Archives of Microbiology最新文献

{"title":"Technical limitations of CRISPR-Cas9 genome editing in bacteria: challenges and future directions","authors":"Abdul Qadeer Shabbir,&nbsp;Javeria Idrees,&nbsp;Ali Arif Khan,&nbsp;Iqbal Ahmad Alvi,&nbsp;Saba Sana,&nbsp;Shafiq ur Rehman,&nbsp;Muhammad Asif","doi":"10.1007/s00203-026-05182-0","DOIUrl":"10.1007/s00203-026-05182-0","url":null,"abstract":"<div><p>The CRISPR-Cas system, which originated as an adaptive immune system in bacteria and archaea, has been repurposed as a precise and programmable tool for genetic manipulation in both prokaryotes and eukaryotes. Its applications in bacteria include targeted genome modifications, antimicrobial resistance studies, functional genomics studies, and the development of engineered strains for industrial and synthetic biology applications. Therefore, the understanding of technical aspects of CRISPR systems and their underlying molecular mechanisms is essential for experimental accuracy, reproducibility, and biosafety. CRISPR editing introduces several challenges in bacteria, including off-target effects, DNA repair limitations, cytotoxicity of Cas nucleases, and host-specific restriction-modification barriers. In addition to these specific challenges, metabolic burden, sgRNA design, and delivery challenges further introduce limitations. Such issues compromise editing efficiency, genomic stability, and cell viability. Recent studies have focused on improved guide RNA design, alternative Cas variants, refined delivery strategies, and host-adapted engineering as promising directions to enhance editing. This review discusses the principal barriers to CRISPR-Cas9 genome editing of bacteria, evaluates the current strategies for addressing these barriers, and highlights emerging approaches aimed at improving the efficiency, reliability and precision in bacterial genome engineering.</p><h3>Graphical abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of Pepper aptamer-based reporter system for bacterial transcription studies","authors":"Feixue Zhang,&nbsp;Yue Wang,&nbsp;Yue Mao,&nbsp;Bingbing Hou,&nbsp;Jiang Ye,&nbsp;Haizhen Wu,&nbsp;Ruida Wang,&nbsp;Huizhan Zhang","doi":"10.1007/s00203-026-05197-7","DOIUrl":"10.1007/s00203-026-05197-7","url":null,"abstract":"<div><p>This study introduces a novel bacterial reporter system using the fluorescent RNA aptamer Pepper to directly monitor mRNA-level transcriptional changes, overcoming limitations of traditional protein-based reporters. First, the Pepper reporter system was used to characterize the strength differences of promoters used in <i>Escherichia coli</i>, and the result were compared with enhanced green fluorescent protein (eGFP) reporter and quantitative real-time PCR (qRT-PCR) analysis. Then the Pepper reporter system was used to examine six pairs of known transcriptional regulatory relationships: RacR activating P_<i>lysN</i> and SoxS activating P_<i>ydbK</i> in <i>E. coli</i>, EsrB activating P_<i>evpP</i> and repressing P_<i>glnA</i> in <i>Edwardsiella piscicida</i>, as well as Spo0A activating P_<i>yloA</i> and AbrB repressing P_<i>yloA</i> in <i>Bacillus subtilis</i>. Additionally, we tested the capacity of Pepper reporter to verify the binding of LmbU, a transcriptional regulator from <i>Streptomyces lincolnensis</i>, to known or putative binding sequences in <i>E. coli</i>. These results demonstrate that the Pepper reporter system is a reliable and versatile tool for probing promoter activity, transcriptional regulation, and regulator-DNA interactions in diverse bacteria.