.128454","url":null,"abstract":"<div><div><em>Listeria monocytogenes</em> (LM) is a significant foodborne pathogen with considerable resilience in diverse environments. Following ingestion via contaminated food, LM can breach the intestinal barrier and infect target organs, causing systemic infection. This breach represents a critical step in its pathogenesis. The gut microbiota, a key component of intestinal defense, can restrict the colonization and invasion of the pathogen through mechanisms such as nutrient competition and bacteriocin production. In response, LM has evolved counterstrategies to enhance its survival and invasiveness in the gut environment. Furthermore, the efficacy of the gut microbiota in resisting LM is influenced by multiple factors, such as population differences and dietary habits, leading to variations in susceptibility to infection among individuals. Currently, antibiotic therapy for listeriosis faces limitations, highlighting the need for alternative control and therapeutic strategies. This review systematically summarizes the mechanisms by which the gut microbiota resists LM, the adaptive strategies of the pathogen, and the factors influencing this interaction. It also discusses current microbiota-based preventive and therapeutic approaches, aiming to provide a theoretical foundation for future research.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128454"},"PeriodicalIF":6.9,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146024356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-15DOI: 10.1016/j.micres.2026.128451
Jingwen Bai, Jinjin Zheng, Chi Wei, Bin Yu, Jingwen Sun, Ziyang Feng, Yu Yang
The global spread of methicillin-resistant Staphylococcus aureus (MRSA) urgently demands novel therapeutic strategies. This study demonstrates that honokiol (HNK), a natural biphenolic compound, is a potent and broad-spectrum agent against MRSA, including clinical isolates. HNK exhibited rapid bactericidal activity, effectively disrupted biofilms, and in a murine abscess model, significantly promoted wound healing while reducing pro-inflammatory cytokines, with excellent biocompatibility. Through an integrated multi-omics, biochemical, and biophysical approach, we identified pyruvate kinase (PYK), the terminal enzyme of glycolysis, as the primary cellular target. Remarkably, HNK employs a dual-targeting strategy, concurrently inhibiting PYK enzyme activity and downregulating pyk gene transcription. Molecular docking, dynamics simulations, and computational mutagenesis delineated the precise binding mode and validated key interaction residues. This concerted attack triggers a catastrophic metabolic cascade severe obstruction of glycolytic flux, impairment of the TCA cycle, profound depletion of ATP/NADH, and oxidative stress ultimately leading to bacterial death and virulence attenuation. Our findings not only elucidate a novel antibacterial mechanism centered on the simultaneous transcriptional and functional inhibition of a metabolic hub but also provide a structural basis for drug design, positioning HNK as a valuable lead compound against multidrug-resistant staphylococcal infections. The definitive genetic validation of PYK as the essential target remains the critical next step to advance this therapeutic strategy.
{"title":"Natural product honokiol exerts anti-methicillin resistant Staphylococcus aureus infection activity by targeting pyruvate kinase to inhibit glucose metabolism","authors":"Jingwen Bai, Jinjin Zheng, Chi Wei, Bin Yu, Jingwen Sun, Ziyang Feng, Yu Yang","doi":"10.1016/j.micres.2026.128451","DOIUrl":"10.1016/j.micres.2026.128451","url":null,"abstract":"<div><div>The global spread of methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) urgently demands novel therapeutic strategies. This study demonstrates that honokiol (HNK), a natural biphenolic compound, is a potent and broad-spectrum agent against MRSA, including clinical isolates. HNK exhibited rapid bactericidal activity, effectively disrupted biofilms, and in a murine abscess model, significantly promoted wound healing while reducing pro-inflammatory cytokines, with excellent biocompatibility. Through an integrated multi-omics, biochemical, and biophysical approach, we identified pyruvate kinase (PYK), the terminal enzyme of glycolysis, as the primary cellular target. Remarkably, HNK employs a dual-targeting strategy, concurrently inhibiting PYK enzyme activity and downregulating <em>pyk</em> gene transcription. Molecular