Microbiological research最新文献

{"title":"Trichoderma specialized metabolites in biocontrol: gene-metabolite links, ecological functions, and translational bottlenecks.","authors":"Mario Riolo, Santa Olga Cacciola","doi":"10.1016/j.micres.2026.128719","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128719","url":null,"abstract":"<p><p>Trichoderma spp. produce a diverse repertoire of metabolites with specific activities that contribute to biocontrol through direct antagonism, ecological signalling, and modulation of plant responses. However, current knowledge remains uneven: many metabolites are chemically described, whereas fewer are supported by robust gene-metabolite associations, experimentally validated ecological functions, and realistic translational evidence. Progress in this field will depend less on expanding compound catalogues than on integrating mechanistic, ecological, and translational evidence. This review examines the specialized metabolism of Trichoderma with emphasis on biosynthetic gene clusters, regulatory networks, ecological roles, and biosafety constraints relevant to biocontrol. Major metabolite classes, including polyketides, terpenoids, peptaibols, siderophores, diketopiperazines, and volatile organic compounds, are discussed together with representative case studies for which genetic and functional evidence is available. We further propose a translational framework to distinguish metabolites with mainly descriptive support from those approaching application readiness, based on four criteria: gene-level validation, demonstrated ecological role, manageable biosafety profile, and feasible delivery/stability. This perspective helps explain why metabolite inventories continue to expand faster than field translation. Recent advances in genomics, transcriptomics, metabolomics, genome editing, and formulation science are reshaping how Trichoderma metabolites are prioritized for future development.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"314 ","pages":"128719"},"PeriodicalIF":8.5,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148897613","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 \"Integrated analysis uncovers exogenous induction and molecular regulation of erinacine A accumulation in Hericium erinaceus\" [Microbiol. Res., 313 (2026) 128690].","authors":"Yue Li, Xinyi Hu, Zhangyuan Tan, Minfeng Huang, Qiuyun Wu, Ling Xie, Zhilan Xia, Xiaoya Song, Wenbing Gong","doi":"10.1016/j.micres.2026.128711","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128711","url":null,"abstract":"","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":" ","pages":"128711"},"PeriodicalIF":8.5,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148887976","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":"Signal perception to bacterial warfare: Two-component systems mediated regulation of type VI secretion system in the intestinal ecosystem.","authors":"Yunteng Geng, Songbiao Chen, Ke Ding, Rongxian Guo","doi":"10.1016/j.micres.2026.128710","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128710","url":null,"abstract":"<p><p>The intestinal tract is a complex ecological interface in which host cells and resident microbiota jointly maintain barrier integrity, immune homeostasis, and metabolic balance. Within this ecosystem, pathogenic bacteria must overcome colonization resistance imposed by commensal communities and host defenses to establish infection. The type VI secretion system (T6SS) is a contact-dependent secretion apparatus that delivers effector proteins into bacterial competitors or host cells, thereby contributing to interbacterial competition, microbiota remodeling, and host-pathogen interactions. However, T6SS activity is not constitutive; rather, it is tightly regulated in response to environmental and host-derived cues. Two-component systems (TCSs) are central to this regulation because they sense intestinal signals, including pH variation, nutrient/metal ion availability and host-associated signals, and can convert these inputs into coordinated control of T6SS expression and activity, including, in some systems, assembly, effector deployment, and attack timing. In this review, we discuss how pathogens deploy TCS‑regulated T6SSs to orchestrate offensive antagonism and defensive countermeasures during intestinal infection. Beyond promoting T6SS-dependent antagonism, some TCSs also participate in damage sensing, envelope repair, counterattack responses, and compensatory defense programs. In certain T6SS-deficient contexts, TCS-mediated induction of capsular polysaccharide synthesis may provide an alternative protective strategy against T6SS-mediated killing, highlighting the regulatory plasticity of bacterial defense systems. By integrating current knowledge from signal perception to effector delivery, this review outlines how TCSs fine-tune bacterial competitiveness and resilience in the intestinal microenvironment and identifies key gaps that limit our understanding of TCS-T6SS regulation in vivo.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"314 ","pages":"128710"},"PeriodicalIF":8.