AMB Express最新文献

{"title":"Microbial diversity and its links to retinol pathways and aroma compounds in ethnic fermented rice beverages of Assam.","authors":"Rohit Das, Madhu Chandana Medhi, Buddhiman Tamang","doi":"10.1186/s13568-026-02062-0","DOIUrl":"10.1186/s13568-026-02062-0","url":null,"abstract":"<p><p>Traditional fermented rice beverages are produced through complex microbial fermentation processes that influence their physicochemical characteristics and metabolite composition. In this study, metagenomic sequencing and GC-MS/MS-based metabolomics were integrated to characterize four indigenous rice beverages: Black Rohi Modh (BR), Rohi Modh (RH), Jou Bidwi (JOU), and Sai Mod (SM). All beverages were mildly acidic, with pH values ranging from 4.1 to 4.5 and titratable acidity between 0.58 and 0.72% lactic acid. Ethanol content varied among samples, with BR showing the highest concentration (8.13% v/v), followed by JOU and RH (approximately 5.5% v/v), while SM exhibited the lowest level (4.28% v/v). Antioxidant activity differed across beverages, with RH and BR demonstrating higher DPPH radical scavenging activity and SM showing the highest ferric reducing antioxidant power (96.93 µmol/mL). Metagenomic analysis generated 57.69 Mb of assembled sequences, identifying 48 microbial phyla and 1,785 species, with Eukarya accounting for 66.12% of the total community. Ascomycota predominated in BR and JOU, whereas Bacillota was more abundant in RH. The genus Saccharomyces was consistently dominant across samples. Functional annotation indicated enrichment in metabolic pathways related to carbohydrate and amino acid metabolism, as well as genes associated with ethanol biosynthesis and retinol metabolism pathways, reflecting microbial metabolic potential rather than direct vitamin production. Metabolomic profiling identified 113-167 metabolites per beverage, with 93 compounds shared among all samples. Correlation analysis revealed significant associations between Saccharomyces cerevisiae and short-chain fatty acids (ρ = 0.62-0.71, FDR < 0.05), indicating a strong positive relationship between microbial abundance and metabolite production.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13550340/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148161538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial activity of echinacea-loaded metal-organic framework against Pseudomonas aeruginosa.","authors":"Fatemeh Ashrafi, Pooria Moulavi, Zahra Jamalipanah, Maryam Jafari, Abolfazl Rafati Zomorodi, Sepideh Asadi","doi":"10.1186/s13568-026-02073-x","DOIUrl":"10.1186/s13568-026-02073-x","url":null,"abstract":"<p><p>This study evaluated the antibacterial and antibiofilm activity of Echinacea-loaded amino-functionalized UIO-66 MOF nanoparticles against clinical Pseudomonas aeruginosa isolates. Echinacea-loaded amino-functionalized UIO-66 metal-organic framework nanoparticles (UIO-66-NH₂-Ea) were synthesized and characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), entrapment efficiency (EE%), in vitro release studies of Echinacea angustifolia, and physical stability assessments. Antibacterial assays, including minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), time-kill assays, and biofilm inhibition assays, were performed. Gene expression of arr-2 and arr-4 was analyzed using quantitative real-time polymerase chain reaction (qRT-PCR) following treatment with UIO-66-NH₂-Ea. Echinacea-loaded UIO-66-NH₂ nanoparticles showed a size of 235.0 ± 7.4 nm, PDI of 0.140 ± 0.013, and entrapment efficiency of 72.53 ± 1.83%. A sustained release (~ 60% at 72 h) was observed compared to nearly complete release of free extract within 24 h. Stability showed significant changes in particle size, PDI, and entrapment efficiency over 60 days (p < 0.001). MIC (15.62-125 µg/mL) and MBC (31.25-250 µg/mL) values were up to four-fold lower than free Echinacea angustifolia (250-500 and 250-1000 µg/mL). Time-kill assays confirmed superior bactericidal activity. Biofilm formation was significantly inhibited (p < 0.001), and arr-2 and arr-4 expression was markedly downregulated compared to free extract (p < 0.001). These findings highlight the in vitro potential of Echinacea-loaded UIO-66-NH₂ nanoparticles as an effective antibacterial and antibiofilm platform against P. aeruginosa isolates. However, further in vivo studies are required to evaluate their safety and efficacy, and to better assess their translational potential.