Frontiers in Microbiology最新文献

{"title":"Editorial: Endophytic fungi: from plant occupants to agricultural allies.","authors":"Rosario Nicoletti, Jolanta Jaroszuk-Ściseł, Beata Zimowska","doi":"10.3389/fmicb.2026.1982175","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1982175","url":null,"abstract":"","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1982175"},"PeriodicalIF":5.8,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13661915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149192712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polystyrene microplastics compromise intestinal health and reduce growth and slaughter performance of Chahua chicken No. 2.","authors":"Kun Wang, Yidan Ma, Shiyu Chen, Chen Liu, Guo Chen, Linna Duan, Le Xu, Xiannian Zi, Tengfei Dou, Qiuye Lin, Shunfen Zhang, Zhenhui Cao","doi":"10.3389/fmicb.2026.1954352","DOIUrl":"10.3389/fmicb.2026.1954352","url":null,"abstract":"<p><p>Microplastics are ubiquitous in livestock settings and raise increasing concern, yet studies on their effects on poultry intestinal health and gut microbiota, particularly in native Chinese breeds, are still scarce. Chahua chicken No. 2 were exposed to drinking water with 0, 0.05, 0.1, or 0.5 mg/d polystyrene microplastics (PS-MPs). At 0.5 mg/d, PS-MPs significantly reduced body weight, average daily gain, and feed intake at 42 and 120 days, while increasing feed conversion ratio and decreasing carcass traits (semi-eviscerated yield, eviscerated yield, breast and thigh muscle weights) at 42 days (<i>p</i> < 0.05). This dose also increased the microplastic-associated fluorescence signal in jejunum and ileum, reduced villus height and villus height/crypt depth ratio, and deepened crypts. It downregulated genes associated with intestinal barrier integrity (<i>ZO-1</i>, <i>Occludin</i>, <i>Claudin-1</i>), upregulated inflammatory cytokines (<i>IL-6</i>, <i>IL-8</i>, <i>IL-1β</i>, <i>TNF-α</i>, <i>MIP-1β</i>), and suppressed genes involved in glucose (<i>SLC5A1</i> and <i>SLC2A2</i>), lipid (<i>SLC27A4</i>, <i>APOA1</i>, <i>APOB</i>, <i>MTTP</i>, <i>CD36</i>, <i>FABP2</i>), and amino acid (<i>SLC15A1</i>, <i>SLC7A1</i>, <i>SLC7A9</i>, <i>SLC3A1</i>, <i>SLC6A19</i>) transport (<i>p</i> < 0.05). 16S rRNA gene sequencing analysis revealed that 0.5 mg/d PS-MPs exposure induced intestinal microbiota dysbiosis in Chahua chicken No. 2, characterized by an increased abundance of <i>norank_o_Clostridia_UCG_014, Mediterraneibacter, Olsenella</i>, and <i>Faecalitalea</i> (<i>p</i> < 0.05). Overall, these findings indicate that PS-MP exposure is associated with alterations in growth performance, intestinal morphology, barrier-related gene expression, inflammatory responses, nutrient transporter expression, and gut microbiota in Chahua chicken No. 2.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1954352"},"PeriodicalIF":5.8,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13661584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149180430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Time-resolved transcriptomic analysis reveals envelope stress-mediated adaptation of <i>Escherichia coli</i> to the LPS transport inhibitor thanatin.","authors":"Renu Bisht, Elisabete C C M Moura, Julien Prados, Alessandra Romanelli, Alessandra M Martorana, Pierre D Charlesworth, Mélanie Roch, William L Kelley, Paola Sperandeo, Alessandra Polissi","doi":"10.3389/fmicb.2026.1920608","DOIUrl":"10.3389/fmicb.2026.1920608","url":null,"abstract":"<p><p>Gram-negative bacteria are a major cause of antibiotic-resistant infections due to their highly impermeable cell envelope which contains lipopolysaccharide (LPS) and prevents antibiotics from entering the cell. LPS biogenesis relies on the activity of the essential LPS transport machinery (Lpt), which represents an attractive and validated target for antibiotic development. The antimicrobial peptide thanatin impairs LPS transport by disrupting the assembly of the Lpt protein machinery, resulting in cell death. However, thanatin is not a suitable drug candidate due to its poor drug-like properties and the rapid emergence of resistance. Therefore, understanding the mechanisms underlying cell resistance and adaptation to thanatin is crucial for developing novel antimicrobial strategies. Here we performed RNA-seq-based kinetic transcriptomic analysis to investigate how bacterial cells respond to thanatin over time followed by a functional validation. We found that thanatin treatment induces a rapid activation of the