Pub Date : 2025-11-01DOI: 10.1016/j.micres.2025.128386
Zhuoren Ling , Ruicheng Zheng , Yanjun Dong , Wenjuan Yin , Lu Qiao , Rong Zhang , Pramod K. Jangir , Qiaoling Sun , Gerald Larrouy-Maumus , Craig MacLean , Yang Wang , Jianzhong Shen , Timothy R. Walsh
Colistin is one of the last treatment options against human infections caused by multi-drug resistant Klebsiella pneumoniae. Colistin resistant K. pneumoniae arises through modifying bacterial lipopolysaccharide (LPS) via two mechanisms: the mgrB inactivation on chromosome and mcr-1 expression - usually plasmid-mediated. Notably, chromosomal-mediated resistance is more common in naturally-occurring clinical K. pneumoniae than plasmid-borne resistance. Herein we demonstrated that K. pneumoniae strain with a mutant mgrB (ΔmgrB) gene exhibited increased pathogenicity compared to those carrying mcr-1, as evidenced in Galleria mellonella and murine bacteraemia model. Strain possessing ΔmgrB showed higher mortality rate, greater bacterial accumulation, and increased damage to host tissue. Although both ΔmgrB and mcr-1 impose fitness cost on K. pneumoniae and enhance bacterial evasion from phagocytosis, ΔmgrB mediated greater bacterial resistance to host defence peptides than mcr-1, providing an evolutionary advantage. These findings indicated distinct features of mgrB-inactivated K. pneumoniae and mcr-1-positive K. pneumoniae in host immunity responses, and promote understanding of how antibiotic-resistant determinants influence host-pathogens interactions.
{"title":"mgrB inactivation confers enhanced pathogenicity and immune evasion over mcr-1 expression in colistin-resistant Klebsiella pneumoniae","authors":"Zhuoren Ling , Ruicheng Zheng , Yanjun Dong , Wenjuan Yin , Lu Qiao , Rong Zhang , Pramod K. Jangir , Qiaoling Sun , Gerald Larrouy-Maumus , Craig MacLean , Yang Wang , Jianzhong Shen , Timothy R. Walsh","doi":"10.1016/j.micres.2025.128386","DOIUrl":"10.1016/j.micres.2025.128386","url":null,"abstract":"<div><div>Colistin is one of the last treatment options against human infections caused by multi-drug resistant <em>Klebsiella pneumoniae</em>. Colistin resistant <em>K. pneumoniae</em> arises through modifying bacterial lipopolysaccharide (LPS) via two mechanisms: the <em>mgrB</em> inactivation on chromosome and <em>mcr-1</em> expression - usually plasmid-mediated. Notably, chromosomal-mediated resistance is more common in naturally-occurring clinical <em>K. pneumoniae</em> than plasmid-borne resistance. Herein we demonstrated that <em>K. pneumoniae</em> strain with a mutant <em>mgrB</em> (Δ<em>mgrB</em>) gene exhibited increased pathogenicity compared to those carrying <em>mcr-1</em>, as evidenced in <em>Galleria mellonella</em> and murine bacteraemia model. Strain possessing Δ<em>mgrB</em> showed higher mortality rate, greater bacterial accumulation, and increased damage to host tissue. Although both Δ<em>mgrB</em> and <em>mcr-1</em> impose fitness cost on <em>K. pneumoniae</em> and enhance bacterial evasion from phagocytosis, Δ<em>mgrB</em> mediated greater bacterial resistance to host defence peptides than <em>mcr-1</em>, providing an evolutionary advantage. These findings indicated distinct features of <em>mgrB</em>-inactivated <em>K. pneumoniae</em> and <em>mcr-1</em>-positive <em>K. pneumoniae</em> in host immunity responses, and promote understanding of how antibiotic-resistant determinants influence host-pathogens interactions.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128386"},"PeriodicalIF":6.9,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145445262","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 : 2025-11-01DOI: 10.1016/j.micres.2025.128385
Ganghua Han , Lei Zhao , Ruixin Li , Ruihua Liu , Yingying Wang , Mark Bartlam
Temperate and virulent phages coexist in natural environments and can collaboratively contribute to the lysis of bacterial biofilms. However, their therapeutic potential and the dynamics of phage-biofilm interactions, particularly in clinical contexts, remain poorly understood. In this study, we demonstrated the strong biofilm-lysing capabilities of the temperate phage PaoP1 and virulent phage PaoP5 against Pseudomonas aeruginosa biofilms, highlighting their potential for phage therapy. RNA-seq analysis revealed a shared host resistance mechanism involving the downregulation of flagellar biosynthesis and enhanced biofilm formation. Despite this common host response, the two phages exhibited distinct infection strategies: PaoP1 integrated quiescently into the host genome, while PaoP5 rapidly and abundantly expressed its genes, potentially hijacking the host transcriptional machinery through an as-yet-unknown mechanism. These findings deepen our understanding of phage-biofilm interactions and support the development of phage-based approaches to treat biofilm-associated infections.