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13429566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148051979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Atmospheric room-temperature plasma mutagenesis and heterologous expression of dextranase in Aspergillus niger.","authors":"Xinyue Huang, Liyan Yang, Wenbo Zhang, Dengfeng Yang, Hao Guo, Bin Zhang, Mingguo Jiang, Lixia Pan","doi":"10.1186/s13568-026-02074-w","DOIUrl":"10.1186/s13568-026-02074-w","url":null,"abstract":"<p><p>Dextranase (DEX) is a high-value biocatalyst with substantial potential in oral hygiene and diverse industrial bioprocesses, yet its practical application is frequently constrained by the insufficient yields of wild-type strains. In this study, a high-efficiency DEX production system was established through an integrated strategy comprising Atmospheric and Room Temperature Plasma (ARTP) mutagenesis, molecular mechanism elucidation, and host-specific promoter engineering. A stable mutant, Chaetomium gracile B12, was isolated, exhibiting a 30.6-fold increase in DEX activity (16.23 U/mL) compared to the parental strain. Sequence analysis and multi-scale computational simulations, including AlphaFold2-based modeling and 100 ns molecular dynamics, generated a testable hypothesis that this mutation may contribute this enhancement. This substitution was found to augment structural rigidity and refine the spatial orientation of the substrate within the active pocket, facilitating a more \"productive alignment\" for catalysis. Furthermore, heterologous expression optimization uncovered a distinct host-specific promoter preference: the heterologous Pcdna1 promoter was most effective in C. gracile, whereas the endogenous inducible PgpdA proved superior in Aspergillus niger. Notably, this pioneering heterologous expression of DEX in A. niger streamlined the production cycle, slashing the fermentation period from 6 days to 48 h. Following systematic optimization of carbon/nitrogen sources and aeration intensity, the engineered A. niger strain H achieved a peak DEX activity of 36.00 U/mL. Biochemical characterization revealed that the recombinant DEX possessed a favorable near-neutral optimal pH (6.0-7.0) and a temperature optimum of 50 °C. Overall, this study reports the first heterologous expression of a dextranase in A. niger, reducing the fermentation period from 6 days to 48 h, and provides a comprehensive strategy for the overproduction of dextranase and offers molecular insights into enzymatic \"fine-tuning\", yielding a high-titer, neutral-pH compatible biocatalyst with significant promise for oral care and industrial applications.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13429565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148040772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of altitude and temperature variation on microbial communities and fermentation quality of natural oat and maize silage on the Qinghai-Tibet Plateau.","authors":"Haiping Li, Jiamin Zhang, Zhifeng Jia, Wenhui Liu, Qingqing Yang, Songyu Fang, Qingping Zhou, Hao Guan","doi":"10.1186/s13568-026-02077-7","DOIUrl":"10.1186/s13568-026-02077-7","url":null,"abstract":"<p><p>To investigate the microbial community dynamics and climatic responsiveness of naturally fermented silage in the Qinghai-Tibet Plateau, 51 silages from 17 distinct geographical locations across Qinghai Province were collected and analyzed. Bacterial community profiling was conducted through high-throughput 16 S rRNA amplicon sequencing, while fermentation characteristics and nutritional composition were systematically evaluated. Significant variations were observed in both fermentation parameters and nutritional quality across samples (P < 0.05). Notably, maize silage from the BHJ.M site exhibited significantly higher acetic acid (AA) content compared to other samples (P < 0.05). Moreover, BMG.O oat had better fermentation quality, indicated by the lowest pH (3.57) and higher lactic acid (LA) content (4.50%DM). Unlike oat silage, maize silage had a lower relative abundance of Lactobacillus and a higher abundance of Lentilactobacillus. Except for the Hainan (HN), the bacterial community in all regions was dominated by Lactobacillus, but the abundance of Lactobacillus was less than 75% in all samples except BMG.O. Correlation analysis indicated that high altitude and large diurnal temperature fluctuations jointly constrained Lactobacillus dominance. This environmental filtering not only shaped the Lactobacillus community structure but may also limit the metabolic functionality of certain strains, contributing to the inconsistent fermentation quality observed in naturally fermented silage on the plateau.