AIMS Microbiology最新文献

{"title":"GCMS-based evaluation, characterization and in silico analysis of antimicrobial metabolites in the crude extract of cold-adapted <i>Alcaligenes pakistanensis</i> LTP10.","authors":"Imran Rabbani, Muhammad Rafiq, Suliman Shah, Tariq Ahmad, Muhammad Irfan, Aamer Ali Shah, Turki M Dawoud, Fariha Hasan","doi":"10.3934/microbiol.2026011","DOIUrl":"10.3934/microbiol.2026011","url":null,"abstract":"<p><p>Antagonistic microorganisms from extreme environments have gained great attention from scientists due to increasing threat of global antimicrobial resistance. In this context, previously isolated cold-adapted isolate from Passu glacier <i>Alcaligenes pakistanensis</i> LTP10 was used to extract their antimicrobial metabolites with organic solvents. MIC and MBC assays of the extract were performed. The synergistic effect of LTP10 ethyl acetate extract was studied with known antibiotics against <i>Staphylococcus aureus</i> and <i>Escherichia coli</i>. The extract was analyzed by FTIR, GC-MS, and in silico studies. Ethyl acetate extract of LTP10 has shown a maximum activity of 20 ± 1.0 and 19.3 ± 1.2 mm against <i>Staphylococcus epidermidis</i> and <i>S. aureus</i>, respectively. MIC of the extract was 0.4 and 1.6 mg/mL against <i>S. aureus</i> and <i>E. coli</i>, respectively. FTIR analysis revealed the presesnce of functional groups belonging to alcohols, aliphatic hydrocarbons, and nitrogen containing organic compouns. GC-MS analysis confirmed the presence of important antimicrobial compounds Dodecanoic acid, 3-hydroxy-, 7,9-Di-tert-butyl-1-oxaspiro(4,5)deca-6,9-diene-2,8-dione, and Pyrimidine-2,4(1H,3H)-dione in ethyl acetate extract of LTP10. A molecular docking study of these compounds has shown that 7,9-Di-tert-butyl-1-oxaspiro(4,5)deca-6,9-diene-2,8-dione has strong binding affinity of -7.8 kcal/mol against dihydrofolate reductase. Moreover, an ADMET study of the compounds has predicted their good intestinal absorption and non-toxic nature. In this work, we uniquely identify and characterize antimicrobial metabolites of glacier-derived <i>Alcaligenes</i>, combining GC-MS profiling with in-silico analysis. It was concluded that <i>Alcaligenes pakistanensis</i> LTP10 could be considered a good source for antimicrobial compound production, which should be further characterized by analytical techniques.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 2","pages":"252-281"},"PeriodicalIF":5.4,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13370262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148457257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of cover cropping on orchard soil microbiomes: Mechanisms and perspectives.","authors":"Guan Guan, Pingzhi He, Yu Miao, Gaofeng Zhou, Guidong Liu","doi":"10.3934/microbiol.2026010","DOIUrl":"10.3934/microbiol.2026010","url":null,"abstract":"<p><p>Orchards have long faced severe soil erosion, acidification of red soils, low nutrient-use efficiency, and frequent soil-borne diseases. Conventional clean tillage combined with intensive chemical inputs often fails to simultaneously improve fruit yield and quality while safeguarding orchard ecological security. Cover cropping (i.e., managed groundcover vegetation) introduces persistent surface plant cover and introduces continuous inputs of root exudates, litter, and residues, while simultaneously modifying soil moisture, temperature, aggregation, porosity, and nutrient availability. Consequently, it reorganizes the soil microbiome from the rhizosphere scale to community-network scales and drives key ecological processes such as carbon sequestration, nitrogen and phosphorus turnover, and disease suppression. Mechanistically, cover crops (i) enhance the supply of labile carbon through root exudation and residue return, stimulating microbial assimilation and enzyme-mediated decomposition and promoting SOC stabilization via microbial necromass formation-mineral association/aggregate protection; and (ii) optimize microbial habitats by improving aggregate architecture, pore structure, and water-holding capacity, and by regulating pH and nutrient availability, thereby increasing the abundance and functional potential of key guilds (e.g., diazotrophs, nitrifiers/denitrifiers, and microorganisms involved in organic-P mineralization) and their functional gene repertoires. In addition, cover cropping may strengthen system stability and suppressiveness through multi-trophic interactions and reconstruction of the soil micro-food web. However, under drought conditions or during the juvenile-tree stage, trade-offs can emerge due to context-dependent tree-groundcover competition for water and nutrients. Future progress requires long-term field experiments integrating multi-omics, isotope tracing, and process-based flux measurements to establish causal evidence chains and scenario-specific models linking management-microbial mechanisms-ecosystem services. Developing operational microbiome-based indicators will provide a scientific basis for groundcover species selection, cover pattern optimization, and fertilizer reduction with improved efficiency, as well as disease mitigation and fruit-quality enhancement.