Frontiers in Microbiology最新文献

{"title":"Gut microbiome and urinary metabolomic alterations in Chinese infants with functional constipation and yin-deficiency constitution.","authors":"Haihong Zhao, Xiuxia Lu, Yanbin Ye, Hui Ye, Weiwei Li, Ziyu Long, Xuezhi Zhang, Jieling Wu, Ji Wang","doi":"10.3389/fmicb.2026.1851053","DOIUrl":"10.3389/fmicb.2026.1851053","url":null,"abstract":"<p><strong>Background: </strong>Functional constipation (FC) is common in early childhood and is closely associated with gut microbiota imbalance. According to Traditional Chinese Medicine (TCM) constitution theory, infants can be categorized into different constitution types, among which the yin-deficiency constitution is particularly linked to a higher risk of FC. However, data specifically addressing this association in infants remain limited.</p><p><strong>Methods: </strong>Infants under 2 years of age were assessed for yin-deficiency and balanced constitutions using a TCM Constitution Questionnaire, and FC was diagnosed according to the Rome IV criteria. The study enrolled 31 infants with yin-deficiency constitution and FC (YINDC) and 31 infants with balanced constitution and without FC (BC, controls). Evaluations included Bristol Stool Scale scores, constipation symptoms, fecal microbiota profiles, and urinary metabolite characteristics.</p><p><strong>Results: </strong>The YINDC group exhibited significantly lower Bristol Stool Scale scores and more severe FC symptoms than the BC group. Marked differences in gut microbial composition and metabolite profiles were observed between the two groups, with main alterations identified in the sphingolipid signaling and metabolism pathways.</p><p><strong>Conclusion: </strong>This study compares gut microbial and urinary metabolomic profiles between infants with the combined yin-deficiency constitution/FC phenotype and balanced non-constipated controls. We identified preliminary microbiota and metabolomic differences between the two groups, involving sphingolipid-related pathways. However, these differences cannot be specifically attributed to yin-deficiency constitution, FC, or their interaction. Our findings provide a preliminary basis for future investigation of the gut microbiome-metabolome axis in TCM-integrated FC management, but require validation in independent cohorts.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1851053"},"PeriodicalIF":5.8,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13522173/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148850238","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":"Broad-spectrum lytic potential of endolysins derived from prophages of clinical <i>Salmonella</i> isolates.","authors":"Yuhui Liu, Xiuxiu Zeng, Hui Su, Jianing Zhao, Jiayi Dong, Fanfan Yang, Shuo Ye, Wenping Lin, Yuanbin Yang, Yuechao Sun","doi":"10.3389/fmicb.2026.1922952","DOIUrl":"10.3389/fmicb.2026.1922952","url":null,"abstract":"<p><p>In the post-antibiotic era, alternative therapeutic strategies were urgently needed. Here, we characterized 514 prophages from 105 clinical <i>Salmonella</i> isolates, assessing their carriage of antimicrobial resistance (AMR) genes and virulence factors (VFs) to evaluate biosafety and evolutionary dynamics. Our analyses revealed significant correlations between the abundance of each prophage and host serotypes, as well as between prophage-borne AMR genes and host age or serotype background. Phylogenetic analysis showed that most prophages are related to known <i>Salmonella</i> phages, though a subset shares homology with <i>Burkholderia</i> viruses, suggesting inter-generic evolutionary connections. A comprehensive screening of prophage-encoded proteins identified a large repertoire of endolysins, with 80.93% of prophages carrying at least one such enzyme. Sequence-based clustering grouped these endolysins into seven families, three of which are widely distributed across the isolate collection. Structural modeling indicated that representative enzymes from these major groups are structurally analogous to thermostable, broad-spectrum lysozymes, which revealed the potential of the proteins as alternatives to antibiotics for treatment. To validate the therapeutic potential of prophage-derived lytic enzymes, we expressed the candidate endolysin <i>Lys2823</i> and demonstrated its lytic activity against outer-membrane-permeabilized <i>Salmonella</i>. These results indicate that <i>Lys2823</i> holds promise as a biocontrol agent for the prevention and treatment of <i>Salmonella</i> infections, thereby contributing to food safety and public health. This study provides experimental evidence supporting the development of prophage-derived endolysins as novel antimicrobial agents.