Microbiological research最新文献

{"title":"c-di-GMP regulates the resistance of Pseudomonas aeruginosa to heat shock and aminoglycoside antibiotics by targeting the σ factor RpoH","authors":"Xinyi Huo ,&nbsp;Lianying Mao ,&nbsp;Chenyu Dong,&nbsp;Wenguang Yang,&nbsp;Heng Zhang,&nbsp;Lei Zhang","doi":"10.1016/j.micres.2025.128347","DOIUrl":"10.1016/j.micres.2025.128347","url":null,"abstract":"<div><div>Cyclic di-GMP (c-di-GMP) is a second messenger molecule that is widely distributed in bacteria and plays various physiologically important regulatory roles through interactions with a variety of effector molecules. Sigma (σ) factors are the predominant transcription factors involved in transcription regulation in bacteria. While c-di-GMP has been shown to bind to a range of transcription factors, c-di-GMP-binding σ factors have never been reported before. In a c-di-GMP/σ factors binding screen, we identified the σ factor RpoH as a c-di-GMP-responsive transcription factor in <em>Pseudomonas aeruginosa</em> PAO1. We further show that the binding of c-di-GMP to RpoH inhibits binding of RpoH to the promoters of its target genes such as <em>asrA</em> and <em>dnaK</em>, thereby downregulating the expression of these genes and reducing the resistance of <em>P. aeruginosa</em> to heat shock and aminoglycoside antibiotics. RpoH from <em>Escherichia coli, Burkholderia thailandensis</em> and <em>Agrobacterium tumefaciens</em> are also capable of binding c-di-GMP, suggesting that c-di-GMP-mediated control of the activity of RpoH is conserved in members of Proteobacteria.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128347"},"PeriodicalIF":6.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155921","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}

{"title":"Corrigendum to “Gut microbiota-driven BCAA biosynthesis via Staphylococcus aureus -expressed acetolactate synthase impairs glycemic control in type 2 diabetes in South China” [Microbiol. Res. 296 (2025) 128145]","authors":"Tingting Liang ,&nbsp;Tong Jiang ,&nbsp;Zhuang Liang ,&nbsp;Longyan Li ,&nbsp;Ya Chen ,&nbsp;Tong Chen ,&nbsp;Lingshuang Yang ,&nbsp;Ni Zhang ,&nbsp;Bo Dong ,&nbsp;Xinqiang Xie ,&nbsp;Bing Gu ,&nbsp;Qingping Wu","doi":"10.1016/j.micres.2025.128344","DOIUrl":"10.1016/j.micres.2025.128344","url":null,"abstract":"","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128344"},"PeriodicalIF":6.9,"publicationDate":"2025-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113720","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}

{"title":"Metabolic control of cytokinesis by glucose cAMP–PKA signaling in fission yeast","authors":"Antonio Marín-Castillo,&nbsp;Sergio León-Zaragoza,&nbsp;Alejandro Franco,&nbsp;Jero Vicente-Soler,&nbsp;Andrés Núñez,&nbsp;Teresa Soto,&nbsp;Marisa Madrid,&nbsp;José Cansado","doi":"10.1016/j.micres.2025.128345","DOIUrl":"10.1016/j.micres.2025.128345","url":null,"abstract":"<div><div>Cytokinesis, the final step of cell division, must be precisely coordinated with the cellular metabolic status, yet the underlying regulatory mechanisms remain poorly understood. Here we show that in <em>Schizosaccharomyces pombe</em>, glucose signaling promotes cytokinesis via the evolutionarily conserved cAMP–PKA signaling pathway. Loss of the Pka1 catalytic subunit delays assembly and constriction of the contractile actomyosin ring (CAR), whereas constitutive PKA activation enhances CAR integrity and accelerates cytokinesis. Mechanistically, Pka1 downregulates the basal activity of the stress-activated MAPK Sty1 under glucose-rich conditions, thereby stabilizing the formin For3 and its nucleated actin cables, which collaborate to regulate CAR dynamics. Remarkably, cAMP–PKA signaling also facilitates cytokinesis through a parallel, actin cable–independent mechanism. Additionally, mitochondrial respiration contributes to cytokinesis in the presence of glucose through a PKA-independent pathway. These findings reveal a multilayered network that links carbon source metabolism to cytoskeletal organization and underscore the importance of tight PKA activity control for robust cell division.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128345"},"PeriodicalIF":6.9,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145118922","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}

