AIMS Microbiology最新文献

{"title":"Uncovering the phenotypic and transcriptional characteristics of biofilm-released cells in <i>Pseudomonas aeruginosa</i>.","authors":"Jason Li, Larry Ayiku, Benjamin Larson, Agam Patel, Dylan Adams, Patrick Moran, Samantha Burgan, Esha Shah, Anthony Bruno, Jaclyn Printz, Tevin Flom, Whitni K Redman","doi":"10.3934/microbiol.2026031","DOIUrl":"https://doi.org/10.3934/microbiol.2026031","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> is a prominent biofilm-forming pathogen associated with chronic infections that are difficult to eradicate due to the protective biofilm matrix. Inducing biofilm dispersion has emerged as a potential therapeutic strategy. Although researchers have compared selected biofilm dispersion mechanisms, the characteristics of cells generated by mechanistically distinct release strategies, particularly enzymatic matrix degradation, remain uncharacterized. In this study, we compared <i>P</i>. <i>aeruginosa</i> cells released from biofilms using four distinct dispersion mechanisms: An external signaling molecule (<i>cis</i>-2-decenoic acid; <i>cis</i>-DA), a nutrient cue (glutamate), an environmental toxin (sodium nitroprusside; SNP), and a matrix-degrading enzyme (amylase). Released cells exhibited distinct antibiotic susceptibility, attachment, and gene expression depending on the release mechanism. Glutamate-released cells exhibited greater tobramycin tolerance and attachment, whereas glutamate and amylase-released populations exhibited differences in the expression of selected genes. Additionally, the release mechanism influenced subsequent biofilm recovery and reformation, and <i>cis</i>-DA significantly enhanced tobramycin-mediated killing of mature biofilms. Collectively, these findings demonstrate that the mechanism used to induce release may influence subsequent bacterial behavior and antibiotic susceptibility. These findings highlight the importance of considering release mechanism when developing dispersion-based strategies for treating biofilm-associated infections.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 3","pages":"718-741"},"PeriodicalIF":5.4,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149170764","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":"Zeolite-amended peat carriers improve long-term survival of <i>Ensifer meliloti</i> and maintain alfalfa nodulation efficiency.","authors":"Olivera Stajković-Srbinović, Mila Pešić, Biljana Sikirić, Vesna Mrvić, Snežana Andjelković, Dušica Delić","doi":"10.3934/microbiol.2026029","DOIUrl":"https://doi.org/10.3934/microbiol.2026029","url":null,"abstract":"<p><p>Microbiological N fertilizers containing native highly effective and competitive rhizobial bacteria placed in a suitable carrier are the best choice for sustainable plant production. This study evaluated the ability of various peat-based formulations with different zeolite/CaCO₃ amendments to support the survival and preservation of symbiotic efficiency of alfalfa rhizobia. 15 different inoculants were tested, including five nitrogen-fixing efficient <i>Ensifer meliloti</i> strains (218, 225, 252, 4148ss and 4193cs) in three different carriers made of peat and perlite and supplemented with micro-zeolite (B1), nanozeolite (B2), and micro-zeolite + CaCO₃ (B3). The number of rhizobia after 90 days of storage at room temperature was above 10¹⁰ CFU/g of inoculant in most of the combinations, after 180 days of storage was 10⁹ CFU/g in all combinations, and in 330^th day stayed above 10⁸ CFU/g of inoculant for strains 218, 4148ss, and 252. Considering the whole period of storage, the most performant carriers were B3, with the addition of micro-zeolite + CaCO₃ and B2 with nanozeolite amendment. The efficiency of all inoculants, measured by the nodulation ability and shoot dry weight (SDW), was confirmed in inoculated alfalfa plants after six and eleven months of storage. The SDW of inoculated alfalfa plants increased from 2.5 up to 5 times compared to non-inoculated plants, while the nitrogen content (mg/plant) was also significantly increased. The SDW was influenced by strain, while the type of carrier and storage of inoculant did not have an effect. The inoculant formulations with zeolite and calcium carbonate showed good potential for rhizobia survival and effectiveness preservation during long-term storage, which should be further tested under field conditions.