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1922952"},"PeriodicalIF":5.8,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13522114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148849608","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":"Comparative analysis of gut and ovarian microbiota in <i>Dactylopius opuntiae</i> (Hemiptera: Dactylopiidae) from distinct Moroccan regions.","authors":"Oumaima Moustaid, Mohamed Idbella, Salah Eddine Azaroual, Karim El Fakhouri, Chaimae Ramdani, Mohamed Ouaarous, Mustapha El Bouhssini, Issam Meftah Kadmiri","doi":"10.3389/fmicb.2026.1890634","DOIUrl":"10.3389/fmicb.2026.1890634","url":null,"abstract":"<p><strong>Introduction: </strong>Investigating the hidden microbial world within insect hosts yields new insights into their biology, ecology, and adaptation. <i>Dactylopius opuntiae</i> (Cockerell), a major invasive pest of the cactus <i>Opuntia ficus-indica</i>, causes severe economic and ecological damage in Morocco and other arid regions. However, little is known about its associated bacterial microbiota and how it varies across environmental gradients. This study explored the bacterial diversity of <i>D. opuntiae</i> and evaluated how it varies across tissue types, developmental stages, and contrasting environmental regions.</p><p><strong>Methods: </strong>We characterized bacterial communities in two tissue types (gut and ovary) of adult females and in whole-body samples of nymphs, collected from two ecologically contrasting regions of Morocco: Marrakech (arid, semi-desert climate) and Al Hoceima (humid, Mediterranean climate). Using 16S ribosomal RNA (rRNA) gene sequencing, we evaluated differences in diversity, composition, and relative abundance across regions and developmental stages.</p><p><strong>Results: </strong>Sequencing generated approximately 2.84 million reads across all samples, of which 91.9% were retained after quality filtering and contaminant removal, and 91.2% were successfully classified to bacterial taxa. Our results revealed clear geographic structuring of the microbiota. In insects from Marrakech, the adult gut and ovary harboured comparatively lower bacterial diversity and were dominated by <i>Pseudomonadota</i>, whereas whole-body nymph samples were dominated by <i>Bacillota</i> (>70% relative abundance). In contrast, samples from Al Hoceima showed consistently higher bacterial richness across stages and tissues, with <i>Pseudomonadota</i> accounting for approximately 60-90% of reads. Differential abundance analysis identified several taxa with nominal tissue- and region-associated differences (<i>p</i> < 0.05), including <i>Thiomonas</i>, <i>Burkholderia</i>, and <i>Acinetobacter baumannii</i> for tissues, and <i>Staphylococcus xylosus</i>, <i>Klebsiella pneumoniae</i>, <i>Salmonella enterica</i>, and <i>Ferrovum myxofaciens</i> for regions. The most represented bacterial orders in Al Hoceima samples were <i>Burkholderiales</i>, <i>Enterobacterales</i>, <i>Nitrosomonadales</i>, and <i>Rhodocyclales</i>.</p><p><strong>Discussion/conclusion: </strong>Together, these findings highlight the spatial variability of insect-microbe association in <i>D. opuntiae</i> and point to candidate bacterial taxa whose distribution covaries with regional environmental conditions. This study provides baseline, descriptive microbiome data and a foundation for future functional investigations of microbial roles in host biology, which may in turn inform microbiome-aware pest management strategies across Moroccan agroecosystems.