{"title":"Coordinated host resistance and distinct phage strategies shape biofilm-phage dynamics in Pseudomonas aeruginosa","authors":"Ganghua Han , Lei Zhao , Ruixin Li , Ruihua Liu , Yingying Wang , Mark Bartlam","doi":"10.1016/j.micres.2025.128385","DOIUrl":"10.1016/j.micres.2025.128385","url":null,"abstract":"<div><div>Temperate and virulent phages coexist in natural environments and can collaboratively contribute to the lysis of bacterial biofilms. However, their therapeutic potential and the dynamics of phage-biofilm interactions, particularly in clinical contexts, remain poorly understood. In this study, we demonstrated the strong biofilm-lysing capabilities of the temperate phage PaoP1 and virulent phage PaoP5 against <em>Pseudomonas aeruginosa</em> biofilms, highlighting their potential for phage therapy. RNA-seq analysis revealed a shared host resistance mechanism involving the downregulation of flagellar biosynthesis and enhanced biofilm formation. Despite this common host response, the two phages exhibited distinct infection strategies: PaoP1 integrated quiescently into the host genome, while PaoP5 rapidly and abundantly expressed its genes, potentially hijacking the host transcriptional machinery through an as-yet-unknown mechanism. These findings deepen our understanding of phage-biofilm interactions and support the development of phage-based approaches to treat biofilm-associated infections.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128385"},"PeriodicalIF":6.9,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145459196","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 : 2025-10-30DOI: 10.1016/j.micres.2025.128383
Yongheng Hou , Shiguang Huang , Xin-zhuan Su , Fangli Lu
Autophagy is a catabolic process that responds to various environmental stresses, such as nutrient deficiency and intracellular pathogen infection. Toxoplasma gondii is an intracellular parasite that acquires nutrients from the host cells for its proliferation; however, the molecular mechanisms of T. gondii parasites’ nutritional acquisition and metabolism are not fully understood. Here, we found that T. gondii type I RH strain induced host cell autophagy for nutrient acquisition and growth. T. gondii RH strain infection induced DNA damage-regulated autophagy modulator 1 (DRAM1) expression in host cells, and mechanistic analyses suggest an involvement of the IL-33-MyD88-p38/NF-κB signaling pathway in this process. DRAM1 knockdown decreased T. gondii parasite growth, while DRAM1 overexpression increased T. gondii parasite growth by hyperactivating autophagy, especially lipophagy, to provide fatty acids for T. gondii proliferation, which led to increased tissue pathology. This study identified DRAM1 as a critical molecule in regulating type I T. gondii-induced lipophagy, parasite proliferation, and liver pathology in mice. The results provide crucial insights into how T. gondii leverages host autophagy for its gain and identify a target for potential disease management, which may offer new avenues for developing novel drugs against this parasite.
{"title":"DNA damage-regulated autophagy modulator 1 (DRAM1)-induced lipophagy facilitates Toxoplasma gondii nutrient acquisition and infection","authors":"Yongheng Hou , Shiguang Huang , Xin-zhuan Su , Fangli Lu","doi":"10.1016/j.micres.2025.128383","DOIUrl":"10.1016/j.micres.2025.128383","url":null,"abstract":"<div><div>Autophagy is a catabolic process that responds to various environmental stresses, such as nutrient deficiency and intracellular pathogen infection. <em>Toxoplasma gondii</em> is an intracellular parasite that acquires nutrients from the host cells for its proliferation; however, the molecular mechanisms of <em>T. gondii</em> parasites’ nutritional acquisition and metabolism are not fully understood. Here, we found that <em>T. gondii</em> type I RH strain induced host cell autophagy for nutrient acquisition and growth. <em>T. gondii</em> RH strain infection induced DNA damage-regulated autophagy modulator 1 (DRAM1) expression in host cells, and mechanistic analyses suggest an involvement of the IL-33-MyD88-p38/NF-κB signaling pathway in this process. DRAM1 knockdown decreased <em>T. gondii</em> parasite growth, while DRAM1 overexpression increased <em>T. gondii</em> parasite growth by hyperactivating autophagy, especially lipophagy, to provide fatty acids for <em>T. gondii</em> proliferation, which led to increased tissue pathology. This study identified DRAM1 as a critical molecule in regulating type I <em>T. gondii</em>-induced lipophagy, parasite proliferation, and liver pathology in mice. The results provide crucial insights into how <em>T. gondii</em> leverages host autophagy for its gain and identify a target for potential disease management, which may offer new avenues for developing novel drugs against this parasite.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"305 ","pages":"Article 128383"},"PeriodicalIF":6.9,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145820122","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 : 2025-10-29DOI: 10.1016/j.micres.2025.128380
