BMC Microbiology最新文献

{"title":"Clinical evaluation of an in-house Xpert Lysate-based Method combined with MALDI-TOF MS for the rapid identification of positive blood cultures.","authors":"Yili Ping, Qiong Chen, Xiling Sun, Haiyan Wang, Shaohua Lin, Bingwei Zhu, Zhejiong Wang, Jun Lu, Junmin Cao","doi":"10.1186/s12866-025-03996-4","DOIUrl":"10.1186/s12866-025-03996-4","url":null,"abstract":"<p><strong>Background: </strong>In clinical practice, bloodstream infections (BSIs) can lead to a very high mortality rate. Rapid identification (ID) of the pathogenic bacteria in positive blood cultures (PBCs) can guide the clinical implementation of effective antibiotic treatment in advance, thereby helping to reduce the mortality rate.</p><p><strong>Methods: </strong>Using the Conventional Culture Method results as criteria, we evaluated the effectiveness of our newly developed in-house method, the Xpert Lysate-based Method, for rapidly identifying pathogens in PBCs across four hospitals.</p><p><strong>Results: </strong>A total of 629 monomicrobial PBCs were investigated. The Xpert Lysate-based Method correctly identified 96.18% of PBCs at the species level and 97.30% at the genus level. When the confidence scores of MALDI-TOF MS were ≥ 2.000, ≥ 1.700, and ≥ 1.500, the percentages of correctly identified PBCs at the species level were 67.47%, 94.24%, and 98.88%, respectively. When the score threshold of species-level ID was set to 1.500, the rates reached 98.25% for Gram-positives (GPs), 93.54% for Gram-negatives (GNs), 70.00% for anaerobes, and 94.74% for fungi, respectively. The median confidence score of ≥ 2.000 indicated high certainty in identifying common BSI pathogens. Additionally, one of the microbial species was correctly identified in 10 out of 11 PBCs with polymicrobial growth. The entire operation process took an average of 10 min of hands-on time and 15 to 20 min for time-to-result.</p><p><strong>Conclusion: </strong>The method of directly identifying microbial pellets using MALDI-TOF MS, extracted via the Xpert Lysate-based Method we developed, is non-inferior to the conventional Culture Method in terms of ID performance. Meanwhile, it is easy to operate and more time-efficient, making it suitable for routine workflow in the rapid etiological ID of PBCs.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"293"},"PeriodicalIF":4.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144076080","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":"Effects of different additives on fermentation characteristics, nutrient composition and microbial communities of Leymus chinensis silage.","authors":"Yuting Yan, Muqier Zhao, Pengbo Sun, La Zhu, Xingquan Yan, Junfeng Hao, Qiang Si, Zhijun Wang, Yushan Jia, Mingjiu Wang, Weifeng Hou, Gentu Ge","doi":"10.1186/s12866-025-04023-2","DOIUrl":"10.1186/s12866-025-04023-2","url":null,"abstract":"<p><strong>Background: </strong>Leymus chinensis (Trin.) Tzvel is a perennial high-quality indigenous grass in China; characterized by high yield, elevated crude protein content, excellent palatability, substantial leaf volume, adaptability, and longevity. This study aimed to examine the impact of Lactiplantibacillus plantarum (LP), Lactobacillus buhneri (LB), their combination (LPLB), and complex enzyme preparation (CE) on the quality and microbial community of Leymus chinensis silage.</p><p><strong>Results: </strong>Throughout silage fermentation, pH levels decreased in all treatment groups relative to the control group. The LPLB group exhibited elevated levels of lactic acid (LA) and water-soluble carbohydrates (WSC) content, alongside reduced concentrations of acidic detergent fibre (ADF), and neutral detergent fibre (NDF) content. It exhibited superior silage outcomes compared to the other groups. Lactobacillus predominated in the treatment groups, but Enterobacter was predominant in the control group. The microbial diversity was decreased in LP and LPLB within the treatment groups due to the suppression of unwanted bacteria. Functional predictions indicated that glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism, glycolysis/gluconeogenesis, amino sugar metabolism, and nucleotide sugar metabolism were the most significant metabolic pathways, with LP being particularly important in each.</p><p><strong>Conclusion: </strong>The experimental results demonstrated that the incorporation of various additives influenced the bacterial community structure, fermentation quality, and nutrient composition of Leymus chinensis silage differently. The LP and LPLB groups decreased pH and ADF levels and amassed a significant quantity of LA during fermentation, while preserving CP and WSC content. The microbial composition exhibited greater stability, which markedly enhanced the quality of Leymus chinensis silage, hence preserving its nutrient composition.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"296"},"PeriodicalIF":4.