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1890634"},"PeriodicalIF":5.8,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13522214/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148849809","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":"Genetic diversity and evolution of nine avirulence genes in South Korean <i>Phytophthora sojae</i> populations.","authors":"Rahel Dinsa Guta, Youngnam Yoon, Jun Hyoung Jeon, Hyeon Su Lee, Seoyeon Hong, Ok Jae Won, Rameswor Maharjan, Yi Hwi Jong, Yun-Woo Jang","doi":"10.3389/fmicb.2026.1909451","DOIUrl":"10.3389/fmicb.2026.1909451","url":null,"abstract":"<p><strong>Introduction: </strong><i>Phytophthora sojae</i>, the causal agent of soybean root and stem rot, is a highly destructive pathogen affecting soybean production worldwide. Rapid evolution of avirulence (<i>Avr</i>) genes poses a major challenge to the development of durable host resistance. However, comprehensive information on the diversity, sequence variation, and evolution of multiple <i>Avr</i> genes in South Korean <i>P. sojae</i> populations remains limited. This study aimed to characterize the pathogenicity, pathotypes, and genetic diversity of nine <i>Avr</i> genes in <i>P. sojae</i> populations from the Republic of Korea.</p><p><strong>Methods: </strong>Fifty <i>P. sojae</i> isolates were collected from soybean-growing regions in the Republic of Korea between 2020 and 2025. Pathogenicity was evaluated in the soybean cultivar 'Daewon', and pathotypes were determined by amplification patterns of nine race-specific <i>Avr</i> genes (<i>Avr1a</i>, <i>Avr1b</i>, <i>Avr1c</i>, <i>Avr1d</i>, <i>Avr1k</i>, <i>Avr3a</i>, <i>Avr3b</i>, <i>Avr3c</i>, <i>Avr4/6</i>). Sequence polymorphism, nucleotide and amino acid variation, and haplotype diversity were analyzed to investigate the evolutionary patterns of these <i>Avr</i> genes.</p><p><strong>Results: </strong>Most isolates were highly virulent on the soybean cultivar 'Daewon', with 70% causing severe disease symptoms. Five distinct pathotypes were identified, with pathotype 3, characterized by the absence of <i>Avr3a</i>, representing the predominant group. Gene deletions occurred most frequently in <i>Avr3a</i> and <i>Avr1a</i>. Sequence analyses revealed extensive nucleotide and amino acid polymorphisms among <i>Avr</i> loci, particularly within the C-terminal regions of effector proteins, whereas <i>Avr4/6</i> remained highly conserved across all isolates. Haplotype analysis demonstrated substantial allelic diversity, with <i>Avr1a</i> exhibiting the highest haplotype diversity and the greatest number of haplotypes. The coexistence of multiple pathotypes and haplotypes within the same geographic regions indicated considerable genetic diversity within local <i>P. sojae</i> populations.</p><p><strong>Discussion: </strong>This study provides the first comprehensive characterization of the diversity and evolution of nine <i>Avr</i> genes in South Korean <i>P. sojae</i> populations. The results demonstrate that both gene loss and sequence diversification contribute to <i>Avr</i> gene evolution and pathogen adaptation. These findings improve our understanding of the evolutionary dynamics of <i>P. sojae</i> populations and highlight the importance of continuous pathogen surveillance to support durable resistance breeding and effective management of soybean root and stem rot.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1909451"},"PeriodicalIF":5.8,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13522140/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148849906","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 metabolomics approach to target the effect of histone protein methyltransferase-specific probe UNC1999 on cryptic metabolites in an endophytic fungus <i>Xylaria papulis</i> Lloyd.","authors":"Shubham Vishwakarma, Jay Hind Nishad, Anjali, Shagun Sinha, Rajnish Bharti, Laxmi Shekhar, Ravindra Nath Kharwar","doi":"10.3389/fmicb.2026.1894461","DOIUrl":"10.3389/fmicb.2026.1894461","url":null,"abstract":"<p><p><i>Xylaria papulis</i> Lloyd, an endophytic fungus, was isolated from the stem of <i>Andrographis paniculata</i> Willd., commonly known as green chiretta, which is native to India and Sri Lanka. To date, no report is available on the epigenetic modulation of <i>X. papulis</i> using the histone methyltransferase inhibitor UNC1999. Hence, this study aims to evaluate the independent effect of this probe. The fungal culture was evaluated for antioxidant (2,2-diphenyl-1-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid radical scavenging assays) and antibacterial potential against six human pathogens: <i>Staphylococcus epidermidis</i> (ATCC 12223), methicillin-susceptible <i>Staphylococcus aureus</i> (MSSA) (ATCC 