Jieting Wu , Haoran Yin , Yuxin Li , Lei Zhao , Haijuan Guo , Chengbin Xu , Jing Shang , Xiaofan Fu , Fang Ma , Ruoning Song
The migration and transformation of polycyclic aromatic hydrocarbons (PAHs) in soil systems are inherently constrained by their low solubility, strong sorption affinity to soil particles, and limited bioavailability for biological uptake and degradation. As a critical ecological interface mediating plant-microbe interactions, the rhizosphere plays a pivotal role in facilitating PAHs mobilization and transformation processes. This review systematically examines the spatiotemporal dynamics of PAHs migration and transformation within rhizosphere systems under plant-microbe collaborative regulation, characterized by sequential temporal phases (initial desorption-solubilization, intermediate absorption-accumulation, and terminal degradation-transformation) and spatial stratification (rhizosphere soil-liquid interface, root surface microenvironment, and internal root tissues). We particularly emphasize the synergistic plant-microbe interactions that drive PAHs desorption, solubilization, phytoaccumulation, and biodegradation. Furthermore, we elucidate four potential mechanistic pathways: AHL analogs in root exudates activate bacterial quorum sensing systems to stimulate surfactant production and PAHs-degrading enzyme synthesis; Microbial-derived IAA enhances H+ -ATPase activity in plants, facilitating PAHs/H+ co-transport mechanisms; Coordinated AHL-IAA signaling promotes Ca2+ uptake and upregulates root nodule symbiosis-related gene expression; ROS in root exudates activate bacterial c-di-GMP signaling pathways to enhance microbial colonization and PAHs-degrading enzyme production. We also analyze the practical limitations affecting rhizoremediation efficacy, including climatic conditions, soil heterogeneity, and variations in pollutant types, and propose corresponding future research directions toward the end of the article. This comprehensive analysis establishes a theoretical framework for understanding the mechanistic basis of plant-microbe synergism in rhizospheric PAHs remediation, offering a foundation for advancing rhizosphere engineering and phytoremediation strategies.
{"title":"Dynamic drivers of PAHs transformation in the spatial and temporal continuum of the rhizosphere: An analysis of plant-microbe synergistic mechanism","authors":"Jieting Wu , Haoran Yin , Yuxin Li , Lei Zhao , Haijuan Guo , Chengbin Xu , Jing Shang , Xiaofan Fu , Fang Ma , Ruoning Song","doi":"10.1016/j.micres.2025.128380","DOIUrl":"10.1016/j.micres.2025.128380","url":null,"abstract":"<div><div>The migration and transformation of polycyclic aromatic hydrocarbons (PAHs) in soil systems are inherently constrained by their low solubility, strong sorption affinity to soil particles, and limited bioavailability for biological uptake and degradation. As a critical ecological interface mediating plant-microbe interactions, the rhizosphere plays a pivotal role in facilitating PAHs mobilization and transformation processes. This review systematically examines the spatiotemporal dynamics of PAHs migration and transformation within rhizosphere systems under plant-microbe collaborative regulation, characterized by sequential temporal phases (initial desorption-solubilization, intermediate absorption-accumulation, and terminal degradation-transformation) and spatial stratification (rhizosphere soil-liquid interface, root surface microenvironment, and internal root tissues). We particularly emphasize the synergistic plant-microbe interactions that drive PAHs desorption, solubilization, phytoaccumulation, and biodegradation. Furthermore, we elucidate four potential mechanistic pathways: AHL analogs in root exudates activate bacterial quorum sensing systems to stimulate surfactant production and PAHs-degrading enzyme synthesis; Microbial-derived IAA enhances H<sup>+</sup> -ATPase activity in plants, facilitating PAHs/H<sup>+</sup> co-transport mechanisms; Coordinated AHL-IAA signaling promotes Ca<sup>2+</sup> uptake and upregulates root nodule symbiosis-related gene expression; ROS in root exudates activate bacterial c-di-GMP signaling pathways to enhance microbial colonization and PAHs-degrading enzyme production. We also analyze the practical limitations affecting rhizoremediation efficacy, including climatic conditions, soil heterogeneity, and variations in pollutant types, and propose corresponding future research directions toward the end of the article. This comprehensive analysis establishes a theoretical framework for understanding the mechanistic basis of plant-microbe synergism in rhizospheric PAHs remediation, offering a foundation for advancing rhizosphere engineering and phytoremediation strategies.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128380"},"PeriodicalIF":6.9,"publicationDate":"2025-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145452372","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 : 2025-10-29DOI: 10.1016/j.micres.2025.128375
Li Cheng , Xinyuan Wang , Qianqian Wang , Kehan Yin, Bo Wang, Biyu Wu, Ping Xu, Hongyi Qiu, Wenjing Ge, Jiali Sun, Qing Shi, Xiujuan Yan , Shengliang Chen
