Archives of Microbiology最新文献

{"title":"Transcriptomics analysis for elucidating the mechanism underlying the enhancement of Arabidopsis Thaliana growth by the endophytic fungus Clonostachys rosea","authors":"Le Yu,&nbsp;Qinger Huang,&nbsp;Ting Wu,&nbsp;Jiaqi Gao,&nbsp;Bo Zhu,&nbsp;Luping Qin","doi":"10.1007/s00203-025-04453-6","DOIUrl":"10.1007/s00203-025-04453-6","url":null,"abstract":"<div><p>Endophytic fungi are nonpathogenic fungi that live symbiotically in the interior of healthy plant tissues and form mutualistic associations with their hosts. These fungi are critically involved in promoting plant development, strengthening plant uptake of nutrients, and improving plant resistance to biotic and abiotic stress conditions. Endophytic fungi improve plant growth by synthesizing phytohormones (e.g., auxins and gibberellins), solubilizing phosphorus, and enabling nitrogen fixation, thereby enhancing nutrient availability and root development. Previously, we isolated an endophytic fungal strain named AE16 from <i>Actinidia eriantha</i> Benth., a traditional Chinese medicinal plant; this strain was found to substantially stimulate <i>Arabidopsis thaliana</i> growth. Here, to investigate the underlying molecular mechanisms, we conducted transcriptome sequencing analysis and used bioinformatics tools to determine the transcriptome profiles of AE16-inoculated <i>A. thaliana</i> root tissues. We obtained 683 genes with differential expressions, including 391 and 292 upregulated and downregulated genes, respectively. We screened and validated 25 selected genes with a role in plant growth promotion (3 photosynthesis-related genes, 14 starch- and glucose metabolism-related genes, 6 plant hormone synthesis-related genes, and 2 cell transport-related genes). These genes, along with the ERF family of transcription factors, might have a crucial role in promoting <i>A. thaliana</i> growth. The strain AE16 was identified as <i>Clonostachys rosea</i> according to its morphological characteristics and ITS sequencing results. These results further clarify the mechanisms of the mutualistic association between <i>A. thaliana</i> and <i>C. rosea</i> and provide theoretical support to obtain sustained agricultural yield of other plants.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 10","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145011500","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":"Integrated machine learning, molecular dynamics, and DFT-based approach to elucidate the inhibitory effect of Ciprofloxacin analogues against fluoroquinolone-resistant Salmonella Typhi","authors":"Romita Guchhait,&nbsp;Sudha Ramaiah","doi":"10.1007/s00203-025-04452-7","DOIUrl":"10.1007/s00203-025-04452-7","url":null,"abstract":"<div><p><i>Salmonella enterica</i> serovar Typhi, the etiological agent of Typhoid fever, remains a critical public health concern associated with high morbidity in many developing countries. The widespread emergence of multidrug-resistant (MDR) <i>Salmonella</i> Typhi strains against the fluoroquinolone group of antibiotics, particularly ciprofloxacin, poses a significant global therapeutic challenge with underlying resistance due to mutations in quinolone-resistance determining region (QRDR) of <i>gyrA</i> gene, encoding DNA gyrase subunit A (GyrA). In pursuit of alternative therapeutic candidates, the present study was designed to evaluate ciprofloxacin analogues against prevalent GyrA mutations (S83F, D87G, and D87N) to overcome fluoroquinolone resistance through machine learning (ML)-based approach. Based on Decision table algorithm with 78% predictive accuracy, 354 potential active ciprofloxacin analogues were identified from a dataset of 400 compounds. Following molecular docking against each mutant variant, top 10 analogues were screened out based on their higher binding affinity than the reference compound, from which 8 compounds revealed acceptable drug-likeness and ADMET properties. Notably, two analogue compounds (C1) and (C5) exhibited highest average binding affinities of −34.17 kJ/mol and −33.61 kJ/mol, respectively. These compounds further yielded validatory results in molecular dynamics (MD) simulation and binding-free energy analysis using Molecular mechanics/Poisson–Boltzmann surface area. Density functional theory (DFT) study of both the compounds indicated least HOMO–LUMO energy gaps, implying enhanced chemical reactivity. Additionally, MEP (Molecular electrostatic potential) surface mapping and Fukui function analysis revealed key reactive regions, supporting favourable binding orientations. Overall, the findings identify promising ciprofloxacin analogues as lead compounds against GyrA mutations, supporting the development of structurally optimised antimicrobial therapeutics.