25923), methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) (MU50), <i>Enterobacter cloacae</i> (ATCC 13047), <i>Klebsiella pneumoniae</i> (ATCC 700603), and <i>E. coli</i> (ATCC 25922). The crude extract, which was recovered from the samples treated with 250 nM of UNC1999, exhibited enhanced antioxidant and antibacterial efficacy against <i>S. epidermidis</i> (ATCC 12223), MSSA (ATCC 25923), MRSA (MU50), <i>E. cloacae</i> (ATCC 13047), and <i>K. pneumoniae</i> (ATCC 700603), compared to the control. The chemical profiles of crude extracts, both treated and untreated, were analyzed using gas chromatography-mass spectrometry and ultra-high-performance liquid chromatography along with high-resolution mass spectrometry). The results highlighted the capacity of UNC1999 to modulate the synthesis of cryptic metabolites in <i>X. papulis</i>, displaying antimicrobial and anticancer potential. This study underlines the importance of further research into the molecular mechanisms regulating these epigenetically modulated metabolic pathways.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1894461"},"PeriodicalIF":5.8,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13522211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148850236","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: Microbial solutions for soil health and remediation: from natural diversity to engineered communities.","authors":"Rui Zhuo, Xuan Zhang","doi":"10.3389/fmicb.2026.1947537","DOIUrl":"10.3389/fmicb.2026.1947537","url":null,"abstract":"","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1947537"},"PeriodicalIF":5.8,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13521911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148849892","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":"Multigene phylogeny and taxonomy of Hydnaceae (Cantharellales, Basidiomycota) reveal <i>Leucopruina abieticola</i> gen. et sp. nov. from Southwest China.","authors":"Zhan-Bo Liu, Jian-Ling Zhang, Ren-Jin Chen, Ke-Ni Meng, Ying-Ge Fan, Han Liu, Guang-Peng Weng, Xiao-Bin Liu, Jing-Xuan Xu, Yu-Tong Zhang, Qing-Chao Zeng, Han Zhao, Shu-Jiang Li","doi":"10.3389/fmicb.2026.1889648","DOIUrl":"10.3389/fmicb.2026.1889648","url":null,"abstract":"<p><p>During a survey of wood-decaying fungi in the subalpine forests of Southwest China, distinctive corticioid specimens were collected from fallen <i>Abies</i> trunks. Based on a combination of morphological characteristics and multigene phylogenetic analyses of the internal transcribed spacer (ITS) and nuclear large subunit (nLSU) sequences, these specimens were found to represent a highly distinct and strongly supported monophyletic lineage within the family Hydnaceae (Order: Cantharellales; Division: Basidiomycota). Consequently, a new genus, <i>Leucopruina</i> gen. nov., is proposed to accommodate the novel species <i>L. abieticola</i> sp. nov. Morphologically, the new species is characterized by its white, pruinose, resupinate basidiomata and a dimitic hyphal system with branched skeletal hyphae. Although it shares urniform basidia bearing 6-8 sterigmata with <i>Sistotremella</i>, <i>Leucopruina</i> is clearly distinguished by its thin-walled, acyanophilous (CB-) basidiospores, in contrast to the thick-walled, cyanophilous (CB+) spores of <i>Sistotremella</i>. This discovery increases the number of recognized genera within Hydnaceae to 19 and highlights the rich but previously underestimated taxonomic diversity of saprotrophic fungi in the high-altitude ecosystems of Southwest China.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1889648"},"PeriodicalIF":5.8,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13522215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148850265","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":"Multi-layer gut microbiome variation in type 2 diabetes despite preserved higher-order community structure.","authors":"Junwei Zhou, Peijie Du, Limin Liu, Li Wang, Suping Liu, Guizhi Yan","doi":"10.3389/fmicb.2026.1902019","DOIUrl":"10.3389/fmicb.2026.1902019","url":null,"abstract":"<p><strong>Background: </strong>Type 2 diabetes (T2D) has been consistently associated with alterations in the gut microbiome, although disease, treatment, diet, and other host factors may contribute to the observed patterns. How these associations are organized across different biological levels of the microbial ecosystem remains incompletely understood.