Circadian rhythm disturbance caused by shift work has become increasingly prevalent, emerging as a risk factor for digestive diseases. Both the host’s and the microbial metabolic pathways and functions might be markedly altered by circadian disruption. However, metabolic changes in the gut during shift work are poorly reported. Here, we demonstrated intestinal metabolome signatures in individuals with shift work disorder and identified sebacic acid as a symptoms-related metabolite. Shift work-related circadian rhythm disturbance leads to enhanced hepatic fatty acid ω-oxidation and a significant increase in dicarboxylic fatty acids in feces. Among these, the increased sebacic acid impaired the intestinal mucus barrier by regulating composition of mucus-related gut bacteria, characterized by an increase in Muribaculaceae and a decrease in Akkermansia abundance, along with activated immune system characterized by increased B cell responses, thereby driving the occurrence of intestinal inflammation. The application of the inhibitor for CYP4A, a key ω-hydroxylase in fatty acid oxidation, effectively improved intestinal dysfunction caused by circadian rhythm disturbance. Our findings provide a deep insight into understanding the role of circadian rhythm in maintaining intestinal homeostasis.
{"title":"Circadian rhythm disturbance impairs intestinal mucus barrier and immune microenvironment via sebacic acid-mediated gut dysbiosis","authors":"Li Cheng , Xinyuan Wang , Qianqian Wang , Kehan Yin, Bo Wang, Biyu Wu, Ping Xu, Hongyi Qiu, Wenjing Ge, Jiali Sun, Qing Shi, Xiujuan Yan , Shengliang Chen","doi":"10.1016/j.micres.2025.128375","DOIUrl":"10.1016/j.micres.2025.128375","url":null,"abstract":"<div><div>Circadian rhythm disturbance caused by shift work has become increasingly prevalent, emerging as a risk factor for digestive diseases. Both the host’s and the microbial metabolic pathways and functions might be markedly altered by circadian disruption. However, metabolic changes in the gut during shift work are poorly reported. Here, we demonstrated intestinal metabolome signatures in individuals with shift work disorder and identified sebacic acid as a symptoms-related metabolite. Shift work-related circadian rhythm disturbance leads to enhanced hepatic fatty acid ω-oxidation and a significant increase in dicarboxylic fatty acids in feces. Among these, the increased sebacic acid impaired the intestinal mucus barrier by regulating composition of mucus-related gut bacteria, characterized by an increase in <em>Muribaculaceae</em> and a decrease in <em>Akkermansia</em> abundance, along with activated immune system characterized by increased B cell responses, thereby driving the occurrence of intestinal inflammation. The application of the inhibitor for CYP4A, a key ω-hydroxylase in fatty acid oxidation, effectively improved intestinal dysfunction caused by circadian rhythm disturbance. Our findings provide a deep insight into understanding the role of circadian rhythm in maintaining intestinal homeostasis.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128375"},"PeriodicalIF":6.9,"publicationDate":"2025-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145418897","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 : 2025-10-28DOI: 10.1016/j.micres.2025.128381
Ning Li , Yuemei Zhang , Zhaolei Qu , Jie Xu , Angang Ming , Hui Sun , Lin Huang
The large-scale cultivation of eucalyptus has led to significant ecological challenges, such as declines in soil microbial diversity and soil degradation. To address these issues, management practices incorporating nitrogen-fixing species and adjusted rotation periods have been proposed. However, their impacts on rhizosphere soil microorganisms and metabolites remain insufficiently understood. This study employed metagenomic and untargeted metabolomics techniques to investigate the response of rhizosphere microorganisms and metabolites in eucalyptus plantations under different management regimes: monoculture plantation, plantation mixed with a nitrogen-fixing tree species, monoculture second-generation plantation, and second-generation mixed plantation. The results revealed that mixed plantation increased microbial diversity compared to continuous cropping. In contrast, second-generation monoculture led to a loss of unique microbial species and reduced microbial community stability compared to the first-generation monoculture. In nutrient-poor pure second-generation plantations, the bacterium Gemmatimonadetes (relative abundance: PF: 0.13 %, PS: 0.39 %, MF: 0.14 %, MS: 0.21 %)—which plays a key role in soil phosphorus cycle—was enriched. Although continuous cropping improved the organic phosphorus mineralization function, it decreased the abundance of genes related to carbon (rbcL and ppc) and phosphorus cycle (phoP and ppk2). The metabolite fluocinolone is negatively correlated with carbon, nitrogen and phosphorus cycle gene components in our dataset, while echinocystic acid and bezitramide are positively correlated. These findings highlight that mixed plantations enhance the ecological niche of eucalyptus rhizosphere by altering the interaction between rhizosphere microbial composition, function, and host plant metabolism.