Cpx envelope stress response system, followed by activation of Rcs phosphorelay and downregulation of the FlhDC regulon. Cpx regulated genes showed enrichment for pathways involved in cationic peptide resistance, stress regulation, protein folding, and peptidoglycan remodelling. Rcs upregulated genes were associated with capsule synthesis and biofilm formation. Finally, late response to thanatin suggests the involvement of phospholipid metabolism modulation and trafficking as a strategy to restore OM asymmetry. Overall, our results delineate the adaptive mechanisms employed by bacterial cells to counteract thanatin-induced stress through an interplay of multiple regulatory pathways controlling envelope integrity, stress responses, motility and biofilm formation.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1920608"},"PeriodicalIF":5.8,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13661569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149180540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biosorption of synthetic dyes by live and dried marine diatom <i>Phaeodactylum tricornutum</i> and freshwater diatom <i>Navicula cryptocephala var. veneta</i>.","authors":"Ceaira Howard, Tahira Tasneem Rahman, Mingyue Li, Kesler Hortin, Chiqian Zhang, Liyuan Hou","doi":"10.3389/fmicb.2026.1891020","DOIUrl":"10.3389/fmicb.2026.1891020","url":null,"abstract":"<p><p>Diatom biomass has emerged as a promising biosorbent for removing dye pollutants from dye-bearing wastewater due to its low cost, sustainability, and abundant surface functional groups. Despite interest in algal biosorption, limited studies have compared live and dried biomass across different diatom species. The relative importance of species identity, biomass state, and operating conditions therefore remains unquantified. This study addresses these gaps by investigating the adsorption of three cationic dyes: crystal violet (CV), malachite green (MG), and basic fuchsin (BF), by two diatom species, <i>Phaeodactylum tricornutum</i> and <i>Navicula cryptocephala var. veneta</i>. The effects of dye concentration, pH, temperature, and biomass state were systematically evaluated. For dry cells, adsorption capacity increased with dye concentration due to enhanced mass transfer driving force. Maximum removal efficiencies by <i>P. tricornutum</i> reached 91.3% for CV, 88.6% for MG, and 85.9% for BF, corresponding to equilibrium adsorption capacities of 16.7, 36.6, and 26.6 mg/g, respectively, while <i>N. veneta</i> showed lower removal (13.8, 31.8, and 20.3 mg/g) and earlier saturation at higher concentrations. Neutral pH yielded optimal performance. However, MG and BF exhibited strong pH dependence because of surface charge effects and dye ionization, while CV was relatively insensitive to pH. Temperature effects were strongest for MG, smaller but significant for BF, and not significant for CV. Species and biomass state were the dominant factors controlling adsorption. <i>P. tricornutum</i> consistently outperformed <i>N. veneta</i> across all dyes and conditions tested. Dried biomass achieved significantly higher removal (CV = 70% to 91%, MG = 75% to 87%, BF = 61% to 84%) than live biomass (CV = 45% to 85%, MG = 70% to 82%, BF = 49% to 79%). This may be due to the drying process removing extracellular polymeric substances and membrane barriers, exposing reactive functional groups (e.g., -COO- and Si-O-) and promoting surface-controlled electrostatic interactions. Isotherm analysis indicated adsorption onto an energetically heterogeneous surface. The concentration range examined did not reach saturation in all systems, so maximum adsorption capacities are reported only where the data constrain them. These findings establish biomass state and species identity as the dominant controls on dye biosorption under the conditions tested. This work highlights dried marine and freshwater diatoms as sustainable biosorbents for broad-spectrum dye remediation.