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13391984/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148025701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploratory gut microbiota-host interaction in parkinson's disease: integrative multi-omics analysis of metabolic and epigenetic pathways.","authors":"Guangli Li, Xiaoping Ye, Tao Zhou, Zhiyou Zhou, Yijia Min, Hui Song, Xinghui Liu","doi":"10.1186/s13568-026-02078-6","DOIUrl":"10.1186/s13568-026-02078-6","url":null,"abstract":"<p><p>Mounting evidence has associated gut microbial composition and systemic metabolic profiles with Parkinson's disease (PD), yet causal pathways and molecular mechanisms remain unclear. We employed a systematic two-stage analytical framework integrating multiple Mendelian randomization (MR) approaches, transcriptome and epigenome-wide regulatory analyses, and colocalization analysis to genetically dissect the microbiota-host regulatory network implicated in PD susceptibility. Initially, two-sample MR was performed using gut microbiota data from the MiBioGen consortium, followed by an independent replication MR analysis using mbQTL data from the Dutch Microbiome Project (DMP). The two-step MR approach was employed to identify potential mediation of blood metabolites. Summary data-based MR (SMR) methods were also used to pinpoint key blood metabolic genes and regulatory regions associated with PD risk, with the combination of PD GWAS data, blood expression quantitative trait loci (eQTLs), and DNA methylation quantitative trait loci (mQTLs). Colocalization analyses were performed to explore interactions between host metabolic gene expression and the gut microbiota using blood expression quantitative trait loci (eQTLs) and fecal microbial quantitative trait loci (mbQTLs). Our multi-stage analyses identified five microbial taxa with nominal positive associations with Parkinson's disease (PD), including class Clostridia, order Bacillales, and genera Clostridium sensu stricto 1, Dorea, and Lachnospiraceae UCG001. By contrast, three additional microbial genera (Butyricimonas, Defluviitaleaceae UCG011 and Marvinbryantia) exhibited nominal protective correlations with PD. Cross-cohort analyses further indicated a shared correlation pattern along the Clostridia-Clostridiales-Clostridiaceae/Lachnospiraceae taxonomics potentially linking to PD risk across both discovery and validation cohorts. Mediation analyses indicated that betaine may mediate the Lachnospiraceae UCG001-PD associations, while androstenediol monosulfate may serve as a mediator linking Clostridium sensu stricto 1 to PD. SMR analysis highlights genes like SH2B1, JUP, as key host metabolic genes with potential causal relevance to PD, with colocalization indicating genetic overlaps supporting their potential involvement in gene-microbiota interactions. These findings deepen our understanding of gut-brain axis dysregulation in PD and may provide novel insights for future mechanistic validation and targeted preventive or therapeutic investigations.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13376093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148004321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimization of fermentation medium for advancing postbiotic antibacterial activity.","authors":"Chajira Garrote-Achou, María J Cantalejo-Díez, Alejandra Flandes-de-Cía","doi":"10.1186/s13568-026-02076-8","DOIUrl":"10.1186/s13568-026-02076-8","url":null,"abstract":"<p><p>Antimicrobial postbiotic compounds have attracted increasing interest due to their potential applications in the food industry, particularly as candidates for biopreservation strategies. From a technological perspective, process optimization represents a valuable strategy for improving the production of postbiotic compounds and supporting the development of efficient fermentation bioprocesses. This study aimed to optimize the culture medium to enhance the antibacterial activity of a postbiotic derived from Pediococcus acidilactici CECT 9879. Plackett-Burman design (PBD) was first used to screen carbon and nitrogen sources, followed by one-factor-at-a-time (OFAT) experiments to evaluate yeast-derived ingredients and MRS-derived basal medium components, and response surface methodology based on a central composite design (CCD-RSM) for final medium optimization. Significant linear, quadratic, and interaction effects of key medium components, particularly yeast-derived ingredients and sodium acetate, were identified, indicating well-defined optimal concentration ranges. Under optimized composition, the minimum inhibitory concentration (MIC) against Escherichia coli decreased from 48.33 ± 2.89% (v/v) in the non-optimized medium to 31.67 ± 2.89% (v/v). The results highlight the role of nutrient optimization in modulating postbiotic antibacterial activity during fermentation and provide insights that may contribute to improving process efficiency in the agri-food sector.