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial small RNAs and extracellular vesicles in inflammatory and osteoimmune diseases: regulatory mechanisms and host–microbe communication","authors":"Juan Fernando Montes-Garcia,&nbsp;Erasmo Negrete-Abascal,&nbsp;Sergio Rafael Carrillo-Patiño,&nbsp;Alejandra Isabel Ortega-Meléndez,&nbsp;Rafael Velázquez-Cruz,&nbsp;Alberto Hidalgo-Bravo,&nbsp;Rogelio Frank Jiménez-Ortega","doi":"10.1007/s00203-026-05224-7","DOIUrl":"10.1007/s00203-026-05224-7","url":null,"abstract":"<div><p>Bacterial small RNAs (sRNAs) functions as post-transcriptional regulators that influnce microbial adaptation, pathobiont behavior, and host–microbe communication. This review analyzes bacterial sRNAs and vesicle-associated RNA signals in inflammatory and osteoimmune diseases, with a focus on gastrointestinal and oral microbial communities. Major sRNA classes and mechanisms are summarized, followed by an evaluation of evidence in gastrointestinal inflammation, periodontitis, rheumatoid arthritis, osteoarthritis, and postmenopausal osteoporosis. Direct disease-related evidence is currently limited. The most robust mechanistic example is <i>Porphyromonas gingivalis</i> vesicle-associated sRNA45033, which targets the 3′ untranslated region (UTR) of <i>CBX5</i> and regulates apoptosis in periodontal ligament cell, <i>P. gingivalis</i> outer membrane vesicles also promote alveolar bone resorption in vivo. Human studies in rheumatoid arthritis provide emerging associative evidence, while evidence in osteoarthritis and osteoporosis remains primarily indirect. Future research integrating small RNA sequencing, metatranscriptomics, extracellular vesicle profiling, and functional validation is required to establish causal roles and biomarker potential.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Bioconversion of sea cucumber (Holothuria sp.) by Lactobacillus plantarum: enhancement of bioactive peptides, gamma-aminobutyric acid, and corresponding bioactivities","authors":"Nurul Hidayah,&nbsp;Baso Manguntungi,&nbsp;Masyitha Wahid,&nbsp;Lismayana Hansur,&nbsp;Apon Zaenal Mustopa,&nbsp;Herman Irawan,&nbsp;Fatimah Fatimah,&nbsp;Musrifah Tahar,&nbsp;Arlinda Puspita Sari,&nbsp;Ariandi Ariandi,&nbsp;M. Fiqriansyah Wahab,&nbsp;Alim Bahmid,&nbsp;Lita Meilina","doi":"10.1007/s00203-026-05202-z","DOIUrl":"10.1007/s00203-026-05202-z","url":null,"abstract":"","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emticicia lacicola sp. nov., isolated from a freshwater reservoir","authors":"Hyun Ju Kim,&nbsp;Ahyoung Choi,&nbsp;Jaeduk Goh,&nbsp;Mi-Hwa Lee,&nbsp;Hyangmi Kim","doi":"10.1007/s00203-026-05195-9","DOIUrl":"10.1007/s00203-026-05195-9","url":null,"abstract":"<div><p>A novel Gram-stain-negative, rod-shaped, non-motile, and orange-pigmented bacterium, designated strain 24SJ17W-69^T, was isolated from freshwater collected from Jeongdo Reservoir, Republic of Korea, in March 2024. 16 S rRNA gene sequence analysis revealed that the isolate belongs to the genus <i>Emticicia</i>, showing the highest similarity to <i>E. aquatica</i> HMF2925^T (97.33%). Whole-genome sequencing yielded a 6.15 Mbp genome with a DNA G + C content of 34.8 mol %. Average nucleotide identity (ANI, 78.8%) and digital DNA–DNA hybridization (dDDH, 22.0%) values with the closest relatives were below the species thresholds, clearly supporting its classification as a distinct species (Chun et al. 2018). Growth occurred at 4 ~ 30 °C, pH 6.0 ~ 8.0, and in the absence of NaCl. The predominant respiratory quinone was menaquinone-7 (MK-7). The major polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids, and five unidentified polar lipids. The dominant fatty acids were summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c) and C_15:0. Based on polyphasic taxonomic analyses, strain 24SJ17W-69^T represents a novel species of the genus <i>Emticicia</i>, for which the name <i>Emticicia lacicola</i> sp. nov. is proposed. The type strain is 24SJ17W-69^T (= KCTC 102529^T =LMG 34446^T =FBCC B20691^T).</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New herbicide-degrading microorganisms for the biogenic synthesis of silver nanoparticles","authors":"Juraeva Rokhila Nazarovna,&nbsp;Ergashev Rustam Baxtiyor ugli,&nbsp;Baymurzaev Erkin Nukusbay uli,&nbsp;Jalilov Javlon Zafar ugli,&nbsp;Turakulov Fozil Mamarayim ugli,&nbsp;Garafutdinov Ravil Rinatovich","doi":"10.1007/s00203-026-05199-5","DOIUrl":"10.1007/s00203-026-05199-5","url":null,"abstract":"<div><p>Herbicide-resistant microorganisms were investigated for their potential in pendimethalin biodegradation and the biogenic synthesis of silver nanoparticles (AgNPs). Among the selected strains, <i>Acinetobacter radioresistens</i> R27, <i>Bacillus pumilus</i> R25, and <i>Streptomyces