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1891020"},"PeriodicalIF":5.8,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13662007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149180526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: New Frontiers in <i>Wolbachia</i> biology 2025.","authors":"Takema Fukatsu, Mark J Taylor, Toshiyuki Harumoto, Yuval Gottlieb, Steve Perlman, Zhiyong Xi, Amelia R I Lindsey, Susumu Katsuma","doi":"10.3389/fmicb.2026.1980203","DOIUrl":"10.3389/fmicb.2026.1980203","url":null,"abstract":"","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1980203"},"PeriodicalIF":5.8,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13661406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149180590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A central hub for convergence: multi-layer genomic networks reveal lineage-specific plasmid compatibility driving hypervirulence and carbapenem resistance in ST11 <i>Klebsiella pneumoniae</i>.","authors":"Xuan Hai, Jun-Ling Wang, Qi Chen, Yi-Fei Lu, Xiu-Ping Li, Cong-Jian Li, Chao-Fu Yue, Jian-Mei Song, Ling-Ling Yang, Min Chen, Hong-Wei Li, Xiao-Yang Zhi","doi":"10.3389/fmicb.2026.1932987","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1932987","url":null,"abstract":"<p><p>The convergence of hypervirulence and carbapenem resistance in <i>Klebsiella pneumoniae</i> represents a critical threat to global public health. However, the genomic mechanisms underlying this convergence, particularly the interplay between chromosomal background and mobile genetic elements, remain incompletely understood. Here, we integrated complete genome data from 102 clinical isolates from Qujing, China, with a global dataset of 4,262 genomes to construct a multi-layer population genomic framework. Using comparative genomics and sequence-similarity network analyses, we characterized the structural organization of the core genome and the population structures of plasmids and prophages. We show that the ST11 lineage serves as a central hub for the convergence of hypervirulence and carbapenem resistance. Plasmids are organized into discrete, functionally specialized communities, among which a dominant community is strongly enriched for hypervirulence and multidrug resistance determinants and preferentially associates with ST11. In contrast, the core genome exhibits a highly constrained structural organization, with most core genes embedded within conserved synteny modules, indicating strong evolutionary constraints on chromosomal architecture. Furthermore, prophages form structured yet more conserved communities that show non-random associations with plasmid types and selectively contribute to the dissemination of resistance genes. Notably, we identified a previously unreported plasmid harboring multiple copies of key virulence loci, underscoring the ongoing modular evolution of high-risk elements. Together, these findings reveal that the convergence of hypervirulence and resistance is driven by lineage-specific plasmid compatibility within a structurally constrained chromosomal background, and they establish a network-based framework for understanding the evolution of high-risk <i>K. pneumoniae</i> lineages.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1932987"},"PeriodicalIF":5.8,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13661990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149192705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pangenomic and machine learning approaches to divergent pathogenic strategies in avian <i>Mycoplasma</i> species: evidence and limitations.","authors":"Miao Yin, Qingrong Jiang, Xing Yu, Qian Wu, Yu Xia, Xin Zhao, Miaoxi Deng, Xuemei Ding, Jinglong Yang, Xiwen Chen, Xuefeng Qi","doi":"10.3389/fmicb.2026.1936311","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1936311","url":null,"abstract":"<p><p>Avian mycoplasmosis, mainly caused by <i>Mycoplasma gallisepticum</i> (MG), <i>Mycoplasma synoviae</i> (MS), and <i>Mycoplasma gallinarum</i> (MGn), remains a persistent constraint on poultry production. These species co-circulate in flocks but differ in tissue tropism, host responses, and clinical outcomes. This review examines how pangenomic analysis and machine learning (ML)-based feature prioritization can clarify these differences while separating computational associations from experimentally supported mechanisms. We first summarize genome reduction, structural variation, accessory gene content, and antimicrobial resistance architecture, and then evaluate ML applications in classification, feature selection, network inference, and candidate prioritization. The evidence is strongest for MG, which combines respiratory adhesion, TLR2/MyD88/NF-κB-mediated inflammation, NLRP3 activation, and oxidative injury. MS appears more synovium-adapted, with evidence of fibroblast reprogramming, ER stress-related responses, and interference with antiviral signaling. MGn remains insufficiently characterized because complete reference genomes, standardized infection models, and functional validation data are lacking. We conclude that pangenomics and machine learning are useful only when linked to validation: They can define candidate repertoires and rank testable hypotheses, but they do not establish pathogenic mechanisms. A controlled three-species comparison and a complete, well-annotated MGn reference genome are the most immediate priorities for addressing the gaps that currently prevent confident cross-species comparison.