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148004318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Odoribacter laneus protects intestinal barrier by bile acid-FXR axis in acute pancreatitis.","authors":"Ruru Gu, Jiazheng Li, Jinfeng Qi, Ruonan Sun, Honglei Wu, Bin Jin","doi":"10.1186/s13568-026-02071-z","DOIUrl":"10.1186/s13568-026-02071-z","url":null,"abstract":"<p><p>Odoribacter laneus (O. laneus) is a promising probiotic. Acute pancreatitis (AP) is an acute abodominal disease accompanied by intestinal barrier dysfunction and gut dysbiosis. However, the effects of O. laneus in AP remain unexplored. We established AP model of C57BL/6 mice. Western blotting and immunohistofluorescence were used to detect the expression of intestinal tight junction proteins and FXR/NLRP3 pathway. The changes of gut microbiota and bile acids (BAs) were analyzed by 16 S rRNA gene and targeted metabolomics sequencing. The fecal microbiota transplantation (FMT) was used to investigate the role of gut microbiota in O. laneus treatment. O. laneus effectively reduced systemic inflammation, pancreatic damage, and intestinal barrier dysfunction in AP mice. We observed significant enrichment of pathogens along with depletion of second BAs (7-KDA) in AP mice, and these alterations were reversed by O. laneus. FMT experiment showed that the protective roles of O. laneus depended on gut microbiota. O. laneus ameliorated AP via activating intestinal FXR and inhibiting NLRP3 inflammasome in vivo. In vitro and vivo studies showed that 7-KDA protected AP. Taken together, O. laneus could mitigate AP-induced intestinal barrier dysfunction by reversing the disorderd gut microbiota, BAs metabolism, and modulating FXR/NLRP3 pathway.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13365277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147980068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 and spectroscopic analysis for antimicrobial metabolite profiling of Microbacterium testaceum endophyte.","authors":"Merihan S Sabra, Amr S Bishr, Lina Jamil M Abdel-Hafez, Ahmed M Elissawy, Khaled M Aboshanab","doi":"10.1186/s13568-026-02063-z","DOIUrl":"10.1186/s13568-026-02063-z","url":null,"abstract":"<p><p>Wild plants harbor distinct endophytes that produce potent antimicrobial metabolites that can be used to combat life-threatening pathogens. In our study, four bacterial endophytes (LP1, LP2, LP3, LP4) were isolated from the inner tissues of leaves of Pluchea dioscoridis (L.) DC (Barnûf). The antimicrobial activity of the respective extracts (P1, P2, P3, and P4) against standard, multidrug-resistant (MDR), and Candida albicans was determined using the cup agar diffusion method. The P4 extract showed broad-spectrum activity against all tested pathogens and promising antiviral activity. The endophytic bacterium LP4 was microscopically and genomically identified by whole-genome sequencing (WGS) as Microbacterium testaceum (M. testaceum) strain CCASU-2025-88. The extract of endophytic M. testaceum CCASU-2025-88 (LP4) exhibited broad-spectrum antimicrobial activity against standard and multidrug-resistant pathogens as well as antiviral activity against Adenovirus 7, Herpes Simplex Virus 1, and Herpes Simplex Virus 2, and cytotoxic activity with a non-toxic concentration of 7.32 μg/mL, reflecting the promising bioactive properties of LP4 metabolites. Chemical profiling using AntiSMASH and LC-ESI-MS analysis suggested the presence of a compound putatively identified as microansamycin B; however, this assignment remains tentative, since the compound exhibits potent antibacterial activity, and it demonstrates the bioactive potential of M. testaceum metabolites. In conclusion, M. testaceum strain CCASU-2025-88 is a potential source of microansamycin B-like compound based on LC-ESI-MS evidence. This is the first report investigating the production of microansamycin B by a locally isolated endophytic bacterium, M. testaceum CCASU-2025-88. Further studies are recommended to optimize its production and isolation in a pure form.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":"16 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13187077/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147969540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In vitro nano‑emodin-associated exosome‑mediated aPDT against Acinetobacter baumannii.","authors":"Samane Teymouri, Hadiseh Mohammadpour, Maryam Pourhajibagher, Abbas Bahador","doi":"10.1186/s13568-026-02069-7","DOIUrl":"10.1186/s13568-026-02069-7","url":null,"abstract":"<p><p>Biofilm-forming Acinetobacter baumannii, particularly multidrug-resistant (MDR) strains, present major challenges in burn wound treatment. This study evaluated the antibacterial and antibiofilm efficacy of