variabilis</i> R35 demonstrated pronounced pendimethalin-degrading activity. At a herbicide concentration of 125 mg/L, biomass increases after 7 days reached 87.5%, 92.0%, and 58.5%, while pendimethalin degradation efficiencies were 92.5%, 86.0%, and 62.0%, respectively. <i>A. radioresistens</i> R27 exhibited the highest degradation efficiency. Biogenic AgNP synthesis was confirmed by UV–Vis spectroscopy and X-ray diffraction, which demonstrated a face-centred cubic crystalline structure. The synthesized AgNPs showed predominantly spherical morphology, with particle sizes varying depending on the biosynthesis conditions. AgNPs synthesized using <i>A. radioresistens</i> R27 at 75 mg/L exhibited a zeta potential of − 20.5 mV. The synthesized AgNPs demonstrated pronounced concentration-dependent antifungal activity against <i>Aspergillus flavus</i>, <i>Alternaria alternata</i>, and <i>Fusarium oxysporum</i>. Thus, the investigated microorganisms, particularly <i>A. radioresistens</i> R27, demonstrated a combination of high pendimethalin-degrading capacity and biogenic AgNP synthesis associated with pronounced antifungal activity.</p><h3>Graphical abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Silybum marianum against multidrug-resistant bacterial pathogens: mechanisms of action, synergistic therapy, nanoformulations, and clinical translation","authors":"Syed Suhaib Ahmed,&nbsp;Bhaswati Das,&nbsp;Punitha Muruganantham,&nbsp;Marakanam Srinivasan Umashankar,&nbsp;Inamul Hasan Madar","doi":"10.1007/s00203-026-05184-y","DOIUrl":"10.1007/s00203-026-05184-y","url":null,"abstract":"<div><p><i>Silybum marianum</i>, commonly known as milk thistle, has a long history of medicinal use as a hepatoprotective plant and has emerged as a potential source of natural antimicrobial agents against multidrug-resistant (MDR) bacterial pathogens. This review provides an objective overview of current knowledge on the antimicrobial mechanisms of S. marianum and its potential utility for targeting resistant bacterial strains. Recent studies have demonstrated that silymarin, the major flavonolignan complex isolated from the seeds of S. marianum, exhibits observable antimicrobial activity against several critical MDR phenotypes, including methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum β-lactamase (ESBL)-producing <i>Escherichia coli</i>, carbapenem-resistant <i>Klebsiella pneumoniae</i>, and <i>Stenotrophomonas maltophilia</i>. The antimicrobial effect of silymarin is concentration-dependent, with ethanolic extracts exhibiting greater antibacterial activity than aqueous extracts. The principal mechanisms underlying the anti-MDR activity of S. marianum include multiple pathways: disruption of bacterial membranes, increasing permeability; inhibition of biofilm formation; modulation of reactive oxygen species; inhibition of efflux pumps; and synergistic enhancement of conventional antibiotic activity. Advanced nanoformulation techniques have been applied to address the poor baseline bioavailability of silymarin, with nano-silymarin systems displaying lower minimum inhibitory concentrations (MICs) than conventional formulations against clinical MDR isolates in laboratory models. Topical delivery systems, such as mucoadhesive gels, offer sustained drug release profiles and enhanced permeation properties. Nevertheless, standardising extraction protocols, optimising dosing regimens, and conducting rigorous clinical trials remain essential steps to translate these preclinical findings into viable human therapeutic applications.