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Prevalence of polymyxin heteroresistance in Klebsiella pneumoniae under sustained antibiotic selection during experimental evolution. 在实验进化过程中持续抗生素选择下肺炎克雷伯菌多粘菌素耐药性的流行。
IF 2.3 3区 生物学
Archives of Microbiology Pub Date : 2025-07-21 DOI: 10.1007/s00203-025-04405-0
Sambit K Dwibedy, Indira Padhy, Gajanan M Bitode, Saswat S Mohapatra
{"title":"Prevalence of polymyxin heteroresistance in Klebsiella pneumoniae under sustained antibiotic selection during experimental evolution.","authors":"Sambit K Dwibedy, Indira Padhy, Gajanan M Bitode, Saswat S Mohapatra","doi":"10.1007/s00203-025-04405-0","DOIUrl":"https://doi.org/10.1007/s00203-025-04405-0","url":null,"abstract":"<p><p>The swift increase in resistance exhibited by Klebsiella pneumoniae, primarily a nosocomial pathogen, against all frontline antibiotics has significantly restricted the available therapeutic options. Additionally, the rising resistance to polymyxins, frequently considered the last-resort antibiotic, has further exacerbated the situation. The molecular mechanisms responsible for developing high levels of polymyxin resistance are well understood. However, the evolutionary trajectory under antibiotic selection that mimics the clinical setting is not fully elucidated. This study aimed to investigate the development of stable polymyxin resistance in K. pneumoniae using adaptive laboratory evolution (ALE). The K. pneumoniae (ATCC 13883) strain was subjected to ALE with stepwise increasing concentrations of polymyxin-B (PB) and colistin (Col) for 17 days (106 generations). Phenotypic characterisation indicated that the MIC of the polymyxins among the evolved strains increased by 64- to 128-fold. The evolved strains produced smaller hypo-mucoid colonies on LB agar than their ancestral strain and produced significantly more biofilm. However, the phenotypic distinction in the LB broth among the ancestral and the evolved strains was not apparent. Cross-resistance between Col and PB and increased resistance to trimethoprim among the evolved strains was observed. Interestingly, the evolved strains developed collateral sensitivity to ampicillin, kanamycin, and gentamycin. Furthermore, the evolved strains showed polymyxin heteroresistance (HR), where a subpopulation of isogenic bacteria exhibits differential antibiotic susceptibility, often responsible for antibiotic treatment failure. HR was detected using the Kirby-Bauer disk diffusion assay and the E-test and further confirmed by population analysis profiling (PAP) assay. Polymyxin resistance and HR phenotypes remained stable for 100 generations even without antibiotic selection. However, nucleotide sequencing of the targeted TCS genes (phoP, phoQ, pmrA, pmrB, mgrB, and pmrD) revealed no mutations in the evolved strains in comparison to the parental strain, suggesting other genetic mechanisms are likely responsible for the observed phenotypes, warranting further investigation.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 9","pages":"201"},"PeriodicalIF":2.3,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673852","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}
引用次数: 0
Bacterial programmed cell death and toxin-antitoxin system in bacteria. 细菌的程序性细胞死亡与毒素-抗毒素系统。
IF 2.3 3区 生物学
Archives of Microbiology Pub Date : 2025-07-21 DOI: 10.1007/s00203-025-04397-x
Iqra Rafiq, Mudassar Mohiuddin, Muhammad Waqar
{"title":"Bacterial programmed cell death and toxin-antitoxin system in bacteria.","authors":"Iqra Rafiq, Mudassar Mohiuddin, Muhammad Waqar","doi":"10.1007/s00203-025-04397-x","DOIUrl":"https://doi.org/10.1007/s00203-025-04397-x","url":null,"abstract":"<p><p>Bacterial programmed cell death (PCD) is a controlled and regulated mechanism of enormous significance in survival, stress adaptation, and biofilm persistence. Bacterial cells actively trigger their death based on internal or external stimuli. This death is not like accidental or passive death (being caused by antibiotics or through lysis, etc.). The toxin-antitoxin (TA) systems are key players in PCD, contributing significantly to antibiotic resistance and bacterial adaptation. The present descriptive review evaluates current literature dealing with the phenomenon of bacterial PCD with particular focus on the molecular biology of Type