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 3","pages":"666-681"},"PeriodicalIF":5.4,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149166647","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":"Molecular biophysics of viral proteins: From mechanistic insights to microbiological and clinical applications.","authors":"Alessandro Paolo Addamo, Floriana D'Angeli, Carlo Genovese","doi":"10.3934/microbiol.2026030","DOIUrl":"https://doi.org/10.3934/microbiol.2026030","url":null,"abstract":"<p><p>Viral proteins are dynamic molecular machines that couple molecular-scale events to microbiological phenotypes, including host-cell tropism, entry efficiency, environmental persistence, strain-specific immune escape, and antiviral resistance. In this review, we critically evaluated how experimental, computational, and biochemical approaches define these links and support clinical translation. We organized the evidence around four key observables: Structure, dynamics, mechanics, and thermodynamics. We then assessed which conclusions remained robust across methods and viral families. Nuclear magnetic resonance spectroscopy, cryogenic electron microscopy, atomic force microscopy, calorimetry, all-atom molecular dynamics (MD), coarse-grained MD, structural bioinformatics, artificial intelligence, and biochemical reconstitution were compared in terms of resolution, sampling, assumptions, and validation requirements. Human immunodeficiency virus type 1 and severe acute respiratory syndrome coronavirus 2 were used as data-rich exemplars, but the resulting conclusions were tested against influenza virus, hepatitis B virus (HBV), human papillomavirus (HPV), Ebola virus, adenovirus, bacteriophages, and other systems. Particular attention was given to force-field selection, enhanced sampling, free-energy calculations, convergence, experimentally restrained modeling, and the multiscale relationship between all-atom and coarse-grained simulations. We also examined integrative workflows, the licensed HBV and HPV virus-like particle (VLP) vaccines, emerging dengue and coronavirus VLP platforms, and clinically validated structure-guided antivirals and prefusion-stabilized antigens. The analysis identified where evidence converges, where method-specific biases or limited taxonomic sampling constrain generalization, and which measurements are required to connect a molecular mechanism to infection, transmission-relevant traits, surveillance, or therapeutic performance. This critical, experimentally anchored framework defines the distinctive contribution of the review.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 3","pages":"682-717"},"PeriodicalIF":5.4,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149170499","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":"Gut microbiota dysbiosis: Pathogenic drivers and emerging phage-based therapeutics.","authors":"Ahmed Dewan, Débora Brito Goulart, Maria Teresa Mascellino","doi":"10.3934/microbiol.2026028","DOIUrl":"https://doi.org/10.3934/microbiol.2026028","url":null,"abstract":"<p><p>Gut microbiota dysbiosis driven by pathogenic and opportunistic bacteria, including <i>Clostridioides difficile</i>, adherent-invasive <i>Escherichia coli</i> (AIEC), <i>Salmonella enterica serovar Typhimurium</i>, <i>Fusobacterium nucleatum</i>, <i>Klebsiella pneumoniae</i>, <i>Enterococcus faecalis</i>, and <i>Campylobacter</i> spp., disrupts colonization resistance, epithelial barrier integrity, and immune homeostasis, thereby contributing to the development of inflammatory and metabolic diseases. In this review, we summarize the mechanisms through which these microorganisms promote gut dysbiosis and critically evaluate current microbiome-targeted therapeutic strategies, including fecal microbiota transplantation (FMT), live biotherapeutic products (LBPs), probiotics, and bacteriophage (phage) therapy. We review the preclinical and emerging clinical evidence supporting phage-based targeting of major dysbiosis-associated pathogens and examine the principal challenges limiting clinical translation, including phage resistance, immune-mediated clearance, safety considerations related to temperate phages, manufacturing and delivery constraints, and regulatory barriers. Although evidence remains predominantly preclinical, advances in phage engineering, artificial intelligence-guided phage selection, and systems-level microbiome modeling are expanding the potential of personalized phage therapeutics. Collectively, these developments position bacteriophage therapy as a promising addition to future microbiome-directed strategies for restoring gut microbial homeostasis and managing dysbiosis-associated disease.