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148887940","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":"Elevated nitrate levels inhibit nitrogen fixation in Azotobacter chroococcum via an ammonium-independent pathway.","authors":"Ping Tian, Jun-Feng Wang, Yu-Dian Xun, Xiao-Hui Shi, Jia-Ni Lin, Ling-Xia Li, Bao-Yan He, Qu-Sheng Li","doi":"10.1016/j.micres.2026.128709","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128709","url":null,"abstract":"<p><p>Nitrate impairs both symbiotic and free-living biological nitrogen fixation (BNF). While nitrate-induced phosphorylation signalling has been implicated in the inhibition of symbiotic BNF, the suppression of free-living BNF has generally been attributed to ammonium generated during nitrate assimilation. However, whether nitrate can inhibit free-living BNF independently of ammonium feedback regulation remains unclear. Here, an ammonium-deregulated mutant of Azotobacter chroococcum (A4) was used to investigate whether nitrate inhibits nitrogen fixation independently of ammonium regulation. Despite the loss of ammonium-mediated inhibition, nitrate significantly suppressed nitrogen fixation. Nitrate at concentrations above 2 mM reduced extracellular ammonium accumulation, with 10 mM nitrate decreasing ammonium production to 61% of that observed under nitrogen-free conditions. Integrated multi-omics analyses revealed that nitrate triggered extensive regulatory reprogramming across multiple molecular layers, with both coordinated and layer-specific responses across transcriptomic, proteomic and phosphoproteomic levels. These responses differed from the typical ammonium-mediated feedback regulation characterized by substantial repression of nitrogen fixation-related genes or proteins, but nevertheless resulted in reduced ammonium excretion, accompanied by enhanced biomass accumulation and extracellular polymeric substance (EPS) production in A4. Together, these findings indicate that, rather than directly repressing the nitrogen fixation machinery, prolonged nitrate exposure suppresses nitrogen fixation output through global regulatory reprogramming that redirects cellular metabolism and resource allocation away from nitrogen fixation. This study provides new insights into nitrate-mediated regulation of free-living diazotrophs and has implications for optimising nitrogen management and improving the application of nitrogen-fixing microorganisms.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"314 ","pages":"128709"},"PeriodicalIF":8.5,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880291","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":"Stressostat cultivation of Lactococcus lactis improves lactate stress resistance through mutations in RNA polymerase.","authors":"Sylviani Hartono, Henriette Lyng Røder, Sjef Boeren, Daan C Swarts, Tjakko Abee, Eddy J Smid, Oscar van Mastrigt","doi":"10.1016/j.micres.2026.128706","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128706","url":null,"abstract":"<p><p>Adaptive laboratory evolution is used to improve the phenotypes of microorganisms and to characterise the mechanisms underlying resistance against complex growth inhibition. Here we focused on lactic acid bacteria (LAB) as starter cultures for food fermentations. Production of LAB starter cultures is challenging due to growth inhibition by organic acids, mainly lactate, produced during fermentation. By utilising stressostat cultivation we generated Lactococcus lactis isolates with enhanced lactate resistance. Using a combination of (meta)genomics, proteomics and pH-controlled batch fermentations, we deciphered the lactate resistance mechanisms of these L. lactis isolates. Proteome responses of L. lactis, combined with similar growth inhibition at high salt, suggest that high lactate mainly causes osmotic stress. We identified RNA polymerase (RNAP) mutations in subunits β (rpoB) and β' (rpoC) as key mutations, causing pleiotropic effects in the proteome. These proteome adaptations are linked to enhanced lactate resistance, particularly the resistance to hyperosmotic stress in absence of glycine-betaine. Combined, our study shows that RNAP mutations enhanced lactate resistance through pleotropic effects in the proteome that changed L. lactis responses against multiple stresses.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"314 ","pages":"128706"},"PeriodicalIF":8.5,"publicationDate":"2026-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880609","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":"Therapeutic potential of oyster peptides against Staphylococcus aureus-induced mastitis via attenuating inflammation, mitochondrial dysfunction and modulating gut microbiota.","authors":"Yue Sun, Guiqiu Hu, Ning Song, Xiyu Gao, Aohan Yan, Xinyi Li, Qianhui Mi, Juxiong Liu, Wenjin Guo, Yu Cao, Bingxu Huang, Shoupeng Fu, Dewei He","doi":"10.1016/j.micres.2026.128702","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128702","url":null,"abstract":"<p><p>Staphylococcus aureus (S. aureus)-induced mastitis represents a significant challenge in dairy production. Oyster peptides (OP), bioactive compounds derived from oysters, exhibit considerable therapeutic value in treating various diseases due to their antibacterial and anti-inflammatory properties. Nevertheless, their role in alleviating mastitis and protecting the blood-milk barrier (BMB) from S. aureus infection remains underexplored. This study reveals that OP effectively attenuates S. aureus-induced inflammation, reduces oxidative stress, and maintains BMB integrity by preserving tight junction protein expression. Mechanistic studies indicate that OP suppresses the S. aureus-induced over-activation of the TLR2-NF-κB and IP3R1/GRP75/VDAC1 signaling pathways, thereby mitigating inflammation and mitochondrial damage. In addition, 16S rDNA sequencing of the gut microbiota demonstrates that OP modulates microbial composition, enhancing the abundance of beneficial bacteria such as Bacteroides acidifaciens while downregulating harmful bacterial populations. Metabolomic analysis also indicates that OP affects intestinal metabolic pathways, increasing the levels of metabolites like 13-Hotre and stearidonic acid. In conclusion, these findings suggest that OP holds promise as a therapeutic agent for the treatment and prevention of S. aureus-induced mastitis.