I and II TA systems (e.g., mazEF, hipBA, hok/sok). Their functions are involved in bacterial stress responses, biofilm growth, and persistence seen in Pseudomonas aeruginosa and Escherichia coli. The TA systems are a combination of toxins that disturb cellular processes (mRNA cleavage, membrane depolarization) and antitoxins that neutralize toxins to modulate PCD. The mazEF TA system blocks protein synthesis, whereas the hok/sok system results in cellular death thereby maintaining plasmid stability. PCD also encourages biofilm formation by eDNA, thereby enhancing antibiotic resistance and structural integrity, which enables bacteria to persist and make infections difficult to treat. Bioinformatic tools and experimental evidence from genetic knock-out and stress response testing studies were combined to clarify the functions of TA systems and regulation under environmental factors. Understanding these mechanisms allows the development of new antibacterial approaches by targeting TA systems to combat antibiotic resistance and reduce persistence. TA systems are redundant; multiple systems with similar mechanisms can synergistically increase persistence, as seen in the deletion of multiple TA loci in E. coli that resulted in reduced persister cell formation. Future studies should explore the interaction between TA systems with other stress-response patterns to develop target intervention mechanisms that can inhibit bacterial survivability without environmental effects.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 9","pages":"200"},"PeriodicalIF":2.3,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673837","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}
引用次数: 0
Transcriptomic analysis reveals differential gene expression in spleen cells of Chinese soft-shelled turtle infected with Bacillus cereus BC12. 转录组学分析显示蜡样芽孢杆菌BC12感染中华鳖脾脏细胞基因表达差异。
IF 2.3 3区 生物学
Archives of Microbiology Pub Date : 2025-07-17 DOI: 10.1007/s00203-025-04401-4
Chun Fang, Wenjie Hu, Xiaowei Fang, Xiongyan Liang, Jing Liu, Yuting Yang
{"title":"Transcriptomic analysis reveals differential gene expression in spleen cells of Chinese soft-shelled turtle infected with Bacillus cereus BC12.","authors":"Chun Fang, Wenjie Hu, Xiaowei Fang, Xiongyan Liang, Jing Liu, Yuting Yang","doi":"10.1007/s00203-025-04401-4","DOIUrl":"https://doi.org/10.1007/s00203-025-04401-4","url":null,"abstract":"<p><p>Bacillus cereus infection has emerged as a leading cause of high mortality of Chinese soft-shelled turtle (Pelodiscus sinensis) in aquaculture. Elucidating the complex physiological processes and differentially expressed genes (DEGs) of P. sinensis in response to bacterial pathogens will help us explore strategies to combat bacterial infection. In this study, Illumina-based RNA-Seq was used to analyze the significantly active DEGs and pathways in the spleen of P. sinensis challenged by B. cereus BC12. A total of 973 DEGs were identified. These DEGs were significantly enriched in 5,421 Gene Ontology (GO) terms and 147 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways through enrichment analysis. The significantly active pathways included NOD-like receptor signaling pathway (pss04621), cytosolic DNA-sensing pathway (pss04623), cell cycle (pss04110) and spliceosome (pss03040). At 48 h post-infection (hpi), the NF-κB signaling pathway was downregulated, and cell cycle-related gene regulation was disrupted. Additionally, the expression of key spliceosome genes was downregulated. In summary, our results demonstrated the active relevant DEGs and pathways in the splenic cells of P. sinensis at 48 hpi with B. cereus BC12. These results offer valuable insights into the investigation of the molecular mechanisms underlying the resistance of P. sinensis to microbial infections.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 9","pages":"198"},"PeriodicalIF":2.3,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144658232","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}
引用次数: 0
Unveiling the potential of antimicrobial peptides to combat Mycobacterium tuberculosis. 揭示抗菌肽对抗结核分枝杆菌的潜力。
IF 2.3 3区 生物学
Archives of Microbiology Pub Date : 2025-07-17 DOI: 10.1007/s00203-025-04393-1
Saurabh Gupta, Rasanpreet Kaur, Anshu Upadhyay, Jitendra Singh, Bhuvnesh Prasad Sharma, Jagdip Singh Sohal