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 3","pages":"632-665"},"PeriodicalIF":5.4,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149170195","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":"Genomic epidemiology of multidrug-resistant <i>Klebsiella pneumoniae</i> reveals lineage-specific resistance patterns with limited virulence determinants.","authors":"Aiman Waheed, Sumera Afzal Khan, Taj Ali Khan, Sajjad Ahmad, Aakash Ahmad Khattak, Taane G Clark, Nigel G Ternan, Fahad Ahmed, Ibrahim M Banat, Zahoor Khan","doi":"10.3934/microbiol.2026027","DOIUrl":"https://doi.org/10.3934/microbiol.2026027","url":null,"abstract":"<p><p>The emergence of multidrug-resistant (MDR) <i>Klebsiella pneumoniae</i> undermines treatment efficacy, while limited genomic epidemiological data constrain understanding of local transmission dynamics. We therefore aimed to investigate the genomic epidemiology and the antimicrobial resistance landscape of <i>K. pneumoniae</i> in tertiary-care settings in Peshawar, Pakistan. A total of 497 clinical samples (urine, blood, sputum, pus, wound swabs, sterile body fluids) were collected from 01 August 2024 to 31 July 2025. <i>K. pneumoniae</i> was identified using the API 20E kit, followed by antimicrobial susceptibility testing (AST), with colistin and tigecycline susceptibility determined by broth microdilution. Whole-genome sequencing (WGS) was carried out on 43 MDR and XDR isolates to resolve clonal diversity, resistome composition, virulence-associated loci, and phylogenetic relationships. Among 497 samples, 152 <i>K. pneumoniae</i> isolates were identified, exhibiting widespread resistance to β-lactams, cephalosporins, fluoroquinolones, aminoglycosides, and carbapenems, while colistin and tigecycline retained substantial <i>in vitro</i> activity. Overall, 37% and 24% of isolates were classified as MDR and XDR, respectively. Forty-three MDR/XDR isolates were subjected to WGS, of which 34 high-quality <i>K. pneumoniae</i> genomes passed quality control and species verification for downstream analysis. Genomic analysis identified 18 sequence types, with ST147 (7/34, 20.6%), ST37 (4/34, 11.8%), ST2629 (3/34, 8.8%), ST39 (3/34, 8.8%), and ST870 (2/34, 5.9%) representing the predominant lineages. The dominant high-risk clones, particularly ST147, ST11, ST231, and ST42-3LV, harbored multiple antimicrobial resistance determinants, including <i>bla</i>CTX-M-15 (20/34) or <i>bla</i>CTX-M-14 (2/34), <i>bla</i>KPC-2 (2/34), <i>blaOXA</i>-48 (1/34), <i>blaOXA</i>-181 (1/34), <i>bla</i>NDM-5 (1/34), aminoglycoside-modifying enzymes, fluoroquinolone resistance determinants, porin disruptions (ompK35/ompK36; 9/34), and colistin resistance-associated mutations in <i>pmrB</i> in 4 isolates. ST147 was the predominant lineage and was consistently associated with the KL64 capsule type and O1/O2-associated O-loci. Virulence profiling demonstrated a predominantly low-virulence population, with 19/34 (55.9%) isolates carrying yersiniabactin as the only detected virulence determinant, whereas aerobactin, colibactin, and <i>rmpA/rmpA2</i> were absent from all genomes. Collectively, these findings demonstrate that MDR <i>K. pneumoniae</i> circulating in Peshawar are dominated by internationally disseminated high-risk clones characterized by extensive antimicrobial resistance but limited virulence potential, underscoring the importance of genomic surveillance to strengthen infection prevention and antimicrobial stewardship.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 3","pages":"610-631"},"PeriodicalIF":5.4,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149169677","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":"The stone-degrading metabolic potential of the urinary microbiome: Sexual dimorphism and dysbiosis in urolithiasis.","authors":"Ying Li, Chengqiang Mo, Yun Xie, Zhixin Huang, Lingwu Chen, Xinqiang Xie, Junhang Luo, Shixuan Huang, Shuangjian Jiang, Tianhao Zhang, Jumei Zhang, Rongpei Wu, Qingping Wu","doi":"10.3934/microbiol.2026026","DOIUrl":"https://doi.org/10.3934/microbiol.2026026","url":null,"abstract":"<p><p>Urolithiasis is a prevalent global health burden characterized by high recurrence rates and marked sexual dimorphism. While the gut microbiome's role in