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"314 ","pages":"128702"},"PeriodicalIF":8.5,"publicationDate":"2026-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880909","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":"Localized root colonization by Trichoderma afroharzianum T22 is associated with host transcriptional reprogramming and beneficial bacterial enrichment under salinity stress in sorghum.","authors":"Ruby Bagchi, Bishrant Pant, Hong Li Wang, Ahmad H Kabir","doi":"10.1016/j.micres.2026.128703","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128703","url":null,"abstract":"<p><p>Salinity is a major abiotic stress that severely restricts crop productivity. Despite considerable potential, the role of Trichoderma afroharzianum T22 in the molecular responses and root microbiome dynamics associated with salinity tolerance remains poorly understood in sorghum. In this study, T. afroharzianum inoculation alleviated salinity-induced stress by improving chlorophyll content, growth parameters, and nutrient balance, while restricting root-to-shoot Na⁺ translocation. Split-root experiments showed that T. afroharzianum application to a single root compartment was insufficient to improve whole-plant performance under salinity, whereas inoculation of both compartments restored growth and chlorophyll-related traits. RNA-seq analysis showed the upregulation of genes involved in symbiosis, hormone signaling, antioxidant defense, and ion homeostasis, accompanied by repression of genes involved in ethylene biosynthesis and senescence in the roots. KEGG enrichment analysis further revealed activation of secondary metabolic pathways involved in stress adaptation. Furthermore, 16S rRNA sequencing showed that T. afroharzianum inoculation was associated with shifts in the root bacterial community without significantly altering alpha diversity, while selectively enriching putatively beneficial taxa, including Dyella mobilis, Luteibacter rhizovicinus, and Luteibacter yeojuensis under salinity. In addition, a conserved core microbiome was retained across treatments and was dominated by Streptomyces, Rhizobium, Dyella, and Labrys. Further, Janibacter was identified as a characteristic indicator taxon of T. afroharzianum inoculation, while Streptomyces showed the highest overall indicator value. Multi-omics integration analysis revealed that T. afroharzianum-associated microbial taxa were strongly associated with hormone signaling, redox homeostasis, mineral transport, and secondary metabolism under salinity stress. Particularly, Streptomyces and Luteibacter were the two genera most strongly associated with plant growth traits, whereas Rhizobium and Mucilaginibacter showed stronger positive correlations with tissue Na⁺ accumulation. Collectively, these findings provide new insights into T. afroharzianum-mediated salinity tolerance in sorghum and highlight its potential as a microbial biostimulant, warranting further validation across diverse sorghum genotypes in field conditions.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"314 ","pages":"128703"},"PeriodicalIF":8.5,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148875450","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":"Synthetic microbial community-assisted regulation of arsenic transport and metabolism reduces grain arsenic accumulation in rice across developmental stages.","authors":"Basudev Majhi, Pradeep Semwal, Deen Dayal Pandey, Shashank Kumar Mishra, Neha Yadav, Puneet Singh Chauhan","doi":"10.1016/j.micres.2026.128704","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128704","url":null,"abstract":"<p><p>Arsenic contamination in paddy soils threatens crop productivity and results in the accumulation of toxic arsenic in rice grains. Here, we demonstrate that a defined synthetic microbial community (SynCom) of Priestia flexa and Pseudomonas putida mitigates arsenic toxicity and restricts arsenic accumulation in rice (Oryza sativa var. Sarju-52). Under arsenic stress [As(III), 18 mg/kg; As(V), 50 mg/kg], plants exhibited impaired growth, reduced photosynthetic performance, and increased oxidative stress. Inoculation with SynCom restored physiological function and metabolic balance, as evidenced by improved photosynthesis, increased soluble sugars, and reduced proline accumulation. Accompanied by attenuation of antioxidant enzyme overactivation, which indicates effective control of reactive oxygen species. Mechanistically, SynCom substantially reduced arsenic accumulation in roots, shoots and grains by coordinate downregulation of arsenic transporter genes (Lsi1, Lsi2, Lsi3, OsNIP1;1, and OsNIP3;3), which limits arsenic uptake and translocation. Metabolomic profiling also indicated stress-associated metabolite suppression and enrichment of growth-related pathways. These results demonstrate that microbiome engineering can reprogram plant responses to arsenic stress and provide a scalable strategy to reduce dietary arsenic exposure from staple crops. Additionally, this study lays a strong foundation for developing SynCom as an effective and sustainable biotechnological intervention to improve food safety and agricultural resilience in arsenic-contaminated areas.