{"title":"Rhizosphere resilience: Exploring microbial diversity and metabolic responses in long-term eucalyptus plantations","authors":"Ning Li , Yuemei Zhang , Zhaolei Qu , Jie Xu , Angang Ming , Hui Sun , Lin Huang","doi":"10.1016/j.micres.2025.128381","DOIUrl":"10.1016/j.micres.2025.128381","url":null,"abstract":"<div><div>The large-scale cultivation of eucalyptus has led to significant ecological challenges, such as declines in soil microbial diversity and soil degradation. To address these issues, management practices incorporating nitrogen-fixing species and adjusted rotation periods have been proposed. However, their impacts on rhizosphere soil microorganisms and metabolites remain insufficiently understood. This study employed metagenomic and untargeted metabolomics techniques to investigate the response of rhizosphere microorganisms and metabolites in eucalyptus plantations under different management regimes: monoculture plantation, plantation mixed with a nitrogen-fixing tree species, monoculture second-generation plantation, and second-generation mixed plantation. The results revealed that mixed plantation increased microbial diversity compared to continuous cropping. In contrast, second-generation monoculture led to a loss of unique microbial species and reduced microbial community stability compared to the first-generation monoculture. In nutrient-poor pure second-generation plantations, the bacterium Gemmatimonadetes (relative abundance: PF: 0.13 %, PS: 0.39 %, MF: 0.14 %, MS: 0.21 %)—which plays a key role in soil phosphorus cycle—was enriched. Although continuous cropping improved the organic phosphorus mineralization function, it decreased the abundance of genes related to carbon (<em>rbcL</em> and <em>ppc</em>) and phosphorus cycle (<em>phoP</em> and <em>ppk2</em>). The metabolite fluocinolone is negatively correlated with carbon, nitrogen and phosphorus cycle gene components in our dataset, while echinocystic acid and bezitramide are positively correlated. These findings highlight that mixed plantations enhance the ecological niche of eucalyptus rhizosphere by altering the interaction between rhizosphere microbial composition, function, and host plant metabolism.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128381"},"PeriodicalIF":6.9,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145418898","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 : 2025-10-28DOI: 10.1016/j.micres.2025.128382
Elina Kadriu, Sophie Qin, Stephanie M. Prezioso, Dinesh Christendat
Carbon utilization strategies are fundamental to microbial proliferation within complex ecosystems like the soil microbiome. These strategies dictate how microbes prioritize, and metabolize available carbon compounds, shaping community dynamics and ecological outcomes. Pseudomonas putida KT2440, a soil bacterium renowned for its metabolic versatility, exemplifies this adaptive capacity. However, the regulatory mechanism it employs to prioritize sugars vs aromatic compounds for their energy requirement remains poorly understood. Here, we investigated two IclR-type transcriptional regulators, LigR1 and LigR2, which control expression of the lig1 and lig2 operons. Functional analyses reveal that LigR1 and LigR2 activate lig1 but repress the lig2 operon. 4-hydroxybenzoate binding to LigR1 represses gene expression, whereas quinate, protocatechuate, and 4-hydroxybenzoate bind to LigR2 to induce lig2 operon expression. Additionally, ligR1 deletion causes growth defects on glucose and 4-hydroxybenzoate, accompanied by cell elongation and aggregation. We propose that the lig1 operon mediates dual influx of glucose and aromatics via its major facilitator superfamily transporter, while the lig2 operon catalyzes aromatic breakdown through a protocatechuate intermediate and meta-cleavage pathway, supplying oxaloacetate to the TCA cycle. Importantly, P. putida prioritizes shikimate pathway intermediates as energy sources under specific metabolic conditions, such as their accumulation. Overall, these findings redefine the metabolic flexibility of soil pseudomonads and reveal a novel mechanism for thriving in chemically diverse environments. By illuminating a dual regulatory system, our study offers new insight into microbial carbon flux and on the traditional biosynthetic paradigm of the shikimate pathway, revealing its unexpected role in supplying the organism with energy generating compounds.