{"title":"Unveiling the potential of antimicrobial peptides to combat Mycobacterium tuberculosis.","authors":"Saurabh Gupta, Rasanpreet Kaur, Anshu Upadhyay, Jitendra Singh, Bhuvnesh Prasad Sharma, Jagdip Singh Sohal","doi":"10.1007/s00203-025-04393-1","DOIUrl":"https://doi.org/10.1007/s00203-025-04393-1","url":null,"abstract":"<p><p>Tuberculosis (TB) is a severe disease that causes considerably high morbidity and mortality in low- and middle-income developing nations. The causative agent of TB, Mycobacterium tuberculosis (Mtb), has evolved medication resistance, which has hampered the treatment of TB. The need for new anti-TB medications has been driven by the growth of multi-drug-resistant (MDR) mycobacterial strains, resistance to current medicines, and a rising financial burden. In this context, antimycobacterial peptides obtained from diverse sources, including human cells, bacteria, mycobacteriophages, plants, and animals, may serve as potential antituberculosis agents. This is because the majority of these peptides exhibit dual benefits, namely, bactericidal activity against Mtb and immunoregulatory properties. AMPs are strong contenders for alternative therapeutic alternatives or adjuvants in TB treatment because some of the peptides have the added benefit of interacting synergistically with antituberculosis drugs as well, improving their efficacy. This review highlights AMPs' potential modes of action, benefits, and drawbacks compared to traditional antibiotics, as well as how to solve usage-related issues to increase their therapeutic potential. We also discuss the difficulties in translating benchside research to the bedside, assess the state of the development pipeline, and examine the anticipated socioeconomic effects worldwide.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 9","pages":"199"},"PeriodicalIF":2.3,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144658233","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}
引用次数: 0
Deciphering mating type and population genetic landscape of Magnaporthe population adapted to millets and rice in blast hotspots of India. 解读印度稻瘟病热点地区稻谷种群的交配类型和种群遗传景观。
IF 2.3 3区 生物学
Archives of Microbiology Pub Date : 2025-07-15 DOI: 10.1007/s00203-025-04398-w
K B Palanna, Gutha Venkata Ramesh, Prasanna S Koti, H D Vinaykumar, Divya Bhandhari, H R Raveendra, T S S K Patro, T V Krishna, T E Nagaraja, R Madhusudhana, C Tara Satyavathi
{"title":"Deciphering mating type and population genetic landscape of Magnaporthe population adapted to millets and rice in blast hotspots of India.","authors":"K B Palanna, Gutha Venkata Ramesh, Prasanna S Koti, H D Vinaykumar, Divya Bhandhari, H R Raveendra, T S S K Patro, T V Krishna, T E Nagaraja, R Madhusudhana, C Tara Satyavathi","doi":"10.1007/s00203-025-04398-w","DOIUrl":"https://doi.org/10.1007/s00203-025-04398-w","url":null,"abstract":"<p><p>Blast disease caused by Magnaporthe spp. is one of the most destructive diseases affecting graminaceous hosts such as rice and millet crops worldwide. Understanding the reproductive biology and the genetic structure of the pathogen is essential for devising effective management strategies. The current study aimed to assess the mating type distribution, fertility status, DNA polymorphism, gene flow and the population structure of Magnaporthe spp. infecting millets and rice across major blast hotspots of India. Mating type-specific PCR amplification of 136 isolates targeting MAT1-1 and MAT1-2 idiomorphs revealed diverse reproductive strategies. Among the millet-infecting isolates (n = 127), 36.22% were male fertile, 26.77% female fertile, 17.32% hermaphroditic and 19.68% unknown. Rice infecting isolates displayed a mixed mating profile, while bajra isolates were unknown. The presence of both mating types and hermaphroditism suggests potential for sexual recombination, posing a risk of increased genetic variability and virulence. The sequence-based polymorphism analysis of 114 isolates (from finger and foxtail millet) revealed 187 segregating sites and 208 mutations, including 117 singleton sites. The population exhibited high Hd (0.982) and moderate nucleotide diversity (π = 0.0053), indicating significant genetic richness and potential for adaptive evolution. Neutrality tests Tajima's D (-2.418), Fu and Li's D* (-5.197), and F* (-4.752) were