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 10","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145011722","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":"Recent progress in macrocyclic trichothecene research: structures, biosynthetic pathways, and biological activities","authors":"Peiwen Yan,&nbsp;Hui Zhang,&nbsp;Li Li","doi":"10.1007/s00203-025-04454-5","DOIUrl":"10.1007/s00203-025-04454-5","url":null,"abstract":"<div>\u0000 \u0000 <p>Macrocyclic trichothecenes are a distinctive class of secondary metabolites produced by Ascomycota characterized by complex macrocyclic scaffolds and diverse biological activities, including antibacterial, antitumor, and immunomodulatory effects. This review provides a comprehensive summary of their classification, biosynthetic pathways, and bioactivities, with a particular focus on research advances from 2015 to 2025. During this period, 30 new macrocyclic trichothecene derivatives have been identified from fungal genera such as <i>Myrothecium</i>, <i>Podostroma</i>, <i>Stachybotrys</i>, <i>Fusarium</i>, and <i>Paramyrothecium</i>. Their biosynthesis is primarily governed by polyketide synthase (PKS) and terpene synthase systems, with key genes such as <i>TRI5</i> and <i>TRI4</i> playing central roles. Structural features—including epoxy moieties and side-chain modifications—have been shown to significantly influence their biological activities. In this review, we emphasize newly discovered compounds and recent insights into their biosynthetic mechanisms as well as the anticancer capabilities of different compounds, aiming to provide a valuable reference for future research on the development, optimization, and application of macrocyclic trichothecene derivatives in medical and agricultural contexts.</p>\u0000 </div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 10","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144934728","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":"Creating a designer cyanobacterial ecosystem for the sustainable production of biomass rich in sun-protecting compounds: mycosporine-like amino acids and scytonemin","authors":"Bhavya Pandey,&nbsp;Abhijeet Sharma,&nbsp;Shanthy Sundaram,&nbsp;Adi Nath","doi":"10.1007/s00203-025-04450-9","DOIUrl":"10.1007/s00203-025-04450-9","url":null,"abstract":"<div><p>This review study examines an innovative biotechnological strategy aimed at creating a specialized cyanobacterial ecosystem designed to produce high-quality biomass abundant in compounds that provide protection against solar radiation, specifically scytonemin and mycosporine-like amino acids (MAAs). The remarkable ability of cyanobacteria to produce biomass that is both sustainable and environmentally friendly has attracted considerable attention in recent years, largely due to its wide-ranging applications in various industries. However, a significant challenge remains: the concentrations of these beneficial metabolites within cyanobacteria are typically very low, rendering industrial-scale production economically unviable. To tackle this limitation, the field of synthetic biology offers a promising avenue for improvement. By utilizing advanced genetic and metabolic engineering techniques, strategically modification can be done in specific cyanobacterial strains to optimize their metabolic pathways. This optimization may lead to enhanced production efficiencies and elevated yields of UV-protective chemicals, which are vital for protecting the organisms from harmful ultraviolet radiation as well as for potential applications in sunscreens and UV-blocking materials. In addition to discussing these engineering strategies, this article delves into the intricate molecular mechanisms underlying UV protection in cyanobacteria. Understanding the role of specific metabolites in shielding these microorganisms from UV damage can provide insight into both the natural resilience of cyanobacteria and the potential for engineered strains to yield higher concentrations of these valuable compounds. Through a comprehensive exploration of these topics, we can better appreciate the dual promise of cyanobacteria: their potential as a sustainable biomass resource and their capabilities in mitigating environmental stressors through enhanced UV protection.