</p><p><strong>Methods: </strong>We performed shotgun metagenomic sequencing of fecal samples from 82 individuals, including 41 patients with T2D and 41 age-, sex-, and body mass index-matched healthy controls. Taxonomic profiling, functional pathway analysis, enterotype characterization, ecological network inference, and interpretable machine-learning approaches were integrated to characterize microbiome variation across multiple organizational levels.</p><p><strong>Results: </strong>Despite clear clinical differences between groups, particularly fasting blood glucose, the overall ecological architecture of the gut microbiome remained broadly preserved. Dominant phylum-level composition and enterotype structure were maintained, whereas variation became apparent at finer biological scales. Species-level analyses identified 42 differentially abundant taxa. Community diversity analysis showed reduced Chao1 richness (<i>P</i> = 0.024), increased Simpson diversity (<i>P</i> = 0.024), unchanged Shannon diversity (<i>P</i> = 0.126), and a modest shift in community composition (PERMANOVA, <i>R</i> ² = 0.040, <i>P</i> = 0.006). Functional profiling showed no pathway-level significance after multiple-testing correction but directional trends across several metabolic modules. Exploratory Spearman-based networks differed in topology between groups; because relative-abundance data are compositional, these differences cannot be interpreted as direct ecological interactions or definitive network rewiring. Machine-learning models achieved a within-cohort cross-validated AUC of up to 0.91, but lacked independent external validation.</p><p><strong>Conclusions: </strong>These findings provide a multi-layer description of T2D-associated gut microbiome variation within this cohort. The data are consistent with preserved higher-order community organization accompanied by finer-scale differences in species composition, functional potential, community-state occupancy, statistical co-occurrence, and within-cohort discriminative features. Medication confounding, compositional effects, technical artifacts, and the absence of external validation limit causal, ecological, and diagnostic interpretation. Larger longitudinal, multi-site, medication-resolved, and independently validated studies are required.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1902019"},"PeriodicalIF":5.8,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13522148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148850273","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":"From low- to high-level resistance: dynamic transcriptional adaptations and efflux pump amplification in cefiderocol-stressed <i>Pseudomonas aeruginosa</i>.","authors":"Ting Zhang, Hanxu Hong, Jun Wang, Yuxuan Liu, Yun Cao, Yang Liu, Wei Zhang","doi":"10.3389/fmicb.2026.1871230","DOIUrl":"10.3389/fmicb.2026.1871230","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> is a bacterium with high antimicrobial resistance to several drugs including carbapenems. Recently, resistance to cefiderocol (FDC), a new siderophore cephalosporin, has been reported despite its rare use in clinical practice. Therefore, this study aimed to investigate the dynamics of different resistance mechanisms in <i>P. aeruginosa</i> that evolve under FDC pressure, as well as the interactions between these mechanisms in evolutionary trajectories to guide clinical medication. <i>P. aeruginosa</i> ATCC 27853 was continuously induced with subinhibitory concentrations of cefiderocol <i>in vitro</i> to generate strains with different resistance levels. Phenotypic adaptability and molecular regulatory networks during the evolution of resistance were systematically elucidated using growth curves, pairwise competition assays, transcriptomics, RT-qPCR and efflux inhibition assays. The minimum inhibitory concentration (MIC) of the induced FDC-resistant strain increased from 0.125 to 64 μg/mL. Simultaneously, the growth rate and peak declined below those of the parental strain. The pairwise competition assay showed that the relative fitness of resistant strains versus parental strains was < 1 in LB and ID-CAMHB broths. Transcriptome analysis revealed that the MIC of the induced FDC-resistant strain was related to the