{"title":"Novel plant-derived compounds modulate gut microbiome dysbiosis in colitis mice: A potential therapeutic avenue for inflammatory bowel disease","authors":"Md. Mizanur Rahaman ,&nbsp;Karma Yeshi ,&nbsp;Mehedi Hasan Bappi ,&nbsp;Md. Zohorul Islam ,&nbsp;Phurpa Wangchuk ,&nbsp;Subir Sarker","doi":"10.1016/j.micres.2025.128343","DOIUrl":"10.1016/j.micres.2025.128343","url":null,"abstract":"<div><div>Inflammatory bowel disease (IBD) is a chronic, multifactorial disorder of the gastrointestinal tract, often associated with dysbiosis in gut microbiota. While the exact cause of IBD remains unclear, alterations in gut microbiome composition and function are recognised as key contributors to IBD pathogenesis. Natural compounds with anti-inflammatory properties are increasingly explored as potential therapeutic options for IBD. This study evaluated the therapeutic effects of two newly isolated galloyl glucosides—galloyl-lawsoniaside A (comp-4) and uromyrtoside (comp-6)—alongside dexamethasone (DEX) on microbiome regulation in a 2, 4, 6-Trinitrobenzene sulfonic acid (TNBS)-induced colitis mouse model. We employed PacBio HiFi full-length 16S rRNA gene sequencing on mouse colon tissue to assess changes in the intestinal microbiome and its associated functional pathways. TNBS-induced colitis significantly altered microbial composition, increasing the abundance of <em>Acutalibacter muris</em>, <em>Monoglobus pectinilyticus</em>, <em>Streptococcus pneumoniae</em>, <em>Parabacteroides merdae</em>, and <em>Haemophilus influenzae</em>, while decreasing <em>Staphylococcus ureilyticus</em> and <em>Mailhella massiliensis</em>. Treatment with comps 4 and 6 effectively restored the imbalanced microbiota. Functional pathway analysis revealed that colitis reduced microbial pathways, including peptidoglycan biosynthesis and the Bifidobacterium shunt. These disruptions were restored following treatment with our plant-derived compounds. Functional improvements were likely associated with reduced IL-6 production and restoring intestinal barrier integrity. Notably, comp-4 exhibited the most pronounced therapeutic efficacy across both microbial and host-associated parameters. <em>In silico</em> docking further supported the anti-inflammatory and immunomodulatory potential of these compounds. Together, our findings highlight the interplay between microbial function and host immunity in IBD and identify plant-derived galloyl glucosides as promising candidates for microbiome-targeted IBD therapeutics.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128343"},"PeriodicalIF":6.9,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145099372","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}

{"title":"LicD-mediated cell wall decoration governs phage sensitivity in Enterococcus faecalis clinical isolates","authors":"Muhammed Awad ,&nbsp;George Bouras ,&nbsp;Sholeh Feizi ,&nbsp;Susanna R. Grigson ,&nbsp;Peter-John Wormald ,&nbsp;Alkis J. Psaltis ,&nbsp;Sarah Vreugde","doi":"10.1016/j.micres.2025.128341","DOIUrl":"10.1016/j.micres.2025.128341","url":null,"abstract":"<div><div><em>Enterococcus faecalis</em> has emerged as a prevalent antibiotic-resistant pathogen in clinical settings. Herein, we report the identification of three novel lytic phages targeting vancomycin-resistant <em>E. faecalis</em>. While the isolated phages all belonged to the <em>Kochikohdavirus</em> genus, there were distinctive differences in their tail fibre proteins, affecting their adsorption. The phages showed strong antibacterial activity with wide host range, infecting &gt; 90 % of the tested <em>E. faecalis</em> clinical and hospital wastewater isolates (n = 13) with variable efficiency. The variation in host range was genomically correlated to the presence of the <em>licD</em> gene in phage sensitive bacteria, which is responsible for phosphorylcholine decoration of the bacterial cell wall. Furthermore<em>,</em> the isolated phages were predicted to harbour genes encoding for depolymerase enzymes, which was confirmed by <em>in vitro</em> testing showing a &gt; 80 % reduction in biofilm biomass. Phages inhibited bacterial growth for ≥ 12 h, followed by the emergence of bacteriophage insensitive mutants (BIMs) that were 4-fold more sensitive to vancomycin compared to parent strains. In addition, the isolated BIMs showed less capability of evading THP-1 macrophage and produced weaker biofilms. These findings underpin the potential of the isolated phages in combating recalcitrant <em>E. faecalis</em> associated biofilm-mediated infections.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128341"},"PeriodicalIF":6.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145075702","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}