oxalate degradation is established, the functional capacity of the local urinary microbiome remains largely unexplored. This study investigated the composition and function of the urinary microbiome in 40 healthy volunteers and 61 urolithiasis patients using 16S rRNA amplicon sequencing, alongside a retrospective analysis of stone composition in 2027 patients. We identified a diverse, ecologically structured microbiome in healthy urine dominated by genera such as <i>Lactobacillus</i>, <i>Streptococcus</i>, and <i>Gardnerella</i>. Significant sex-dependent differences were observed: While males exhibited higher microbial α-diversity, females demonstrated a distinct compositional structure with superior predicted functional capacity for stone degradation. Specifically, the female microbiome was enriched with enzymes including oxalyl-CoA decarboxylase, formyl-CoA transferase, urate oxidase, and purine nucleosidase. Correlation analysis identified <i>Lactobacillus</i>, <i>Enterococcus</i>, and <i>Gardnerella</i> as key contributors to this litholytic potential. Conversely, urolithiasis patients displayed significant dysbiosis, characterized by disrupted microbial networks and a marked reduction in these stone-degrading enzymes. Clinical data supported these findings, revealing a significantly higher prevalence of uric acid stones in males, consistent with their lower microbial degradation capacity. These findings suggest that the healthy urinary microbiome functions as a metabolically active defense system against stone formation. The observed sex-specific variations in microbial composition and enzymatic function provide a novel mechanistic explanation for the epidemiological sex disparities in urolithiasis, highlighting the urinary-kidney axis as a potential therapeutic target.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 3","pages":"595-609"},"PeriodicalIF":5.4,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652743/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149171397","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":"Biocontrol of phytopathogenic fungi by <i>Bacillus</i> spp.: Strain screening, regulatory mechanisms, and field application.","authors":"Feng Wang, Shuang Zhang, Ling Xu, Jingya Qian, Bin Zou, Shuhao Huo, Anzhou Ma, Guoqiang Zhuang","doi":"10.3934/microbiol.2026025","DOIUrl":"https://doi.org/10.3934/microbiol.2026025","url":null,"abstract":"<p><p><i>Bacillus</i> species, which are among the most extensively studied and widely used rhizobacteria, have demonstrated potent antagonistic activity against a broad spectrum of phytopathogenic fungi, making them ideal microorganisms for biological control. Phytopathogenic fungi cause severe preharvest and postharvest losses in global crop production, significantly reducing yield and quality. The prolonged and heavy reliance on traditional chemical fungicides has resulted in environmental pollution and poses risks to human health. In this context, <i>Bacillus</i>-based biological control has emerged as an environmentally friendly, cost-effective, and sustainable alternative strategy. In this review, we provide a comprehensive overview of the screening of <i>Bacillus</i> strains for the biocontrol of phytopathogenic fungi. The possible mechanisms, including the production of a wide array of antifungal metabolites, the induction of systemic resistance in host plants, and indirect suppression through competition for nutrients and space, were also evaluated. Furthermore, the effects of multistrain synergistic consortia and the development of multifunctional <i>Bacillus</i> strains on biocontrol efficacy are discussed, and research advances in the application of <i>Bacillus</i> spp. in the control of soilborne diseases and phytopathogenic fungi are summarized. Finally, this review provides suggestions for the development of efficient <i>Bacillus</i>-based biocontrol agents, thereby promoting sustainable agricultural development.