{"title":"The interplay between glucose and aromatic compound regulation by two IclR-type transcription factors, LigR1 and LigR2, in Pseudomonas putida KT2440","authors":"Elina Kadriu, Sophie Qin, Stephanie M. Prezioso, Dinesh Christendat","doi":"10.1016/j.micres.2025.128382","DOIUrl":"10.1016/j.micres.2025.128382","url":null,"abstract":"<div><div>Carbon utilization strategies are fundamental to microbial proliferation within complex ecosystems like the soil microbiome. These strategies dictate how microbes prioritize, and metabolize available carbon compounds, shaping community dynamics and ecological outcomes. <em>Pseudomonas putida</em> KT2440, a soil bacterium renowned for its metabolic versatility, exemplifies this adaptive capacity. However, the regulatory mechanism it employs to prioritize sugars vs aromatic compounds for their energy requirement remains poorly understood. Here, we investigated two IclR-type transcriptional regulators, LigR1 and LigR2, which control expression of the <em>lig1</em> and <em>lig2</em> operons. Functional analyses reveal that LigR1 and LigR2 activate <em>lig1</em> but repress the <em>lig2</em> operon. 4-hydroxybenzoate binding to LigR1 represses gene expression, whereas quinate, protocatechuate, and 4-hydroxybenzoate bind to LigR2 to induce <em>lig2</em> operon expression. Additionally, <em>ligR1</em> deletion causes growth defects on glucose and 4-hydroxybenzoate, accompanied by cell elongation and aggregation. We propose that the <em>lig1</em> operon mediates dual influx of glucose and aromatics via its major facilitator superfamily transporter, while the <em>lig2</em> operon catalyzes aromatic breakdown through a protocatechuate intermediate and meta-cleavage pathway, supplying oxaloacetate to the TCA cycle. Importantly, <em>P. putida</em> prioritizes shikimate pathway intermediates as energy sources under specific metabolic conditions, such as their accumulation. Overall, these findings redefine the metabolic flexibility of soil pseudomonads and reveal a novel mechanism for thriving in chemically diverse environments. By illuminating a dual regulatory system, our study offers new insight into microbial carbon flux and on the traditional biosynthetic paradigm of the shikimate pathway, revealing its unexpected role in supplying the organism with energy generating compounds.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128382"},"PeriodicalIF":6.9,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145418811","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 : 2025-10-27DOI: 10.1016/j.micres.2025.128379
Alberto Bombelli , Natalia Crespo Tapia , Marcel H. Tempelaars , Sjef Boeren , Heidy M.W. den Besten , Tjakko Abee , Yue Liu
Biofilm formation is key in Listeria monocytogenes’ transmission and persistence in food processing environments. To further understand the mechanisms contributing to biofilm formation, an experimental evolution system was used to isolate strong biofilm producing strains of L. monocytogenes EGDe (reference strain) and FBR16 (hypermutator food isolate). After cycles of plastic surface colonisation, biofilm formation, dispersal and attachment to new surfaces, evolved variants (EV) strains were isolated and found to produce up to seven-fold more biofilm than their respective ancestral (AN) strains. Phenotypic assays revealed an increase in cell surface hydrophobicity as a shared dominant feature of EGDe and FBR16 EV isolates. Proteomic analysis showed proteins Lmo1798, a predicted glucosyltransferase, and Lmo1799, a putative peptidoglycan binding protein with 226 Ala-Asp tandem repeats, to be the most upregulated proteins in both EV strains compared to the AN strains. Genomic analysis of the EGDe EV strain identified a single-nucleotide insertion in the upstream region of lmo1799 and an in-frame deletion of 42 nucleotides in lmo1799, conceivably resulting in high-level expression of a functional protein with 219 Ala-Asp repeats. To evaluate the impact of Lmo1799 on the EV phenotypes and the overall biofilm capacity of L. monocytogenes, EGDe EV mutants lacking lmo1799 and/or the upstream insertion were constructed. Notably, both constructed mutants showed reduced biofilm formation and lower surface hydrophobicity compared to the EV strain, indicating the importance of these mutations for the strong biofilm capacity. Overall, these observations indicate a critical role of Lmo1799 in L. monocytogenes cell surface characteristics and biofilm formation.