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 2","pages":"224-251"},"PeriodicalIF":5.4,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13370275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148457228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolomics analysis reveals diverse nematicidal metabolites from spore-forming bacteria.","authors":"Ziqiang Zheng, Yonghong Zhou, Pengxi Cao, Lingling Gong, Chaofan Zheng, Yujiao Huang, Yu Li, Wenjing Le, Jinliang Zhang, Xianwei Zhou, Jing Tan, Chenfei Guo, Yuanxiang Xu, Chang Chen, Ningchang Yang, Luqing Li, Yuhan Sun, Shen-Cai Hu, Fang Peng, Luhong Sun, Shuang Yu, Hongxun Wang","doi":"10.3934/microbiol.2026009","DOIUrl":"10.3934/microbiol.2026009","url":null,"abstract":"<p><p>Plant-parasitic nematodes are very important plant pathogens that can damage almost all crops worldwide. There has been a progressive decline in the use of chemical compounds because of their high toxicity to humans, livestock, and the environment. Spore-forming Bacilli as excellent biological agents are an effective and eco-friendly solution to control nematodes. However, our previous study showed that genomes of some highly nematicidal strains contain less virulent factor genes. Metabolomics studies based on mass spectrometry (MS) have shown that spore-forming strains can produce five classes of nematicidal secondary metabolites, including macrolide compounds (MCs; selamectin), triazines (Ts; prometon), piprazine derivatives (PDs; diethylcarbamazine), benzene and six-membered heterocyclic compounds (BSMHCs; crotamiton, amodiaquine and diethyltoluamide), and simple aromatic compounds (SACs; phenylacetic acid, benzyl benzoate, and benzyl alcohol). Among the spore-forming species with high nematicidal activity, <i>Cytobacillus firmus</i> synthesizes all five classes of nematicidal metabolites, with a ratio over 30% of PDs, BSMHCs, and SACs. Moreover, <i>B. wiedmannii</i> ZZQ-15, <i>B. mycoides</i> ZZQ-1576, and <i>B. thuringiensis</i> ZZQ-1522, ZZQ-1524, ZZQ-1551, ZZQ-1552, and ZZQ-1553 synthesize novel cyclopeptides with potential nematicidal activity. This study provides a useful method to identify nematicidal metabolites of bacteria.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 2","pages":"211-223"},"PeriodicalIF":5.4,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13370276/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148457287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-ensiling corn silage with <i>Pleurotus</i>-based spent mushroom substrate and oilseeds: Impacts on rumen fermentation, digestibility, and methane emissions in a RUSITEC system.","authors":"Chika C Anotaenwere, Omoanghe S Isikhuemhen, Peter A Dele, Ahmed E Kholif, Michael Wuaku, Oludotun O Adelusi, Deborah O Okedoyin, Joel O Alabi, Kelechi A Ike, John O Adebayo, Kiran Subedi, Uchenna Y Anele","doi":"10.3934/microbiol.2026008","DOIUrl":"10.3934/microbiol.2026008","url":null,"abstract":"<p><p>The present study examined the effects of partially replacing corn silage (CS) with <i>Pleurotus</i>-based spent mushroom substrate (SMS) and oilseeds (OS) on rumen fermentation characteristics, nutrient digestibility, volatile fatty acid (VFA) profiles, and greenhouse gas emissions using a rumen simulation technique (RUSITEC). Four silages were evaluated: A control diet containing 100% CS and three co-ensiled treatments in which CS was partially replaced with <i>Pleurotus</i>-based SMS and OS. The oilseed fraction consisted of equal proportions of soybean and canola seeds. The treatments were: CS90 (90% CS + 5% SMS + 2.5% soybean seed + 2.5% canola seed), CS80 (80% CS + 10% SMS + 5% soybean seed + 5% canola seed), and CS60 (60% CS + 20% SMS + 10% soybean seed + 10% canola seed). Dry matter (DM), organic matter, and crude protein contents were not affected by treatment, whereas ash content increased (P < 0.001) with increasing SMS-OS inclusion. Increasing SMS-OS inclusion significantly reduced non-fiber carbohydrates, hemicellulose and cellulose, while ether extract, neutral detergent fiber, acid detergent fiber, and acid detergent lignin concentrations were increased (P < 0.05). Ruminal fermentation pH, effluent volume, and total gas production showed only numerical differences or trends. DM digestibility increased markedly with SMS-OS inclusion (P < 0.001), rising from 38.7% in the control to 53.0, 49.9, and 52.5% in CS90, CS80, and CS60, respectively, representing improvements of approximately 29-37%. In CS90, organic matter digestibility remained high (P < 0.001) and fiber digestibility was largely the same. Moreover, CS90 had the highest total VFA and acetate, whereas CS60 had the highest propionate proportion (P < 0.05). All SMS-OS diets substantially reduced methane production (P = 0.003) and carbon dioxide emissions (P = 0.014) relative to the control. Methane output declined by approximately 60, 45, and 35% in CS90, CS80, and CS60, respectively (34.2-55.6 vs. 85.7 mg/g DM), while carbon dioxide emissions were reduced by about 49, 26, and 17% (134.7-218.4 vs. 264.0 mg/g DM). In conclusion, co-ensiling corn silage with SMS and oilseeds improved DM utilization while influencing methane production, with reductions observed in all the treatments compared with the control without adversely affecting rumen fermentation stability or fiber digestion under RUSITEC conditions.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 2","pages":"192-210"},"PeriodicalIF":5.4,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13370278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148457282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the probiotic potential of <i>L. rhamnosus</i> strain 044AE by genomic and phenotypic characterization.","authors":"Aruna Inamdar, Vikash Kumar, Akanksha Chauhan, Yogini Dixit, Namrata Bhingardeve, Kunali Ambavale, Dina Saroj","doi":"10.3934/microbiol.2026007","DOIUrl":"10.3934/microbiol.2026007","url":null,"abstract":"<p><p>Probiotics are living microorganisms that improve overall human health by modulating the gut microbiota and enhancing absorption of nutrients and host immunity. Due to the growing demand for probiotics, efforts are being made to search for and characterize new probiotics. Whole genome sequencing has played a significant role in the identification and characterization of many probiotic candidates. In the present study, hybrid assembly (Illumina and Nanopore-based), genomic analyses, and phenotypic evaluations of <i>Lactobacillus rhamnosus</i> 044AE isolated from a dairy sample were carried out to investigate its probiotic potential. The assembled genome of <i>L. rhamnosus</i> 044AE showed maximum homology with <i>L. rhamnosus</i> BIO5326. Downstream analysis of the genome revealed safety, stability, and gut survival features. In the phenotypic assays, <i>L. rhamnosus</i> 044AE exhibited favorable adhesion, aggregation, gut stability (88.96% viability under fasting conditions; 92%-96% viability under fed conditions), antimicrobial, antioxidant, and enzyme activities. Therefore, <i>L. rhamnosus</i> 044AE appears as a potential probiotic candidate for applications in the food, pharmaceutical, and nutraceutical industries.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 2","pages":"173-191"},"PeriodicalIF":5.4,"publicationDate":"2026-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13370279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148457301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Climate-driven restructuring of sediment microbiomes and ecosystem functions in aquaculture systems.","authors":"Antonia Mataragka, Einar Ringø, Anastasios Klavdianos Papastathis","doi":"10.3934/microbiol.2026006","DOIUrl":"10.3934/microbiol.2026006","url":null,"abstract":"<p><p>Aquaculture expansion is occurring under accelerating climatic pressure. Warming, marine heatwaves, deoxygenation, salinity fluctuation, and intensified nutrient loading act simultaneously in aquaculture sediments, altering redox gradients and substrate fluxes that structure microbial communities. These stressors strengthen deterministic environmental filtering, reorganize interaction networks toward reduced-state dominance, and redistribute functional investment within sediment microbiomes; the biogeochemical engines regulating nutrient cycling, water quality, and disease dynamics. Such restructuring is associated with altered nitrogen processing, modified greenhouse gas fluxes, sulfide accumulation, enhanced pathogen performance, and enrichment of antimicrobial resistance determinants, with direct implications for production stability and disease risk. Evidence is synthesized to integrate quantified environmental forcing, ecological assembly mechanisms, and molecular functional responses into a unified framework linking microbial restructuring to ecosystem performance and operational resilience. Structural and functional microbial indicators suitable for early detection of redox compression and functional destabilization are evaluated, alongside resilience-oriented strategies spanning ecological design, microbiome management, engineering control, and adaptive monitoring. Despite substantial empirical progress, major gaps remain in resolving compound-stressor interactions, temporal reversibility, cross-system threshold comparability, and predictive modeling of microbial assembly under multi-driver forcing. Addressing these gaps is essential for developing mechanistically grounded, climate-resilient aquaculture systems.