dose of efflux pumps, together with a layer-by-layer regulation of gene expression, to adapt to environmental stress. In the initial resistant strain, efflux pumps were slightly upregulated, and energy metabolism was downregulated. Conversely, in the strain with a MIC of 64 μg/mL, efflux pumps were significantly up-regulated and drove bacterial reprogramming to induce resistance, particularly the RND efflux pump component oprM, along with multiple ABC transporters. RT-qPCR validated the significant upregulation of oprM, opuC, and opuBD (<i>p</i> < 0.05), confirming their central role. Furthermore, in the presence of the efflux pump inhibitor phenyl-arginine β-naphthylamide (PAβN), the resistant strains exhibited significantly reduced MICs for FDC. In conclusion, these data indicate that multiple mechanisms of action are involved in the antibacterial activity of <i>P. aeruginosa</i> against FDC. Notably, the evolution of resistance was associated with the dose-dependent upregulation of core efflux pumps, complemented by stage-specific global physiological remodeling; however, it also came at a fitness cost.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1871230"},"PeriodicalIF":5.8,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13518359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148839848","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":"Genomic sequencing of vineyard-isolated <i>Bacillus</i> strains and comparison with closely related <i>Bacillus</i> species reveals a putative new lineage, distinct pan-genome architecture and secondary metabolism potential.","authors":"Adeoye J Kayode, Edwin I Wanjofu, Mathabatha Evodia Setati","doi":"10.3389/fmicb.2026.1871298","DOIUrl":"10.3389/fmicb.2026.1871298","url":null,"abstract":"<p><strong>Introduction: </strong><i>Bacillus</i> species are ubiquitous in nature, and they display diverse traits of biotechnological importance, including the production of various enzymes and secondary metabolites. In this study, we profiled the genomes of vineyard-derived <i>Bacillus</i> strains shown to inhibit <i>Botrytis cinerea</i> mycelial growth and spore germination through the production of cyclic lipopeptides and cell wall-degrading enzymes.</p><p><strong>Methodology: </strong>Long-reads-whole genome sequencing was conducted using PacBio Sequel II Single-Molecule Real-Time platform, followed by genome assembly, phylogenetic analysis and functional annotation using different bioinformatics pipelines.</p><p><strong>Results: </strong>The strains possess ~3.900,000 bp genome size and %GC ranging between 45%-46.7%, as expected in <i>Bacillus</i> species. Phylogenetic analysis separated the vineyard-derived strains into two lineages. Strains B4003 and B4005 grouped with <i>B. velezensis</i>. Notably, three <i>Bacillus</i> strains (B4022, B4001, and B4023) clustered with the undescribed strains with placeholders \"sp018613535\", an undescribed taxon in the genome taxonomy database, supported by the Average Nucleotide Identity (ANI) score above 96%. Putative biosynthetic gene clusters (BGCs) involved in secondary metabolite production were identified by AntiSMASH analysis among the isolates. Orthologous cluster analysis further identified 3203 genes conserved across all strains, constituting a stable core genome that supports essential cellular and metabolic functions. Comparative pan-genome analysis of the <i>Bacillus velezensis</i> and <i>Bacillus</i> spp. revealed clear species-level differentiation alongside a conserved functional backbone. Furthermore, functional annotation revealed strain-specific enrichment in metabolic and environmental response pathways, emphasizing the ecological specialization and adaptive diversification.</p><p><strong>Discussion: </strong>Overall, these findings emphasize the dynamic interplay between genomic conservation and flexibility within the <i>Bacillus</i> genus and support the biological control potential of these strains. Furthermore, genomic evidence strongly indicates that B4001, B4022 and B4023, represent members of a putatively novel species.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1871298"},"PeriodicalIF":5.8,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13518137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148839788","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}