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 10","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144934727","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":"Diatoms in low pH environments: diversity, adaptations, mechanisms, ecological roles, and applications","authors":"Hirak Parikh,&nbsp;Gayatri Dave,&nbsp;Archana Tiwari","doi":"10.1007/s00203-025-04455-4","DOIUrl":"10.1007/s00203-025-04455-4","url":null,"abstract":"<div><p>Diatoms inhabit a broad pH spectrum, from neutral lakes to highly acidic waters shaped by natural organic acids and anthropogenic inputs such as acid mine drainage (AMD). This review outlines the key chemical drivers of low-pH environments, including natural and industrial acidification. We then synthesize diatom community responses to acid stress—declining taxonomic richness, dominance of acidophilic taxa, and frustule deformities—highlighting how proton toxicity can be a dominant structuring force in highly acidic environments, although in many AMD systems it interacts synergistically with metal stress to shape assemblage composition. At the cellular level, diatoms exhibit adaptive traits including proton-pumping ATPases, dynamic carbon concentrating mechanisms, pH-modifying frustule surface chemistry, and flexible silicon uptake. Genomic studies reveal DNA regulatory elements linked to energy conservation, metabolic rewiring, and enhanced proton/metal homeostasis. Ecologically, acid-tolerant diatoms contribute to carbon, silica, and trace metal cycling, support unique trophic webs, and serve as reliable indicators in biomonitoring and palaeoecological reconstructions. Despite limited experimental data, acidophilic diatoms offer promise for biotechnological applications, including biomimetic nanomaterials, lipid-rich biofuels in acidic photobioreactors, and biofilm-based remediation. We identify key research gaps in genomic resources, taxonomic resolution, and cultivation methods, and propose a multidisciplinary agenda integrating omics, eDNA, and engineered bioreactors. This synthesis underscores the ecological and biotechnological value of acid-tolerant diatoms in understanding and addressing aquatic acidification.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 10","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144927087","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":"Decoding microbial ecology and functions: metagenomic profiling of activated sludge contaminated with chlorolignin compounds in a pulp-paper mill treatment system","authors":"Vineet Kumar,&nbsp;Sirat Sandil,&nbsp;Pradeep Verma,&nbsp;Fuad Ameen","doi":"10.1007/s00203-025-04443-8","DOIUrl":"10.1007/s00203-025-04443-8","url":null,"abstract":"<div><p>This study aimed to profile the dynamics of indigenous bacterial communities in activated sludge, assess the pollutant load, and unlock the functional genes involved during the activated sludge treatment process. The physicochemical analyses of activated sludge revealed high amounts of phosphate, sulfate, chloride, and lignin, along with heavy metals like Fe, Zn, Cu, Ni, and Pb. Simultaneously, the GC–MS/MS technique identified decane, 1 bromo-2-methyl, pentadecanoic acid, methyl ester, benzene dicarboxylic acid, stigmasterol, borinic acid, diethyl, 2-hydroxymethyl cyclopropane, 2-methoxy-4-ethyl-phenol, 3,4,5-trichlorophenol, octadecanoic acid, and tetracosanic acid as major compounds. Furthermore, taxonomic classification of operational taxonomic unit (OTU) data revealed that <i>Proteobacteria</i> was the most abundant phylum, comprising 44.54% of the microbial community. In addition, other phyla, such as <i>Bacteriodetes</i>, <i>Acidobacteria</i>, <i>Planctomycetes</i>, <i>Chlorolfexi</i>, <i>Actinobacteria</i>, and <i>Verrucomicrobia</i> were also recorded within a range between 13.27 and 4.1% in the sludge. At the genus and species levels, the dominant organisms were unclassified (3.62%) and belonged to the family Rhodospirillacea. Further, PICRUSt2-based KEGG Orthology (KO) analysis showed enriched energy metabolism as the most abundant category, driven by oxidative phosphorylation and the TCA cycle. Furthermore, the MetaCyc analysis revealed a robust and adaptable microbial community with the dominant pathways of aerobic respiration I (cytochrome c) and fatty acid biosynthesis pathways, such as cis-vaccenate biosynthesis. The EC assignments highlighted a broad range of enzymatic functions, with a strong emphasis on oxidoreductases and transferases involved in energy production and biosynthesis. This research offers valuable insights into microbial community dynamics in wastewater treatment processes and identifies their functional role in a chlorolignin waste-polluted environment.