significantly negative (p < 0.02) supporting recent population expansion or purifying selection. Population differentiation analyses showed low Gst (0.0217), moderate Fst (0.0797) with high gene flow (Nm = 11.27) reflecting limited population subdivision with ongoing genetic exchange. Haplotype network analysis identified 95 unique haplotypes with most being singletons, supporting high mutational diversity. A central haplotype (Hap_39), comprising 15 isolates of different mating types represents a potential ancestral or broadly adapted lineage. Interestingly, hermaphroditic isolates predominantly clustered in a distinct clade suggesting reproductive isolation and host-specific evolutionary trajectories. AMOVA revealed that 93.27% of genetic variation existed within populations and 6.73% among populations (Φ<sub>ST</sub> = 0.067) reinforcing the conclusion of a predominantly panmictic structure with localized differentiation. Findings of this study provides novel insights into the mating type dynamics and genetic diversity of Magnaporthe spp. infecting millets and rice in India, emphasizing the evolutionary potential of this pathogen and the need for vigilant monitoring and resistant cultivar deployment.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 9","pages":"197"},"PeriodicalIF":2.3,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144636044","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}
引用次数: 0
Metabolic and fermentation engineering of Klebsiella Pneumoniae for high-level production of 3-hydroxypropionic acid. 高水平生产3-羟基丙酸的肺炎克雷伯菌代谢与发酵工程
IF 2.3 3区 生物学
Archives of Microbiology Pub Date : 2025-07-15 DOI: 10.1007/s00203-025-04395-z
Qing-Yi Cao, Hui-Ying Xu, Bang-Ce Ye, Ying Zhou
{"title":"Metabolic and fermentation engineering of Klebsiella Pneumoniae for high-level production of 3-hydroxypropionic acid.","authors":"Qing-Yi Cao, Hui-Ying Xu, Bang-Ce Ye, Ying Zhou","doi":"10.1007/s00203-025-04395-z","DOIUrl":"https://doi.org/10.1007/s00203-025-04395-z","url":null,"abstract":"","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 9","pages":"196"},"PeriodicalIF":2.3,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144636045","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}
引用次数: 0
Integrated genomic and proteomic analysis of local Bacillus thuringiensis isolates for targeted insect pest control and functional insight. 苏云金芽孢杆菌本地分离物的基因组和蛋白质组学分析及其在害虫防治中的应用。
IF 2.3 3区 生物学
Archives of Microbiology Pub Date : 2025-07-11 DOI: 10.1007/s00203-025-04388-y
Sumarin Soonsanga, Amporn Rungrod, Mongkon Utamatho, Chutchanun Trakulnaleamsai, Peeraphat Paenpong, Wirulda Pootakham, Narumon Phaonakrop, Sittiruk Roytrakul, Boonhiang Promdonkoy
{"title":"Integrated genomic and proteomic analysis of local Bacillus thuringiensis isolates for targeted insect pest control and functional insight.","authors":"Sumarin Soonsanga, Amporn Rungrod, Mongkon Utamatho, Chutchanun Trakulnaleamsai, Peeraphat Paenpong, Wirulda Pootakham, Narumon Phaonakrop, Sittiruk Roytrakul, Boonhiang Promdonkoy","doi":"10.1007/s00203-025-04388-y","DOIUrl":"https://doi.org/10.1007/s00203-025-04388-y","url":null,"abstract":"","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 9","pages":"193"},"PeriodicalIF":2.3,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607250","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}
引用次数: 0
Synergistic antimicrobial effect and mechanism of enterocin Gr17 and cinnamaldehyde against Escherichia coli and Candida albicans. 肠球菌素Gr17和肉桂醛对大肠杆菌和白色念珠菌的协同抑菌作用及机制。
IF 2.3 3区 生物学
Archives of Microbiology Pub Date : 2025-07-11 DOI: 10.1007/s00203-025-04391-3
Wen-Yu Ma, Kai-Sheng Shen, Zhao Wang, Qi Liu, Xin-Jie Diao, Guo-Rong Liu