{"title":"Dual roles of MWCNTs on plant growth and remediation efficiency during PGPR-assisted phytoremediation of Cd-Ni contaminated soil","authors":"Wenqing Zhou,&nbsp;Xiaoxian Cai,&nbsp;Ke Chen,&nbsp;Lixue Zheng,&nbsp;Huijun Guan,&nbsp;Tianlong Hao,&nbsp;Jingjing Yang,&nbsp;Lihua Qi,&nbsp;Chunfeng Guan","doi":"10.1016/j.micres.2025.128339","DOIUrl":"10.1016/j.micres.2025.128339","url":null,"abstract":"<div><div>As the main elements causing soil heavy metals (HMs) pollution, cadmium (Cd) and nickel (Ni) can cause irreversible harm to crops and ecosystems. Currently, research on plant growth-promoting rhizobacteria (PGPR)-assisted phytoremediation techniques for contaminated soil has received more attention. Meanwhile, multi-walled carbon nanotubes (MWCNTs) have also been explored for HMs pollution remediation in recent years due to their high specific surface area and strong adsorption. MWCNTs might improve phytoremediation efficiency of HMs-contaminated soil by directly immobilizing HMs and indirectly promoting plant growth, but less research has been devoted to the possible dual-enhancing roles of MWCNTs in PGPR-assisted phytoremediation process. Therefore, this study innovatively investigated the potential role of MWCNTs application in PGPR-assisted phytoremediation with Cd-Ni contaminated soil by rice. The results indicated that the presence of MWCNTs further improved the remediation efficiency of PGPR in assisting phytoremediation, reducing soil Cd^2 + and Ni²⁺ contents by 20.4 % and 13.7 %, respectively, superior to strain BT treatment individually. Scanning electron microscopy micrographs demonstrated that PGPR could attach to MWCNTs surface and be immobilized in MWCNTs. Meanwhile, MWCNTs application in PGPR-assisted phytoremediation could enhance rice survival under Cd and Ni stresses by stimulating antioxidant system and regulating Na⁺/K⁺ level in rice. Moreover, the increase in soil enzyme activities and relative abundance of beneficial microorganisms accelerated nitrogen and phosphorus nutrient cycling in the soil. In conclusion, MWCNTs might be used as adsorbent materials to directly immobilize Cd²⁺ and Ni²⁺ in soil, and also synergized with rice or PGPR to indirectly improve the phytoremediation efficiency of HMs.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128339"},"PeriodicalIF":6.9,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145045477","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}

{"title":"Multiple catabolism contributes to biodegradation of phthalate-based plasticizers in Acinetobacter baumannii","authors":"Yapeng Li ,&nbsp;Huixin Fan ,&nbsp;Boqiao Li ,&nbsp;Xiaobo Liu","doi":"10.1016/j.micres.2025.128338","DOIUrl":"10.1016/j.micres.2025.128338","url":null,"abstract":"<div><div>Phthalates (PAEs) have been widely used as plasticizers in the production of plastics. Unfortunately, PAEs released into the environment during plastic aging pose a threat to human life and health. Although microbial biodegradation of PAEs has proven to be an emerging bioremediation approach to modern plastic pollution, the microbial catabolism of PAEs remains elusive. Here, we isolate a PAE-degrading bacterium (identified as <em>Acinetobacter baumannii</em> EMB-1) from crude oil wastewater using Di-n-octylo-phthalate (DnOP) as the sole carbon source and unravel the PAE degradation pathway through a multi-omics approach. We observe that <em>A. baumannii</em> EMB-1 grows well both at low (2–5 g/L) and high (20–50 g/L) concentrations of DnOP but cannot grow on glucose due to a lack of hexokinase. The multi-omics analyses reveal that <em>A. baumannii</em> EMB-1 employs multiple catabolic pathways, including phenylacetic acid degradation, protocatechuic acid (PCA) degradation, and benzoate degradation, which synergistically degrade DnOP. Interestingly, phenylacetate and benzoate catabolism is directly linked to the tricarboxylic acid cycle, whereas partial PCA degradation is used to generate substrates for synthesizing aromatic amino acids. Our findings advance the understanding of microbial PAE catabolism and expand microbial resources that could benefit biological upcycling and bioremediation of recalcitrant phthalate-based plasticizers.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128338"},"PeriodicalIF":6.9,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145045476","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}