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 1","pages":"150-172"},"PeriodicalIF":5.4,"publicationDate":"2026-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13047319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial drivers of Black Soldier Fly biowaste valorization: from microbiome functions to scalable insect-microbe systems.","authors":"Hugo Luttenschlager, Grégoire Noel, Taofic Alabi, Joachim Carpentier, Frédéric Francis, Rudy Caparros Megido","doi":"10.3934/microbiol.2026005","DOIUrl":"10.3934/microbiol.2026005","url":null,"abstract":"<p><p>Biowaste and agro-industrial co-products continue to increase with population growth and rising living standards, calling for scalable valorization strategies that go beyond simple mineralization. The black soldier fly (BSF) has emerged as a practical bioconversion platform capable of channeling biodegradable organic waste into high-value proteins, lipids, and chitin. In parallel, microbial interventions are increasingly recognized as key levers for substrate conditioning, process stabilization, and performance optimization in BSF-based systems. In this review, we adopted a function-first perspective to examine how microbial processes shape and connect three major biological valorization routes: aerobic composting, anaerobic digestion (AD), and BSF bioconversion. Rather than focus on taxonomic inventories, we synthesized evidence on microbial functions that matter in practice, including extracellular hydrolysis of complex polymers, regulation of short-chain fatty acids, detoxification and pathogen suppression, and process stabilization. We further reviewed microbe-assisted strategies, such as lactic pre-fermentation, directed acidogenesis, and probiotic or defined consortia and their effects on waste reduction, conversion efficiency, product quality, and sanitary safety. Finally, we translated these microbial mechanisms into scalable design principles for configuring and operating integrated insect-microbe systems, highlighting how microbial functions underpin reproducible, enterprise-ready performance across composting, AD, and BSF-integrated workflows.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 1","pages":"126-149"},"PeriodicalIF":5.4,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13047329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Host restriction factors and p17-Driven inflammaging in HIV-1: From molecular pathogenesis to functional cure.","authors":"Thomas Nitsotolis, Stelios F Assimakopoulos, Elli Kouriannidi, Maria Lagadinou, Alexia Papalexandrou, Petros Ioannou, Markos Marangos, Haralampos Milionis, Eirini Christaki","doi":"10.3934/microbiol.2026004","DOIUrl":"10.3934/microbiol.2026004","url":null,"abstract":"<p><p>Despite the widespread success of combination antiretroviral therapy (cART) in suppressing plasma viremia to undetectable levels, people living with HIV-1 (PLWH) continue to face a significantly elevated risk of chronic inflammation and Serious Non-AIDS Events (SNAEs). In this narrative review, we bridge the critical gap between molecular virology, immunometabolism, and clinical pathology by examining the complex interface of intrinsic immunity and viral persistence. We analyzed the evolutionary \"arms race\" between conserved host restriction factors, including TRIM5α, APOBEC3G, SAMHD1, BST-2, MX2, and SERINC, and the sophisticated viral evasion mechanisms that facilitate reservoir establishment. We further examined the role of bacterial translocation and gut barrier dysfunction in perpetuating systemic inflammation, emphasizing how HIV-1-mediated depletion of mucosal Th17 cells and disruption of tight junction proteins create a \"leaky gut\" that permits microbial product translocation despite suppressive therapy. Among viral proteins that may contribute to residual pathology during suppressive cART, we focused on the HIV-1 matrix protein p17, which has been proposed to function as a secreted \"viral cytokine\" from latent reservoirs, acting through CXCR1/CXCR2 receptors and the RACK1-JAK1-STAT1 pathway. Although primarily characterized in in vitro and ex vivo models, emerging data suggested that p17 may sustain systemic immune activation and metabolic reprogramming; however, its relative contribution compared with other viral proteins (Tat, Nef, gp120) in virologically