{"title":"Synergistic antimicrobial effect and mechanism of enterocin Gr17 and cinnamaldehyde against Escherichia coli and Candida albicans.","authors":"Wen-Yu Ma, Kai-Sheng Shen, Zhao Wang, Qi Liu, Xin-Jie Diao, Guo-Rong Liu","doi":"10.1007/s00203-025-04391-3","DOIUrl":"https://doi.org/10.1007/s00203-025-04391-3","url":null,"abstract":"<p><p>Bacteriocins and essential oils have potential synergistic antimicrobial effects against pathogens, but the poor understanding of their antimicrobial mechanisms, especially against Gram-negative bacteria and fungi, restricts their practical use in public health. Enterocin Gr17 (ENT) is a novel class IIa bacteriocin that exhibits synergistic effects with cinnamaldehyde essential oil (CEO) against some pathogenic Gram-negative bacteria and fungi. This study aimed to further understand the synergistic antimicrobial activity and mechanisms of ENT and CEO against pathogenic Escherichia coli and Candida albicans from the perspectives of cell wall and membrane, morphological structure, respiratory metabolism and gene expression. Results showed that the ENT-CEO combination induced sublethal damage to E. coli and C. albicans, synergistically limiting their growth in a time-dependent manner. For E. coli, ENT and CEO synergistically disrupted the cell wall structure via interfering with membrane potential and targeting cell wall components, then enhanced membrane permeability and formed non-selective pores, leading to K<sup>+</sup> and adenosine triphosphate efflux and severe damage of morphology and intracellular organization. Furthermore, their combination also suppressed the hexose monophosphate respiratory pathway and the expression of growth and virulence-related genes, ultimately accelerating cell death. On the other hand, ENT combined with CEO minimally affected C. albicans morphology but severely disrupted its intracellular organization, indicating mechanistic differences from E. coli. Initially, ENT and CEO synergistically destabilized membrane potential and destroyed C. albicans cell wall homeostasis, facilitating their cellular internalization. They subsequently disrupted cell membrane permeability and integrity, impaired energy metabolism by inhibiting tricarboxylic acid cycle pathway, and down-regulated the growth and virulence-related gene expression, thereby leading to C. albicans cell death. This study provides theoretical support for the industrial application of bacteriocin-essential oil synergistic antimicrobial technology.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 9","pages":"195"},"PeriodicalIF":2.3,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607251","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}
引用次数: 0
Advancing fungal phylogenetics: integrating modern sequencing, dark taxa discovery, and machine learning. 推进真菌系统发育:整合现代测序,暗分类群发现和机器学习。
IF 2.3 3区 生物学
Archives of Microbiology Pub Date : 2025-07-11 DOI: 10.1007/s00203-025-04392-2
Syed Atif Hasan Naqvi, Aqleem Abbas, Ammarah Hasnain, Zeshan Bilal, Fahad Hakim, Muhammad Shabbir, Ahsan Amin, Muhammad Umer Iqbal
{"title":"Advancing fungal phylogenetics: integrating modern sequencing, dark taxa discovery, and machine learning.","authors":"Syed Atif Hasan Naqvi, Aqleem Abbas, Ammarah Hasnain, Zeshan Bilal, Fahad Hakim, Muhammad Shabbir, Ahsan Amin, Muhammad Umer Iqbal","doi":"10.1007/s00203-025-04392-2","DOIUrl":"https://doi.org/10.1007/s00203-025-04392-2","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The study of fungal genetics has undergone transformative advancements in recent decades, profoundly reshaping our understanding of fungal diversity, evolution, and pathogenesis. This review synthesizes cutting-edge molecular techniques revolutionizing fungal diagnostics, with a focus on DNA fingerprinting, next-generation sequencing (NGS), and third-generation sequencing (TGS), alongside their applications in species identification, phylogenetic reconstruction, and disease management. We critically evaluated the utility of molecular markers such as the Internal Transcribed Spacer (ITS), Large Subunit (LSU), and protein-coding genes (e.g., RPB1, RPB2, TEF1-α), which have emerged as indispensable tools for resolving taxonomic ambiguities and cryptic species complexes. While ITS remains the gold standard for fungal barcoding due to its high interspecific variability, multi-locus strategies integrating loci like β-tubulin and CaM enhance resolution in challenging genera such as Aspergillus, Fusarium, and Penicillium. The review underscores the limitations of traditional morphology-based taxonomy, particularly its inability to address cryptic speciation or non-reproductive fungal phases. Advances in NGS platforms (e.g., Illumina, PacBio, Oxford Nanopore) have overcome these barriers, enabling high-throughput genomic analyses that reveal unprecedented fungal diversity in environmental and clinical samples. TGS technologies, with their long-read