{"title":"Evolution of Listeria monocytogenes to a strong biofilm producer via the overexpression of Lmo1799","authors":"Alberto Bombelli , Natalia Crespo Tapia , Marcel H. Tempelaars , Sjef Boeren , Heidy M.W. den Besten , Tjakko Abee , Yue Liu","doi":"10.1016/j.micres.2025.128379","DOIUrl":"10.1016/j.micres.2025.128379","url":null,"abstract":"<div><div>Biofilm formation is key in <em>Listeria monocytogenes</em>’ transmission and persistence in food processing environments. To further understand the mechanisms contributing to biofilm formation, an experimental evolution system was used to isolate strong biofilm producing strains of <em>L. monocytogenes</em> EGDe (reference strain) and FBR16 (hypermutator food isolate). After cycles of plastic surface colonisation, biofilm formation, dispersal and attachment to new surfaces, evolved variants (EV) strains were isolated and found to produce up to seven-fold more biofilm than their respective ancestral (AN) strains. Phenotypic assays revealed an increase in cell surface hydrophobicity as a shared dominant feature of EGDe and FBR16 EV isolates. Proteomic analysis showed proteins Lmo1798, a predicted glucosyltransferase, and Lmo1799, a putative peptidoglycan binding protein with 226 Ala-Asp tandem repeats, to be the most upregulated proteins in both EV strains compared to the AN strains. Genomic analysis of the EGDe EV strain identified a single-nucleotide insertion in the upstream region of <em>lmo1799</em> and an in-frame deletion of 42 nucleotides in <em>lmo1799</em>, conceivably resulting in high-level expression of a functional protein with 219 Ala-Asp repeats. To evaluate the impact of Lmo1799 on the EV phenotypes and the overall biofilm capacity of <em>L. monocytogenes</em>, EGDe EV mutants lacking <em>lmo1799</em> and/or the upstream insertion were constructed. Notably, both constructed mutants showed reduced biofilm formation and lower surface hydrophobicity compared to the EV strain, indicating the importance of these mutations for the strong biofilm capacity. Overall, these observations indicate a critical role of Lmo1799 in <em>L. monocytogenes</em> cell surface characteristics and biofilm formation.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128379"},"PeriodicalIF":6.9,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145445186","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 : 2025-10-26DOI: 10.1016/j.micres.2025.128378
Wilfred Mabeche Anjago , Siqiao Chen , Yishen Zhao , Jiaqi Lu , Yajuan Chen , Dongmei Zhou , Irina S. Druzhinina , Lihui Wei , Paul Daly
The breakdown of oomycete necromass is an important source of organic matter for composting. How Trichoderma harzianum, an important composting fungus, regulates gene expression and produces exo-proteins for degradation of oomycete necromass is poorly understood, especially related to cellulose, an important component of oomycete necromass. Complementary techniques of chemical compositional analysis, transcriptomics, exo-proteomics, enzymatic assays, and fungal genetics were used to analyze the degradation of inactivated oomycete mycelial powder – a surrogate for oomycete necromass. In total, 1556 genes were upregulated and 212 exo-proteins were produced in T. harzianum oomycete mycelial powder cultures, and about 25 % of the produced proteins showed corresponding gene upregulation. The enzymes detected, such as β-1,3-glucanases, and β-1,4-glucanases (cellulases), matched well with the composition of oomycete mycelial powder. Linkage compositional analysis showed that the mycelial powder contained ∼ 60 % 1,3 linkages and ∼19 % 1,4 linkages. The enzyme cocktail from the submerged cultures converted approximately one-third of the mycelial powder to glucose by in vitro assays. The conversion of the mycelial powder to glucose was not substantially reduced by deletion of the cellulolytic transcriptional activator XYR1. Deletion of XYR1 did decrease cellulase activity but only ∼1 % of mycelial powder-induced genes appeared to be XYR1-regulated. In conclusion, T. harzianum produces suitable enzyme cocktails for oomycete mycelial powder degradation, with β-1,3-glucanases likely playing a more important role than cellulases. T. harzianum cellulases may either be relatively unimportant for the degradation, or may not be co-activated alongside CAZymes degrading less recalcitrant parts of the mycelial powder.