suppressed patients remains to be fully delineated in human studies. Furthermore, we examined how HIV-1 hijacks cellular bioenergetics by shifting host cells from oxidative phosphorylation to aerobic glycolysis. We present an integrative model that connects restriction factor biology, p17-mediated chronic inflammation, immunometabolic dysregulation, and gut barrier dysfunction into a unified pathogenic framework, distinguishing established mechanisms from working hypotheses. Last, we assessed emerging therapeutic strategies, including CRISPR/Cas9-mediated enhancement of restriction factors, modulation of the mTOR pathway, and novel \"Shock and Kill\" approaches, stratified by development stage and demonstrated endpoints, offering potential pathways toward a functional cure.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 1","pages":"92-125"},"PeriodicalIF":5.4,"publicationDate":"2026-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13047328/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering the holobiont: Synthetic biology strategies for reversing bioenergetic collapse in radiation enteritis.","authors":"Yingqi Li, Jiuping Liang, Hui Yin, Tao Liu","doi":"10.3934/microbiol.2026003","DOIUrl":"10.3934/microbiol.2026003","url":null,"abstract":"<p><p>Radiation enteritis (RE) constitutes a catastrophic collapse of the intestinal holobiont, fundamentally constraining the curative potential of abdominopelvic radiotherapy. Current clinical management, limited by a reductionist focus on host DNA damage, often overlooks the maladaptive ecological feedback loops driving chronic pathology. This review advocates for a definitive transition from empirical probiotic supplementation to microbial synthetic biology for the rational reprogramming of the gut ecosystem. We delineate strategies for thermodynamic engineering, utilizing engineered commensals as living oxygen sinks to scavenge luminal oxygen and nitrate, thereby starving proteobacterial blooms and restoring the physiological hypoxia essential for mucosal recovery. Addressing the <i>Akkermansia</i> paradox, in which nutrient deprivation drives beneficial microbes toward mucin-degrading pathogenicity, we propose genetic domestication (e.g., sulfatase deletion) to decouple immunogenicity from barrier erosion. Furthermore, we explore the design of biological computers equipped with Boolean logic gates to resolve the immunological timing paradox by precisely modulating the cGAS-STING axis and reprogramming macrophage metabolism via the itaconate shunt. Integrating armored polydopamine delivery, genetic entanglement (STALEMATE) for biocontainment, and Gut-on-a-Chip validation, we outline a roadmap for colonic terraformation. This engineering-driven approach aims to actively reconstruct homeostasis, uniquely decoupling epithelial regeneration from tumor protection to improve long-term cancer survival.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 1","pages":"63-91"},"PeriodicalIF":5.4,"publicationDate":"2026-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13047322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering <i>Trichoderma</i>-mediated plant defense against bacterial phytopathogens: Micro-and nanobiotechnological strategies.","authors":"Zaryab Shafi, Mohammad Shahid, Atul Singh, G Bhupal Raj, Akhtar Rasool","doi":"10.3934/microbiol.2026002","DOIUrl":"10.3934/microbiol.2026002","url":null,"abstract":"<p><p>Bacterial phytopathogens such as <i>Ralstonia</i>, <i>Xanthomonas</i>, and <i>Pectobacterium</i> pose a serious threat to global food security, while overuse of chemical pesticides has led to resistance and environmental concerns. <i>Trichoderma</i>, traditionally known for antifungal activity, is emerging as a versatile antagonist of bacterial diseases through antibacterial metabolites, immune response, nutrient competition, and rhizosphere modulation. Multi-omics advances have revealed novel biosynthetic gene clusters and host interaction mechanisms, while CRISPR-based genome editing and synthetic biology approaches are enabling the tailored strains with enhanced biocontrol efficiency. Nanotechnology further contributes by facilitating nanoparticle-mediated biosynthesis and controlled-release formulations, improving stability and targeted field delivery. Despite remaining challenges related to field translation, biosafety, and regulation, the integration of omics, genetic engineering, and nanotechnology establishes <i>Trichoderma</i> as a next-generation platform for sustainable and precision crop protection.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 1","pages":"27-62"},"PeriodicalIF":5.4,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13047323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}