exosomes associated with nano-emodin (NE-Exos) combined with antimicrobial photodynamic therapy (aPDT) against A. baumannii. Antibacterial and antibiofilm activities were evaluated against the standard strain (ATCC 19606) and clinical isolates of A. baumannii, including MDR, extensively drug-resistant (XDR), and non-MDR/non-XDR strains. Minimum inhibitory and bactericidal concentrations (MIC, MBC), biofilm-inhibitory and eradication concentrations (MBIC, MBEC), drug release, hemolysis, and expression of biofilm-associated genes (abaI, bap) were evaluated. Nano-emodin and NE-Exos showed inhibitory and antibacterial activities with MIC and MBC values ranging from 15 to 39 μg/mL and 30 to 156 μg/mL, respectively. NE-Exos showed better antibiofilm efficacy compared to nano-emodin alone, especially in MDR isolates. The release of nano-emodin from NE-Exos reached 30.73% nano-emodin release at pH 5.5 after 300 min, compared to 27.56% and 23.76% at pH 7.4 and 8.5, respectively, and was associated with minimal hemolysis (0.015%). Furthermore, NE‑Exos combined with aPDT significantly downregulated the biofilm‑associated genes abaI and bap, with reductions of up to 10.96‑fold and 5.33‑fold, respectively (p < 0.001). Exosomes may have contributed to the observed antimicrobial effects, although their role appears to be as a carrier for nano‑emodin. These findings support NE‑Exos combined with aPDT as a promising in vitro strategy against A. baumannii biofilms; however, the lack of direct quantification of nano‑emodin encapsulation should be considered a study limitation.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13350769/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147961895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 analysis of Pantoea alfalfae HF1 isolated from shot hole lesions in peach leaves and symptom reproduction by wound inoculation.","authors":"Yi-Run Wu, Xue Xu, Yan Hu, Jin-Wei Zhou, Xiao-Juan Tan","doi":"10.1186/s13568-026-02067-9","DOIUrl":"10.1186/s13568-026-02067-9","url":null,"abstract":"<p><p>Bacterial leaf shot-hole disease has become an increasingly serious threat to peach production and related industries. Here, we isolated a bacterial strain, designated HF1, from symptomatic peach leaves infected with shot holes in Hefei City, Anhui Province, China. 16S rRNA gene sequencing revealed that the isolate belongs to the genus Pantoea. Furthermore, we used Illumina and MinION Nanopore sequencing technologies to analyze the whole-genome sequence of this strain. The complete genome comprises four distinct genomic elements: one circular chromosome measuring 4,008,864 bp (G + C content of 55.37%) and three circular plasmids measuring 527,106, 161,006, and 104,931 bp long, with G + C contents of 53.13%, 52.34%, and 53.92%, respectively. Multilocus sequence analysis of five housekeeping genes revealed that strain HF1 belongs to a clade containing Pantoea alfalfae CQ10, which was isolated from alfalfa. Average nucleotide identity and DNA-DNA hybridization analyses supported the phylogenetic proximity of HF1 to P. alfalfae CQ10. Based on these results, strain HF1 was reclassified as P. alfalfae HF1. In addition, HF1 was compared with three genetically related representative strains: P. alfalfae CQ10, P. ananatis DZ-12, and P. vagans C9-1. A comparative analysis was conducted using a bacterial pan-genome pipeline, and virulence factors were identified using a virulence factor database. The findings revealed that HF1 contains a number of genes associated with potential virulence traits involved in bacterium-host interactions, including motility, biofilm formation, the type VI secretion system (T6SS), and nutrient acquisition. Compared with its closest pathogenic relative, P. alfalfae CQ10, HF1 possesses three distinct T6SS clusters, including several copies of genes encoding predicted effector proteins such as Hcp, VgrG, and PAAR. Interestingly, incomplete AHL-mediated quorum-sensing system was identified in both P. alfalfae strains, and HF1 was unable to synthesize AHL; in vitro experiments corroborated these findings. Under wound inoculation conditions, strain HF1 reproduced symptoms resembling shot hole disease in peach leaves. Collectively, these findings indicate that strain HF1 is a Pantoea species associated with leaf shot hole symptoms in peach trees. This strain harbors diverse genetic features potentially related to virulence, including motility, biofilm formation, and the T6SS, which may contribute to its ability to induce symptoms under the tested conditions.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13350584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147959480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}