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 3","pages":"564-594"},"PeriodicalIF":5.4,"publicationDate":"2026-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652741/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149166879","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":"Gut microbiota and the gut-brain axis in autism spectrum disorder and attention-deficit/hyperactivity disorder: A scoping review of shared and disorder-specific mechanistic pathways.","authors":"Shifan Khanday, Afra Al Darmaki, Rokia Malahifci, Rima Alvavi, Sana Ahmed, Dina S Nasr","doi":"10.3934/microbiol.2026024","DOIUrl":"https://doi.org/10.3934/microbiol.2026024","url":null,"abstract":"<p><strong>Background: </strong>Autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD) are among the most prevalent neurodevelopmental conditions worldwide, yet the biological mechanisms driving their onset and phenotypic variability remain incompletely understood. The gut-brain axis (GBA), a bidirectional network linking intestinal microbial communities to central nervous system function through endocrine, immune, neural, and metabolic pathways, has emerged as a candidate mechanism through which environmental factors interact with genetic susceptibility to shape neurodevelopmental outcomes.</p><p><strong>Objective: </strong>To systematically map the peer-reviewed evidence on gut microbiome-related mechanistic pathways in ASD and ADHD, we delineated features common to both disorders and identified areas of divergence and knowledge gaps requiring further investigation.</p><p><strong>Methods: </strong>A scoping review was performed following the PRISMA Extension for the Scoping Reviews (PRISMA-ScR) framework. PubMed, Scopus, and Google Scholar were searched for peer-reviewed studies published January 2018 through March 2025. Studies addressing gut microbiome composition, GBA signaling, or microbiome-directed interventions in ASD or ADHD were eligible for inclusion. Extracted data were synthesized using inductive thematic analysis via Covidence software.</p><p><strong>Results: </strong>Forty-five studies satisfied the eligibility criteria. Inductive analysis produced five mechanistic themes: Endocrine dysregulation and microbial metabolite signaling; neuronal signaling and neurotransmitter modulation; immune activation and neuroinflammation; gene-microbiota-environment interactions; and microbiota-targeted interventions. Studies on both disorders demonstrated modifications involving taxa with short-chain-fatty-acid-producing capacity; however, findings were varied and did not prove a common reduction in butyrate production. ASD was marked by pronounced dysregulation of the serotonergic system and tryptophan-kynurenine pathway and increased hypothalamic-pituitary-adrenal (HPA) axis responsiveness. On the other hand, the results in ADHD were majorly cross-sectional or preliminary, and the widely-m recognized dopaminergic dysfunction in ADHD has not been associated to specific microbiota alterations to date.</p><p><strong>Conclusions: </strong>Evidence demonstrates the GBA as a useful research conceptual for investigating ASD and ADHD, although the strength of mechanistic evidence differs substantially between the two disorders. Translating these insights into therapeutic strategies will require longitudinal, multi-omic research designs capable of establishing causality and enabling patient stratification for precision microbiome-based interventions.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 3","pages":"548-563"},"PeriodicalIF":5.4,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149170672","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":"Mechanistic insights into the antimicrobial activity of a novel essential oil blend against <i>Bacillus subtilis</i> using RNA sequencing.","authors":"Breyana N Robinson, Kelechi A Ike, Amsiray Padilla-Arroyo, Lori N King, James M Enikuomehin, John O Adebayo, Ahmed E Kholif, Uchenna Y Anele","doi":"10.3934/microbiol.2026023","DOIUrl":"https://doi.org/10.3934/microbiol.2026023","url":null,"abstract":"<p><p>The growing need for alternatives to conventional antibiotics has intensified interest in essential oils as multitarget antimicrobial agents. This study investigated the global transcriptional response of <i>Bacillus subtilis</i> to a novel essential oil blend (EOB1) composed of garlic, lemongrass, cumin, lavender, and nutmeg. The minimum inhibitory concentration (MIC) of EOB1 against <i>B. subtilis</i> was determined to be 25% (v/v), and a subinhibitory concentration of 12.5% (v/v) was used for transcriptomic analysis. Exposure to EOB1 caused widespread transcriptional changes, with 2178 genes identified as differentially expressed, including 1044 upregulated and 1134 downregulated transcripts. After filtering at a false discovery rate (FDR) of <0.05 and an absolute log2 fold change of >1, 1682 differentially expressed genes remained, comprising 981 upregulated