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biochemical and molecular characterization of Xanthomonas citri pv. mangiferaeindicae causing bacterial black spot of mango in Pakistan","authors":"Hajra Azeem,&nbsp;Rashida Perveen,&nbsp;Ummad-ud-din Umar","doi":"10.1007/s00203-026-05212-x","DOIUrl":"10.1007/s00203-026-05212-x","url":null,"abstract":"<div><p>Bacterial black spot (BBS) disease of mango (<i>Mangifera indica</i> L.) is associated with <i>Xanthomonas citri</i> pv. <i>mangiferaindicae</i> (Xcm) and can cause substantial production and fruit-quality losses in susceptible orchards. This study was investigated to isolate and characterize Xcm associated with symptomatic mango samples from major mango-growing areas of South Punjab, Pakistan, using phenotypic, biochemical, pathogenicity, PCR, sequencing, and phylogenetic approaches. Symptomatic mango samples were collected from surveyed orchards, and Xcm isolates were obtained, purified, and characterized based on colony morphology and biochemical tests, including gelatin hydrolysis, starch hydrolysis (amylase activity), catalase, and oxidase assay. Pathogenicity assays were performed to evaluate the ability of selected isolates to produce disease symptoms. Molecular identification was performed by PCR amplification with the primers targeting the 16 S rRNA gene (27 F/1492R) and the pthA region (VM3/VM4), followed by sequencing and phylogenetic analysis. The isolates produced yellow or offwhite, mucoid colonies, while biochemical assays provided supporting phenotypic characteristics for their identification. BLAST analysis showed 99.9% identity with previously reported Xcm sequences fromChina. Phylogenetic analysis further demonstrated that the Pakistani isolates clustered closely with Xcm isolates reported from mango in china revealed that the Pakistani isolates are clustered closely with the Xcm isolates reported from mango in China and an isolate associated with Ambarella in France The combined phenotypic, pathogenicity, PCR, sequencing, and phylogenetic evidence supported the association of Xcm with bacterial black spot of mango in the surveyed areas of Pakistan. This study confirmed the association of Xcm with bacterial black spot of mango on molecular basis in Pakistan for the first time and provide baseline information for future additional molecular markers diagnosis such as gyrB, rpoD, dnaK, fyuA, or multilocus sequence analysis, to better understand the genetic diversity of Xcm and facilitate improved disease diagnosis and management.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Seed biopriming with a novel endophytic Bacillus licheniformis strain RGS enhances drought tolerance and recovery in tomato","authors":"R. Harish,&nbsp;Y. R. Manasa,&nbsp;H. S. Santhosh Kumar,&nbsp;R. G. Sharathchandra","doi":"10.1007/s00203-026-05206-9","DOIUrl":"10.1007/s00203-026-05206-9","url":null,"abstract":"","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fungi to the rescue: recent advances, mechanistic insights and omics-based perspectives in heavy metal mycoremediation","authors":"Shristy Maurya,&nbsp;Priyanka Sharma,&nbsp;Bhupendra Narayan Singh Yadav,&nbsp;Gyan Prakash Gupta,&nbsp;Neha Tiwari,&nbsp;Rajiv Kumar Yadav","doi":"10.1007/s00203-026-05187-9","DOIUrl":"10.1007/s00203-026-05187-9","url":null,"abstract":"<div><p>Heavy metal (HM) contamination arising from rapid industrialization poses critical threats to global ecosystem integrity and public health. Conventional physicochemical approaches are limited by high costs, incomplete removal, and toxic waste generation, necessitating sustainable alternatives. Mycoremediation, which harnesses the remarkable, diverse capacities of fungi to tolerate and mitigate HM stress through sophisticated biological mechanisms, has emerged as a promising and sustainable approach to address HM pollution. This review examines the sources and ecotoxicological impacts of HM pollution, alongside the intracellular and extracellular mechanisms underlying fungal tolerance and removal, including biosorption, precipitation, membrane transport, antioxidant defense, chelation, bioaccumulation, and biotransformation. It further synthesizes fungal-based bioremediation strategies, while examining how metagenomic, metatranscriptomic, transcriptomic, proteomic, and metabolomic approaches are advancing understanding of fungal community structure and active detoxification pathways. This work uniquely integrates community- and isolate-level multi-omics data, explicitly bridges mechanistic understanding with omics-driven insights, and extends this into translational roadmap for applied bioremediation.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148987044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}