docking, dynamics simulations, and computational mutagenesis delineated the precise binding mode and validated key interaction residues. This concerted attack triggers a catastrophic metabolic cascade severe obstruction of glycolytic flux, impairment of the TCA cycle, profound depletion of ATP/NADH, and oxidative stress ultimately leading to bacterial death and virulence attenuation. Our findings not only elucidate a novel antibacterial mechanism centered on the simultaneous transcriptional and functional inhibition of a metabolic hub but also provide a structural basis for drug design, positioning HNK as a valuable lead compound against multidrug-resistant staphylococcal infections. The definitive genetic validation of PYK as the essential target remains the critical next step to advance this therapeutic strategy.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128451"},"PeriodicalIF":6.9,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145981352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-14DOI: 10.1016/j.micres.2026.128443
Chi Young Hwang , Eui-Sang Cho , Soyoung Jeong , Jong-Hyun Jung , Myung-Ji Seo
The environmental impacts of climate change highlight the need for sustainable bioprocesses using low-cost feedstocks. Microbial fermentation offers an eco-friendly method to produce value-added compounds from renewable resources. Deinoxanthin, a unique carotenoid pigment produced by radiation-resistant bacteria, Deinococcus, has pharmaceutical and food industry applications. However, most microorganisms preferentially utilize glucose as their primary carbon source, limiting their capacity to ferment byproducts or waste-derived resources effectively. Here, we hypothesized that identifying microbial hosts capable of metabolizing a broader range of nutrients could improve fermentation efficiency. Through whole-genome sequencing, we identified that D. yunweiensis KCTC3955 possesses multiple nutrient transporters and is capable of efficiently utilizing glycerol and various nitrogen sources for carotenoid production. Using one-factor-at-a-time and response surface methodologies, we optimized conditions with glycerol, achieving a 4.45-fold increase in carotenoid yield. Notably, key biosynthetic genes (dxr, idi, ispF, ispH, and cruF) were highly up-regulated under mixed nutrient conditions. Fed-batch fermentation with mixed renewable resources such as glycerol and corn steep liquor reached 23.22 mg/L carotenoid production and 15.48 mg/L/day productivity after 36 h, representing over 11- and 15-fold improvements compared to non-optimized conditions. These results highlight D. yunweiensis KCTC3955 as a strong candidate for carotenoid production from mixed renewable substrates
{"title":"Genomic insights into high-yield carotenoid production from renewable resources in radiation-resistant Deinococcus yunweiensis KCTC3955 and its optimization through fed-batch fermentation","authors":"Chi Young Hwang , Eui-Sang Cho , Soyoung Jeong , Jong-Hyun Jung , Myung-Ji Seo","doi":"10.1016/j.micres.2026.128443","DOIUrl":"10.1016/j.micres.2026.128443","url":null,"abstract":"<div><div>The environmental impacts of climate change highlight the need for sustainable bioprocesses using low-cost feedstocks. Microbial fermentation offers an eco-friendly method to produce value-added compounds from renewable resources. Deinoxanthin, a unique carotenoid pigment produced by radiation-resistant bacteria, <em>Deinococcus</em>, has pharmaceutical and food industry applications. However, most microorganisms preferentially utilize glucose as their primary carbon source, limiting their capacity to ferment byproducts or waste-derived resources effectively. Here, we hypothesized that identifying microbial hosts capable of metabolizing a broader range of nutrients could improve fermentation efficiency. Through whole-genome sequencing, we identified that <em>D. yunweiensis</em> KCTC3955 possesses multiple nutrient transporters and is capable of efficiently utilizing glycerol and various nitrogen sources for carotenoid production. Using one-factor-at-a-time and response surface methodologies, we optimized conditions with glycerol, achieving a 4.45-fold increase in carotenoid yield. Notably, key biosynthetic genes (<em>dxr, idi, ispF, ispH</em>, and <em>cruF</em>) were highly up-regulated under mixed nutrient conditions. Fed-batch fermentation with mixed renewable resources such as glycerol and corn steep liquor reached 23.22 mg/L carotenoid production and 15.48 mg/L/day productivity after 36 h, representing over 11- and 15-fold improvements compared to non-optimized conditions. These results highlight <em>D. yunweiensis</em> KCTC3955 as a strong candidate for carotenoid production from mixed renewable substrates</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128443"},"PeriodicalIF":6.9,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146024361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-13DOI: 10.1016/j.micres.2026.128441