</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":"207 10","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144920464","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":"Phytochemical diversity of the metabolite profiles relates to the biostimulatory potential of agriculturally beneficial cyanobacteria","authors":"Ravi Mourthy Nivedha,&nbsp;Radha Prasanna","doi":"10.1007/s00203-025-04449-2","DOIUrl":"10.1007/s00203-025-04449-2","url":null,"abstract":"<div><p>Cyanobacteria interact with biota, including higher plants, through the secretion of metabolites, which provide nutrition or elicit immunity, thereby establishing beneficial linkages. However, the phytochemical diversity, in relation to their plant-growth promoting and biofertilizing roles is less understood. Towards this endeavour, the metabolite profiles of three cyanobacterial cultures-<i>Anabaena laxa</i> (C11), <i>Nostoc carneum</i> (BF2), and <i>Anabaena doliolum</i> (BF4)-were evaluated. Biochemical attributes were analysed at 14 and 21 DAI (Days After Inoculation), followed by untargeted GC–MS (Gas Chromatography–Mass Spectrometry) analyses of the metabolite profiles at 21 DAI. Partial Least Squares Discriminant Analysis (PLS-DA), supported by Volcano plot and Correlation network analyses, were employed to highlight the key metabolites. Partial Least Squares Discriminant Analysis (PLS-DA), supported by Volcano plot and Correlation network analyses, illustrated the predominance of organic compounds, in particular, sugars, amino acids and their conjugates, illustrating the significance of C–N metabolism in all the cultures. The metabolites were also rich in response molecules to environmental stressors and a multiplicity of bioactive molecules (particularly glyceryl glycoside, glycerol, lactose, sucrose, and glutamic acid). <i>A. laxa</i> yielded the most hits across several chemical classes, including sugars, organic compounds, amino acids, and nucleotides. Comparison with previously documented metabolite profiles highlighted the differential relative abundance of these compounds, representative of the core metabolome of these agriculturally-significant cyanobacteria. This phytochemical-analysis guided investigation provided insights into the biostimulatory role of cyanobacterial metabolites in nutritional and signalling mechanisms, underscoring their significance as biological options for boosting crop growth and soil fertility.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 10","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144920493","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":"Recent advancements in drug development for pulmonary tuberculosis","authors":"Koushik Mukherjee,&nbsp;Pritam Saha,&nbsp;Kirat Kumar Ganguly,&nbsp;Somjyoti Chakraborty,&nbsp;Swarnali Ghosh,&nbsp;Gopal Kundu","doi":"10.1007/s00203-025-04415-y","DOIUrl":"10.1007/s00203-025-04415-y","url":null,"abstract":"<div><p>Tuberculosis (TB), caused by <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>), is a global health threat. Despite advances in diagnostics and treatment regimens, it infects millions annually. It remains a significant global health challenge, particularly due to the appearance of resistance towards anti-tuberculosis drugs (ATD), mainly multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Mtb poses resistance towards the currently used first- and second-line regimen. Recent advancements in drug development have introduced therapeutic options focussed on improving treatment outcomes for both drug-sensitive and drug-resistant TB. This includes the implementation of a shorter 6-month regimen, a combination of bedaquiline, pretomanid, linezolid, and moxifloxacin (BPaLM), and all-oral treatment regimens (nine months treatment) for patients with MDR/Rifampicin TB-resistance. Another longer 18–20-month regimen is also accessible for patients with TB resistance, for whom all other regimens or treatments are not feasible due to various factors. Ongoing research into new drug molecules, adjunct therapies, and advancement in faster diagnosis aims to enhance the efficacy and tolerability of TB treatment while tackling challenges related to adherence and resistance. This review will discuss the limitations of current treatment regimens, and recent developments in the pharmacological landscape of TB management, highlighting innovative strategies and the necessity for continued efforts to combat the evolving threat of this headstrong pathogen. The findings underscore the importance of a patient-centered approach in TB treatment to achieve equitable and sustainable health outcomes globally.