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"314 ","pages":"128704"},"PeriodicalIF":8.5,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148887903","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":"Bacteriophages as emerging modulators of antitumor immunity in the tumor microenvironment.","authors":"Xiaoyan Chen, Junfeng Zhang, Feng Gao, Huijun Du","doi":"10.1016/j.micres.2026.128700","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128700","url":null,"abstract":"<p><p>The tumor microenvironment (TME) is increasingly recognized as a complex ecosystem shaped by dynamic interactions among tumor cells, immune cells, and microbial components. While growing evidence has established the microbiota as a key regulator of antitumor immunity and immunotherapy response, the contribution of bacteriophages, the most abundant biological entities within microbial communities, has remained largely overlooked. Recent studies suggest that bacteriophages are not merely passive regulators of bacterial populations but can actively modulate host immune responses and influence tumor-associated immune landscapes. In this review, we summarize emerging evidence suggesting that bacteriophages may influence antitumor immunity through both direct and indirect mechanisms. Evidence from immune-cell and non-cancer experimental systems indicates that phage nucleic acids can engage TLR9-dependent sensing and, for selected phages, STING-associated inflammatory signaling; however, the relevance of these pathways within human tumors remains to be established. Indirectly, phages may alter microbial community structure and metabolic outputs, which could influence systemic immune tone and the composition of immune infiltrates within the TME. We further discuss accumulating data linking phageome features with tumor progression and responses to immune checkpoint blockade and other cancer therapies. However, much of the available evidence remains preclinical, indirect, or correlative, and causal roles for endogenous phages in human tumor immunity still require further validation. Distinct from the putative ecological and immunological roles of naturally occurring phages, engineered bacteriophages are being developed as therapeutic platforms for cancer immunotherapy, including tumor-antigen display, targeted delivery of immune agonists, cytokines or nucleic acids, and combination strategies with existing treatments. Finally, we address key methodological, mechanistic, and safety challenges that must be overcome to translate phage-based immunomodulation into clinical applications. Collectively, this review highlights the phageome as an emerging regulatory layer of tumor immunity and a promising, yet underexplored, target for therapeutic intervention.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"314 ","pages":"128700"},"PeriodicalIF":8.5,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148875487","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":"In genomes we trust: Assessing genomic reliability within the family Nectriaceae.","authors":"Alessandra Villani, Veronica Ghionna, Antonia Susca, Andrea Menicucci, Antonio Prodi, Luigi Faino, Antonio Moretti, Riccardo Baroncelli","doi":"10.1016/j.micres.2026.128705","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128705","url":null,"abstract":"<p><p>Reliable evolutionary inference increasingly depends on public genome resources, and the effects of uneven assembly quality, incomplete metadata, and biased taxonomic sampling remain poorly quantified. Using the species-rich fungal lineage Nectriaceae as a model system, we analysed 1530 genome sequence assemblies to assess metadata completeness, sampling representation, and genome quality. One-third of the assemblies lacked essential metadata, sequencing was heavily skewed toward a few agriculturally important lineages, and sampling of many genera was limited or nonexistent. BUSCO and QUAST metrics revealed substantial heterogeneity in assembly quality, with widespread fragmentation and numerous assemblies falling outside expected quality thresholds. From 763 single-copy orthologs identified in 576 higher-quality genomes, we reconstructed a phylogenomic backbone and quantified gene- and site-level concordance across the tree. Although major clades were broadly recovered, extensive gene-tree discordance and a polyphyletic Fusarium nisikadoi species complex revealed unresolved boundaries and conflict among loci. These results show how data quality, incomplete sampling, and discordant genomic histories can constrain phylogenomic resolution, and provide a general framework for improving comparative genomic resources and large-scale evolutionary inference.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"314 ","pages":"128705"},"PeriodicalIF":8.5,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148891949","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}