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1936311"},"PeriodicalIF":5.8,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13662640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149192207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome sequencing of <i>Lactobacillus helveticus</i> HP-B1137 and its biotransformation capacity toward calycosin-7-O-β-D-glucoside.","authors":"Shu-Hang Zhang, Lan-Fang Li, Zhao-Sen Fan, Shao-Yang Hou","doi":"10.3389/fmicb.2026.1962579","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1962579","url":null,"abstract":"<p><strong>Introduction: </strong><i>Astragalus</i>, as a traditional tonic herb, has alycosin-7-O-β-D-glucoside as one of its main active components.</p><p><strong>Methods: </strong>In this study, a strain of <i>Lactobacillus helveticus</i> HP-B1137 was isolated from raw milk in Mudan District, Heze City, Shandong Province. The probiotic properties, and ability to biotransform calycosin-7-O-β-D-glucoside were systematically evaluated.</p><p><strong>Results and discussion: </strong>Genome analysis revealed that HP-B1137 possesses a circular chromosome (2,098,901 bp) comprising 2,161 CDs, 63 tRNAs and 12 rRNAs. Two circular plasmids were also identified, with sizes of 23,906 bp and 6,414 bp and GC contents of 38.54 and 34.49%, respectively. Functional annotation showed that the strain is rich in carbohydrate metabolism genes, with 29 glycoside hydrolase genes annotated by the CAZy database, providing a genetic basis for its glycoside-hydrolyzing capability. <i>In vitro</i> probiotic tests demonstrated that the strain maintained high viable cell counts after 3 min of heat treatment at 50 °C, achieved a survival rate of 108.33% after 150 min in artificial gastric juice at pH 2.7. It also inhibited 11 pathogenic bacteria, producing inhibition zones ranging from 9.83 to 16.37 mm. Whole-cell transformation experiments indicated that HP-B1137 could nearly completely convert 0.5 mg/mL calycosin-7-O-β-D-glucoside into calycosin within 36 h. Further cloning and expression of the recombinant BgsH enzyme revealed optimal reaction conditions at 37 °C and pH 7.0; under optimized conditions-0.1% substrate concentration, 10 U/mL enzyme activity, and 12-h incubation-the conversion efficiency exceeded 96.3%. In summary, <i>L. helveticus</i> HP-B1137 is a functional strain integrating efficient biotransformation, excellent probiotic characteristics, tolerance to extreme environments, and broad-spectrum antimicrobial activity, showing significant potential for developing functional foods derived from <i>Astragalus</i> and green bio-manufacturing of active aglycones.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1962579"},"PeriodicalIF":5.8,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13661924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149192502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA-based characterization of ribosomally active microbial communities during beef slaughtering.","authors":"Muhammad Sharjeel Chaughtai, Franz-Ferdinand Roch, Sarah Thalguter, Tea Movsesijan, Beate Conrady, Monika Dzieciol, Martin Wagner, Evelyne Selberherr","doi":"10.3389/fmicb.2026.1946469","DOIUrl":"10.3389/fmicb.2026.1946469","url":null,"abstract":"<p><strong>Inroduction: </strong>Microbiological contamination on beef carcasses shortens shelf-life and poses substantial food-safety risks. The application of RNA-based analysis nowadays enables insights into the potentially active fraction of microbial communities by targeting ribosomal RNA rather than DNA.</p><p><strong>Methods: </strong>Here, we profiled the rRNA-derived microbiota present at three critical stages of cattle slaughter, skinning, splitting, and chilling, in an Austrian slaughterhouse, using 16S rRNA cDNA sequencing (Illumina MiSeq).