{"title":"Impacts of mobile genetic elements on antimicrobial resistance genes in gram-negative pathogens: Current insights and genomic approaches","authors":"Bethany J. Cross ,&nbsp;Sally R. Partridge ,&nbsp;Anna E. Sheppard","doi":"10.1016/j.micres.2025.128340","DOIUrl":"10.1016/j.micres.2025.128340","url":null,"abstract":"<div><div>Antimicrobial resistance threatens to take 10 million lives per year by 2050. It is a recognised global health crisis and understanding the historic and current spread of resistance determinants is important for informing surveillance and control measures. The ‘inheritance’ of resistance is difficult to track because horizontal transfer is common. Antimicrobial resistance genes (ARGs) spread rapidly between bacteria, plasmids and chromosomes due to different mobile genetic elements (MGEs). This movement can increase the range of species carrying an ARG, simplify acquisition of multi-resistance, or otherwise alter the selective advantage associated with carriage of the ARG. MGE activity is therefore a significant factor in understanding routes of ARG dissemination. Characterising the combinations of MGEs contributing to the movement of individual ARGs is crucial. Each MGE category has unique genetic characteristics, and distinct impacts on the location and expression of associated ARGs. Here, the ways in which MGEs can meaningfully associate with ARGs are discussed. Approaches for extracting information about MGE associations from bacterial genome sequences are also considered. Accurate and informative annotations of the genetic contexts of relevant ARGs provide crucial insight into the presence of MGEs and their locations relative to ARGs. Combining this genomic information with knowledge about relevant biological processes allows more accurate conclusions to be drawn about transmission and dissemination of ARGs.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128340"},"PeriodicalIF":6.9,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155918","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}

{"title":"Corrigendum to “A molecular overview of the polymyxin-LPS interaction in the context of its mode of action and resistance development” [Microbiol. Res. 283 (2024) 127679]","authors":"Indira Padhy,&nbsp;Sambit K. Dwibedy,&nbsp;Saswat S. Mohapatra","doi":"10.1016/j.micres.2025.128335","DOIUrl":"10.1016/j.micres.2025.128335","url":null,"abstract":"","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128335"},"PeriodicalIF":6.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145030155","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}

{"title":"Lactococcus formosensis and its metabolite 4-acetamidobutanoic acid induced caspase-11 dependent myenteric neuronal pyroptosis in intractable functional constipation","authors":"Xiaoqian Dong ,&nbsp;Mengshi Chen ,&nbsp;Haifeng Liu ,&nbsp;Simin Zhou ,&nbsp;Menglin Sun ,&nbsp;Liwei Wang ,&nbsp;Yuwei Li ,&nbsp;Hao Zhang ,&nbsp;Chen Xu ,&nbsp;Bangmao Wang ,&nbsp;Weilong Zhong","doi":"10.1016/j.micres.2025.128328","DOIUrl":"10.1016/j.micres.2025.128328","url":null,"abstract":"<div><div>Intractable functional constipation (IFC), a severe form of chronic constipation characterized by slow transit and resistance to conventional treatments, posed a significant clinical challenge. Here, we identified <em>Lactococcus formosensis</em> (<em>Lf</em>), a Gram-positive bacterium prevalent in IFC patients, as a novel contributor to intestinal motility impairment. Clinically, IFC patients exhibited increased colonic mucosal colonization of <em>Lf</em> and significant myenteric neuronal loss and pyroptosis, particularly in excitatory choline acetyltransferase (ChAT)⁺ neurons, but not inhibitory neuronal nitric oxide synthase (nNOS)⁺ neurons. In mice, <em>Lf</em> and its supernatant impaired intestinal motility, reducing fecal water content, prolonging transit times, and inhibiting spontaneous contractions and maximum contractile force in isolated intestinal segments. RNA sequencing revealed that <em>Lf</em> disrupted neurochemical signaling, implicating neuronal damage in its pathogenic effects. Mechanistically, <em>Lf</em> and its supernatant selectively induced pyroptosis in ChAT⁺ neurons via caspase-1 activation. Metabolomic profiling identified 4-acetamidobutanoic acid (4-ABA) as a key metabolite shared between <em>Lf</em> supernatant and IFC patient feces. 4-ABA induced ChAT⁺ neuronal pyroptosis through a caspase-11-dependent pathway, further impairing intestinal motility, which was confirmed in <em>Casp11⁻/⁻</em> mice. This study uncovered a previously unrecognized pathway of single microbiota-induced neuronal damage in IFC and provided a foundation for novel diagnostic and therapeutic strategies targeting gut microbiota-ENS interactions</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"302 ","pages":"Article 128328"},"PeriodicalIF":6.9,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144997840","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}