{"title":"Regulation of Trichoderma harzianum gene expression and protein production in submerged cultures with inactivated oomycete mycelium","authors":"Wilfred Mabeche Anjago , Siqiao Chen , Yishen Zhao , Jiaqi Lu , Yajuan Chen , Dongmei Zhou , Irina S. Druzhinina , Lihui Wei , Paul Daly","doi":"10.1016/j.micres.2025.128378","DOIUrl":"10.1016/j.micres.2025.128378","url":null,"abstract":"<div><div>The breakdown of oomycete necromass is an important source of organic matter for composting. How <em>Trichoderma harzianum</em>, an important composting fungus, regulates gene expression and produces exo-proteins for degradation of oomycete necromass is poorly understood, especially related to cellulose, an important component of oomycete necromass. Complementary techniques of chemical compositional analysis, transcriptomics, exo-proteomics, enzymatic assays, and fungal genetics were used to analyze the degradation of inactivated oomycete mycelial powder – a surrogate for oomycete necromass. In total, 1556 genes were upregulated and 212 exo-proteins were produced in <em>T. harzianum</em> oomycete mycelial powder cultures, and about 25 % of the produced proteins showed corresponding gene upregulation. The enzymes detected, such as β-1,3-glucanases, and β-1,4-glucanases (cellulases), matched well with the composition of oomycete mycelial powder. Linkage compositional analysis showed that the mycelial powder contained ∼ 60 % 1,3 linkages and ∼19 % 1,4 linkages. The enzyme cocktail from the submerged cultures converted approximately one-third of the mycelial powder to glucose by <em>in vitro</em> assays. The conversion of the mycelial powder to glucose was not substantially reduced by deletion of the cellulolytic transcriptional activator XYR1. Deletion of XYR1 did decrease cellulase activity but only ∼1 % of mycelial powder-induced genes appeared to be XYR1-regulated. In conclusion, <em>T. harzianum</em> produces suitable enzyme cocktails for oomycete mycelial powder degradation, with β-1,3-glucanases likely playing a more important role than cellulases. <em>T. harzianum</em> cellulases may either be relatively unimportant for the degradation, or may not be co-activated alongside CAZymes degrading less recalcitrant parts of the mycelial powder.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128378"},"PeriodicalIF":6.9,"publicationDate":"2025-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145505595","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 : 2025-10-24DOI: 10.1016/j.micres.2025.128377
Xueqiang Xin , Kai Peng , Qiaojun Wang , Mashkoor Mohsin , Antonio Ruzzini , Zhiqiang Wang , Ruichao Li
The escalating prevalence of antimicrobial resistance (AMR) constitutes a global public health crisis. This is exacerbated by the continuous emergence of new variants and the discovery of previously unrecognized antibiotic resistance genes (ARGs). While advanced AMR surveillance efforts include time-consuming epidemiological investigations and retrospective analyses, critical gaps often remain towards our understanding of the sources of newly identified ARGs. Here, we established a framework integrating omics-based epidemiological investigations, genomic feature analysis of ARGs-carrying bacteria and evolution analysis of novel ARGs. We took the novel resistance gene estT as an example and analyzed it following this framework. Our study revealed that the estT gene was widely prevalent, capable of cross-phyla transmission, and predominantly present in human- and animal-derived bacteria. We explored the genomic characteristics of estT-positive Escherichia coli, Bacillus spp., Mannheimia haemolytica, and Riemerella anatipestifer, uncovering their public health risks. Evolution analysis of estT homologs found historical connections between estTs and tet(X)s. This study provides a systematic strategy for the proactive surveillance of emerging ARGs, enabling omics-data-driven monitoring of ARG evolution and dissemination to mitigate the escalating crisis of AMR.
{"title":"An omics-based framework for investigating the emerging antibiotic resistance gene: The case of estT","authors":"Xueqiang Xin , Kai Peng , Qiaojun Wang , Mashkoor Mohsin , Antonio Ruzzini , Zhiqiang Wang , Ruichao Li","doi":"10.1016/j.micres.2025.128377","DOIUrl":"10.1016/j.micres.2025.128377","url":null,"abstract":"<div><div>The escalating prevalence of antimicrobial resistance (AMR) constitutes a global public health crisis. This is exacerbated by the continuous emergence of new variants and the discovery of previously unrecognized antibiotic resistance genes (ARGs). While advanced AMR surveillance efforts include time-consuming epidemiological investigations and retrospective analyses, critical gaps often remain towards our understanding of the sources of newly identified ARGs. Here, we established a framework integrating omics-based epidemiological investigations, genomic feature analysis of ARGs-carrying bacteria and evolution analysis of novel ARGs. We took the novel resistance gene <em>estT</em> as an example and analyzed it following this framework. Our study revealed that the <em>estT</em> gene was widely prevalent, capable of cross-phyla transmission, and predominantly present in human- and animal-derived bacteria. We explored the genomic characteristics of <em>estT</em>-positive <em>Escherichia coli</em>, <em>Bacillus</em> spp., <em>Mannheimia haemolytica</em>, and <em>Riemerella anatipestifer</em>, uncovering their public health risks. Evolution analysis of <em>estT</em> homologs found historical connections between <em>estT</em>s and <em>tet</em>(X)s. This study provides a systematic strategy for the proactive surveillance of emerging ARGs, enabling omics-data-driven monitoring of ARG evolution and dissemination to mitigate the escalating crisis of AMR.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"303 ","pages":"Article 128377"},"PeriodicalIF":6.9,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145401201","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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