Prasanga M. Kumarage , Tasbiha Gul , Nicholas J. Green , Samuel J.T. Wardell , M. Azam Ali , Minati Choudhury , Daniel Pletzer
Gold (Au) and zinc oxide (ZnO) nanoparticles (AuNPs/ZnONPs, respectively) are well-established antimicrobial nanomaterials with broad-spectrum activity and multifaceted mechanisms of action. This review highlights recent advances, focusing on their antibiofilm activity, novel antimicrobial mechanisms, and therapeutic potential in in vivo infection models. Beyond traditional antibacterial effects, these nanoparticles exhibit potent antibiofilm activity and disrupt multiple cellular targets, including cell wall biosynthesis, membrane transport and efflux pumps, energy metabolism, biofilm formation, quorum sensing pathways, and DNA replication and repair, thereby targeting microorganisms on several fronts simultaneously. In vivo studies, particularly biofilm-relevant infection models, remain comparatively limited; however, available evidence indicates that AuNPs/ZnONPs can reduce bacterial burden, promote wound healing, and improve survival, positioning them as promising candidates for next-generation therapeutics. However, despite promising outcomes, challenges such as nanoparticle cytotoxicity, stability, and delivery efficiency remain significant hurdles to clinical translation. Careful optimization of nanoparticle physicochemical properties, along with the development of advanced functionalization and targeting strategies, will be crucial for enhancing the therapeutic index and safety. Moreover, combining these nanoparticles with existing antibiotics and leveraging computational tools, including artificial intelligence, could accelerate the design of next-generation nanotherapeutics.
{"title":"Recent advances in gold and zinc oxide nanoparticles: Antibiofilm action, mechanisms beyond ROS generation, and in vivo efficacy","authors":"Prasanga M. Kumarage , Tasbiha Gul , Nicholas J. Green , Samuel J.T. Wardell , M. Azam Ali , Minati Choudhury , Daniel Pletzer","doi":"10.1016/j.micres.2026.128441","DOIUrl":"10.1016/j.micres.2026.128441","url":null,"abstract":"<div><div>Gold (Au) and zinc oxide (ZnO) nanoparticles (AuNPs/ZnONPs, respectively) are well-established antimicrobial nanomaterials with broad-spectrum activity and multifaceted mechanisms of action. This review highlights recent advances, focusing on their antibiofilm activity, novel antimicrobial mechanisms, and therapeutic potential in <em>in vivo</em> infection models. Beyond traditional antibacterial effects, these nanoparticles exhibit potent antibiofilm activity and disrupt multiple cellular targets, including cell wall biosynthesis, membrane transport and efflux pumps, energy metabolism, biofilm formation, quorum sensing pathways, and DNA replication and repair, thereby targeting microorganisms on several fronts simultaneously. <em>In vivo</em> studies, particularly biofilm-relevant infection models, remain comparatively limited; however, available evidence indicates that AuNPs/ZnONPs can reduce bacterial burden, promote wound healing, and improve survival, positioning them as promising candidates for next-generation therapeutics. However, despite promising outcomes, challenges such as nanoparticle cytotoxicity, stability, and delivery efficiency remain significant hurdles to clinical translation. Careful optimization of nanoparticle physicochemical properties, along with the development of advanced functionalization and targeting strategies, will be crucial for enhancing the therapeutic index and safety. Moreover, combining these nanoparticles with existing antibiotics and leveraging computational tools, including artificial intelligence, could accelerate the design of next-generation nanotherapeutics.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"306 ","pages":"Article 128441"},"PeriodicalIF":6.9,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145981353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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