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 10","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144918533","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":"Prediction of protein structural changes mediated by NS-SNPs in antibiotic resistance determinants in Streptococcus pneumoniae","authors":"Wenjia Liu,&nbsp;Xin Rao","doi":"10.1007/s00203-025-04444-7","DOIUrl":"10.1007/s00203-025-04444-7","url":null,"abstract":"<div><p><i>Streptococcus pneumoniae</i> (<i>S. pneumoniae</i>) is a gram-positive bacterium, which is a human pathogen that colonises the human nasopharyngeal region. The evolution of its resistance to many antibiotics has become a major clinical and public health problem. In a study of <i>S. pneumoniae</i>, it was found that resistant strains contained more non-synonymous single nucleotide polymorphisms (NS-SNPs) than sensitive strains. These findings motivate us to further understand the role of NS-SNP mutation in bacterial drug-resistance and how it mediates the development of <i>S. pneumoniae</i> drug-resistance. NS-SNP is a molecular genetic marker that has been widely used in the field of disease and microbial drug-resistance. However, few studies have analyzed the characteristics and related mechanisms of microbial drug-resistance through the effect of NS-SNP mutation on protein conformation and function. Therefore, based on NS-SNP mutation, this study predicted the homologous resistance proteins related to <i>S. pneumoniae</i> and explored the resistance mechanism of homologous proteins mediated by NS-SNP mutation. SNP identification was first implemented by using MUMmer 3 software for whole-genome sequence alignment. The self-designed Fast Feature Selection (FFS) and Codon Mutation Detection (CMD) machine learning algorithms were used for feature extraction and NS-SNPs detection, respectively, ten NS-SNPs mutations were finally selected. The protein/homologous protein structure was predicted and evaluated by ab initio method and Swiss-Model server. Subsequently, Molecular Operating Environment (MOE) software was used to compare protein structure and superposition. Finally, the impact of NS-SNPs on the electrostatic surface of proteins was also evaluated by PyMOL software. This study found that three NS-SNPs mutation-mediated homologous proteins were closely related to drug-resistance of <i>S. pneumoniae</i>, namely NS-SNPs (ID 247805, 817989) mutations-mediated antibiotic resistant ABCF (ARE-ABCF) transporter, and NS-SNP (ID 1101585) mutation-mediated NorM protein promoting antibiotic resistance of <i>S. pneumoniae</i>. Moreover, the resistance might be caused by the difference in electrostatic potential energy resulting from the NS-SNP mutations. This suggests that changes in the electrostatic environment might affect antibiotic binding affinity, revealing a novel mechanism of bacterial drug resistance. Furthermore, this study also provides information on the antibiotic resistance of <i>S. pneumoniae</i>, laying the foundation for its clinical research, diagnosis and medication to treat bacterial infections.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 10","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144918287","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":"Prediction of virulence factors in bacterial hypothetical proteins","authors":"Anchita Prasad,&nbsp;Vijayaraghava Seshadri Sundararajan,&nbsp; JayaramanValadi,&nbsp;Vinod Kumar Nigam,&nbsp;Prashanth Suravajhala","doi":"10.1007/s00203-025-04447-4","DOIUrl":"10.1007/s00203-025-04447-4","url":null,"abstract":"<div><p>A large number of genes in bacterial genomes encode hypothetical proteins (HPs) with unknown functions that require annotation. These HPs have recently been linked to pathogenicity due to potential virulence factors. Understanding the key elements influencing their virulence is a crucial goal. In our study, we analyzed protein domain families from the Pfam database in select Gram-positive and Gram-negative bacteria to identify virulent factors using a scoring system. We employed computational tools such as VICMpred and VirulentPred to identify virulent domains in different bacteria and used regression and Support Vector Machine (SVM) with Weka to find the best candidates. Genotypes with higher adherence suggest that diverse adhesin expression contributes to varying virulence potential, making strains with higher adhesin expression more aggressive. We believe our methods for predicting bacterial protein functions can aid in developing drugs and vaccines by enabling the prediction of virulence proteins.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 10","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144918365","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}