and 701 downregulated genes. This corresponds to approximately 41% of the 4100 annotated protein-coding genes of the <i>B. subtilis</i> 168 genome. Principal component analysis showed clear separation between treated and control samples, with the first principal component explaining 97% of the total variance, indicating a strong global transcriptional effect of EOB1 on bacterial gene expression; because library preparation and sequencing were performed in a single batch and replicates within each condition clustered tightly, this separation is attributable to the treatment rather than to technical or batch-related variability. Among the most significantly induced genes were <i>arsB</i>, <i>copA</i>, <i>cadA</i>, <i>pchE</i>, <i>htrB</i>, <i>cypX</i>, <i>arsC</i>, and <i>nfrAB</i>, suggesting the activation of metal detoxification pathways, oxidative and envelope stress responses, secretion stress pathways, and secondary metabolite-associated responses. In contrast, genes involved in cell wall remodeling and nutrient uptake, including <i>cwlO</i> and <i>gltT</i>, were strongly downregulated. Gene Ontology enrichment analysis further supported these patterns, with significant overrepresentation of fatty acid β-oxidation, oxidoreductase activity acting on nicotinamide adenine dinucleotide phosphate (NAD(P)H), stress response pathways, amino acid biosynthetic processes, and cytoplasmic components. Collectively, these findings indicate that EOB1 disrupts multiple aspects of the physiology of <i>B. subtilis</i> and triggers coordinated metabolic, redox, and envelope-associated stress responses. This study provides mechanistic insight into the antimicrobial activity of EOB1 and supports the potential of essential oil blends as alternative antimicrobial agents.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 3","pages":"526-547"},"PeriodicalIF":5.4,"publicationDate":"2026-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149172024","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":"Characterization of duckweed-associated bacteria from the <i>Wolffia globosa</i> microbiome: Strain-level effects on host growth and key determinants.","authors":"Yuparat Saimee, Ryusuke Okada, Daisuke Inoue, Michihiko Ike","doi":"10.3934/microbiol.2026022","DOIUrl":"https://doi.org/10.3934/microbiol.2026022","url":null,"abstract":"<p><p><i>Wolffia</i>, a rootless duckweed in the family Lemnaceae, is increasingly recognized as a sustainable bioresource for food, animal feed, bioenergy, and biomaterials. Its productivity depends strongly on the associated microbiome, yet the functional roles of individual duckweed-associated bacteria (DAB) remain poorly understood. In this study, we evaluated the effects of DAB isolated from <i>Wolffia globosa</i> microbiomes on host plant growth and characterized their physiological traits. A total of 98 DAB strains were isolated from seven <i>W. globosa</i> microbiomes and individually co-cultivated with <i>W. globosa</i>, exhibiting diverse effects on host growth ranging from promotion to inhibition, with -14.6 to +12.9% of final effects on plant growth. Ten strains consistently promoted host growth and nine strains inhibited growth, which were identified as plant growth-promoting and growth-inhibiting bacteria, respectively. Of these, seven and four strains were identified within the core taxa of <i>W. globosa</i> microbiomes. At the community level, growth-promoting strains tended to be enriched in the growth-promoting microbiomes, whereas neutral or negative strains appeared to be enriched in the growth-inhibiting microbiomes. Taxonomic evaluation demonstrated that prominent promotive and inhibitory phenotypes occurred across six and five genera, respectively, with strain-level characteristics likely determining plant growth effects. Indole-related compound production by DAB emerged as a key physiological determinant associated with <i>Wolffia</i> growth. These findings provide a traceable strain set to advance our understanding of <i>Wolffia</i>-microbiome interactions and offer practical clues on microbiome engineering strategies to enhance <i>Wolffia</i> biomass productivity.</p>","PeriodicalId":46108,"journal":{"name":"AIMS Microbiology","volume":"12 3","pages":"508-525"},"PeriodicalIF":5.4,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13652746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149169667","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}