capabilities (&gt; 10 kb), now facilitate the assembly of complex genomes, identification of structural variants, and exploration of horizontal gene transfer events, offering new insights into fungal adaptation and pathogenicity. Despite these breakthroughs, challenges persist in resolving intragenomic variation, reconciling gene tree discordance, and standardizing workflows for large-scale fungal population studies. The integration of multi-omics approaches (transcriptomics, proteomics, metabolomics) and machine learning algorithms promises to address these gaps, enabling predictive modeling of antifungal resistance and host-pathogen interactions. Collaborative efforts among mycologists, clinicians, and bioinformaticians are critical to harmonizing data sharing, refining diagnostic pipelines, and translating genomic insights into precision therapies. Fungal-related diseases pose escalating threats to global agriculture, healthcare, and ecosystem stability. Climate change further exacerbates pathogen spread and antifungal resistance, necessitating innovative management strategies. Emerging tools such as CRISPR-based diagnostics, portable sequencers (MinION), and synthetic biology platforms hold promise for real-time pathogen surveillance and engineered biocontrol solutions. By bridging genomic innovation with interdisciplinary collaboration, this review charts a roadmap for advancing fungal diagnostics, enhancing taxonomic clarity, and mitigating the socio-economic impacts of fungal diseases in an era of rap","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 9","pages":"192"},"PeriodicalIF":2.3,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607248","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}
引用次数: 0
Biofilm-dispersal patterns in ESKAPE pathogens. ESKAPE病原菌的生物膜扩散模式。
IF 2.3 3区 生物学
Archives of Microbiology Pub Date : 2025-07-11 DOI: 10.1007/s00203-025-04394-0
Abhijeet Sahu, Sejal Jain, Mrunalini Junghare, Ankita Mishra, Rohit Ruhal
{"title":"Biofilm-dispersal patterns in ESKAPE pathogens.","authors":"Abhijeet Sahu, Sejal Jain, Mrunalini Junghare, Ankita Mishra, Rohit Ruhal","doi":"10.1007/s00203-025-04394-0","DOIUrl":"https://doi.org/10.1007/s00203-025-04394-0","url":null,"abstract":"<p><p>Biofilm formation is now universal behavior of microbes to protect themselves from harsh environment. For ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumanii, Pseudomonas aeruginosa and Enterobacter) pathogens it is one of the strategies to deal with antibiotic tolerance. Biofilms formation involves following major steps initial adhesion of planktonic cells, microcolony formation, biofilm maturation, and finally dispersal. In recent, interest of researchers to understand biofilm dispersal is considered important as it can make us to recognize infection dynamics, antibiofilm strategies, bacterial ecology and antibiotic resistance. A widely supported strategy for combating biofilms involves promoting their dispersal followed by the application of antibiotic therapy to enhance treatment efficacy. But different molecular studies regarding transition of bacteria to biofilms and back to dispersal have highlighted unique physiology and phenotype which might impact treatment strategies. For example, enzymatic degradation using Dispersin B or DNase I have been shown to decrease biofilm mass by over 70% in S. aureus and P. aeruginosa models, significantly increasing antibiotic susceptibility. Similarly, in E. faecalis, combining proteases with antibiotics has demonstrated up to 3-log reductions in viable biofilm cells. Thus, we discuss how native dispersal cues helps the cells in biofilms to decide for dispersal, while how matrix degradation-based dispersal can develop antibiofilm strategies. Considering ESKAPE as priority pathogens and known for biofilm formation hence we discuss patterns of dispersal focused on them only. We believe dispersing biofilms by targeting biofilm matrix components have much potential for future treatments as signaling cues may generate virulent phenotype.</p>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 9","pages":"194"},"PeriodicalIF":2.3,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607249","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}
引用次数: 0
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