</p><p><strong>Results: </strong>While microbial alpha diversity was similar across the three processing stations, PERMANOVA revealed a statistically significant effect of the processing step on microbial community composition. Carcasses at skinning and chilling harbored high relative abundances of rRNA-derived <i>Pseudomonas</i> and the <i>Escherichia-Shigella</i> group. The high relative abundance of <i>Pseudomonas</i> spp., a psychrotrophic spoilage-associated genus, suggests potential metabolic activity and a possible contribution to quality deterioration at low temperatures, while the <i>Escherichia-Shigella</i> group is commonly used as an indicator of possible fecal contamination and hygiene deficiencies. <i>Eperythrozoon (Mycoplasma)</i> was more abundant at the splitting stage and, to a lesser extent, at the chilling stage, suggesting that some cattle may enter the slaughter already colonized and facilitating cross-contamination during carcass manipulation. The subsequent decline during chilling aligns with the cold sensitivity and limited environmental persistence of <i>Eperythrozoon (Mycoplasma)</i>.</p><p><strong>Discussion: </strong>These findings demonstrate the value of RNA-based approaches for delineating the active fraction of carcass-associated microbiota, with potential to inform interventions that enhance meat hygiene and safety.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1946469"},"PeriodicalIF":5.8,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13662132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149180508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global evolutionary dynamics of peste des petits ruminants virus reveals geographic lineage structuring and clade-defining mutational signatures.","authors":"Sarowar Haque, Md Mahfuj Islam, Anupam Das, Safayet Hossain Piyel, Tanvir Ahmed, Roni Mia, Sharmin Akter, Tofazzal Islam, Md M N Azim, Salima Akter, Mohammad Yaseen Ahmad, Amama Rani, Bonglee Kim, Md Golzar Hossain","doi":"10.3389/fmicb.2026.1944163","DOIUrl":"10.3389/fmicb.2026.1944163","url":null,"abstract":"<p><p>Peste des petits ruminants virus (PPRV) is recognized as one of the most economically significant transboundary pathogens affecting small ruminants. However, despite the increasing availability of whole-genome sequences, comprehensive global analyses integrating evolutionary history, phylogeography, and genome-wide lineage-defining molecular markers remain limited. This study investigated the global genomic diversity, evolutionary history, and molecular characteristics of PPRV using whole-genome sequences. A total of 212 temporally informative whole-genome sequences, retrieved from GenBank (between 1969 and 2025) representing all four recognized PPRV lineages, were analyzed using comparative genomics, Bayesian time-scaled phylogenetic reconstruction, and genome-wide candidate phylogenetic marker; single nucleotide polymorphism (SNP) analysis and codon-based selective-pressure analyses. The results demonstrated high genomic conservation across all genomes despite their broad geographic distribution. Bayesian analysis estimated a mean evolutionary rate of 5.07 × 10^-4 substitutions per site per year (95% HPD: 4.79 × 10^-4 to 5.35 × 10^-4) and dated the most recent common ancestor of PPRV to 1839 (95% HPD: 1829 to 1848) which likely reflects the ancestry of currently sampled viral diversity rather than the historical emergence of PPRV. Lineage IV, the predominant contemporary lineage, was further subdivided into four geographically structured subclades: A, B.1, B.2a, and B.2b. A total of 125 subclade-associated fixed SNP signatures were identified, primarily within the L gene, with most variants resulting in nonsynonymous substitutions. The overlapping P, V, and C coding regions underscored the complex functional consequences of lineage-defining mutations. Gene-wide dN/dS values were below 1 for all six genes, indicating predominant purifying selection, while functional mapping identified several SNP related amino acid substitutions within experimentally characterized antigenic regions; however, these substitutions were not supported as positively selected in the present analyses. These results provide a comprehensive genomic framework for understanding PPRV evolution and identify candidate phylogenetic markers for lineage discrimination to support genomic surveillance, molecular epidemiology, and the Food and Agriculture Organization (FAO)-World Organisation for Animal Health (WOAH) Global PPR Eradication Programme.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1944163"},"PeriodicalIF":5.8,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13662165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149180608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}