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144076085","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":"Nodules-associated Klebsiella oxytoca complex: genomic insights into plant growth promotion and health risk assessment.","authors":"Sameh H Youseif, Fayrouz H Abd El-Megeed, May S Soliman, Amr Ageez, Akram H Mohamed, Saher A Ali, Amani A El-Kholy","doi":"10.1186/s12866-025-04002-7","DOIUrl":"10.1186/s12866-025-04002-7","url":null,"abstract":"<p><p>The swift emergence of antibiotic resistance genes (ARGs) across interconnected One Health compartments poses a significant global threat. Although plant growth-promoting (PGP) bacteria possess numerous attributes beneficial to host plants, many of these bacteria also harbor ARGs, necessitating a focused assessment of their negative implications. In this context, here we performed whole genome sequencing of 14 PGP endophytic strains isolated from root nodules of faba beans, belonging to three Klebsiella oxytoca species complex (KoSC): K. grimontii (n = 5), K. michiganensis (n = 5), and K. pasteurii (n = 4). We performed comparative genomics, molecular typing, and pangenome analyses on these strains. We identified significant diversity within the KoSC population, classifying the strains into five sequence types (STs), three of which are novel to this study (ST-542, ST-569, and ST-629). Phylogenomic analysis revealed that the bacterial strains clustered more closely by ST than by their source of isolation. Annotation of gene clusters indicated that all assembled genomes are enriched with genes involved in PGP activities, alongside a robust array of genes conferring tolerance to abiotic stresses. Importantly, our findings disclosed that the 14 assembled genomes harbored multiple ARGs, conferring resistance to various antibiotic classes, with 71% of the population classified as multidrug-resistant based on the in vitro antibiotic susceptibility assay. Furthermore, all genomes contained an array of virulence factors critical for survival, pathogenesis, biofilm formation, and root colonization. In conclusion, this study substantiates the hypothesis that certain PGP bacteria may serve as potential reservoirs of multidrug resistance, posing significant public health risks. Thus, the future advancement of bacteria-based biofertilizers should integrate environmental considerations and monitor their impact on antibiotic resistance dissemination in soil ecosystems.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"294"},"PeriodicalIF":4.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144076087","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":"Characterization and purification of Pseudomonas aeruginosa phages for the treatment of canine infections.","authors":"Anne Dalponte, Viviane Filor, Antina Lübke-Becker, Marcus Fulde, Thomas Alter, Mathias Müsken, Wolfgang Bäumer","doi":"10.1186/s12866-025-04005-4","DOIUrl":"https://doi.org/10.1186/s12866-025-04005-4","url":null,"abstract":"<p><strong>Background: </strong>Pseudomonas aeruginosa is an opportunistic pathogen that causes infections in both human and veterinary medicine, presenting significant challenges in treatment because of biofilm production and its intrinsic resistance. This problem is exacerbated by the increase in acquired antimicrobial resistance. Bacteriophage (phage) therapy has emerged as a promising alternative for treating infection classically treated with antibiotics, offering a targeted approach to combat this infection. This study aimed to evaluate the therapeutic potential of 7 phages, focusing on their suitability for treating canine infections, as well as their purification and safety analysis for therapeutic use.</p><p><strong>Results: </strong>Two self-isolated phages and five provided phages were analysed. All tested phages reduced bacterial load in vitro; however, their efficacy varied across different concentrations. The host range analysis revealed a spectrum between 9.8 and 68.6% of canine clinical P. aeruginosa isolates. In our in vitro tests 3 out of 7 phages were able to significantly reduce the biofilm biomass, achieving reductions up to 93.38%. The sequence analysis did not discover known virulence factors and genes connected to antimicrobial resistance mechanisms. The self-isolated phages were classified as lysogenic, whereas the other phages had a lytic infection cycle. Through the purification of the phages, high-titre phage preparations (> 10¹¹ PFU/ml) were generated with high stability for at least 1.5 years. The tested endotoxin units are below the regulatory limits.</p><p><strong>Conclusion: </strong>Investigating phages as alternative treatment option seems promising with lytic phages covering a broad host range and a genomic potential for biofilm degradation. These findings support the development of phage cocktails as a targeted alternative for treating canine P. aeruginosa infections, particularly in cases of antibiotic resistance, and highlight the importance of selecting well-characterized lytic phages for therapeutic efficacy and safety.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"289"},"PeriodicalIF":4.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12076904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144076078","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":"Antimicrobial susceptibility at intensive care units in Sudan, antibiogram development.","authors":"Ghada Omer Hamad Abd El-Raheem, Mohamed Elhadi Ahmed Dihesh, Mohamed Elmutaz Babikir Elmardi, Hana Eltayeb Salih Elamin, Latifa Elsir Abas Zeinelabdin, Dalia Omer Suliman Ahmed, Misa Abdelmajid Alhaj Mudather, Omema Abdelkrem Abdelftah Gaber, Hanadie Mustafa Ebrahim Abdalla","doi":"10.1186/s12866-025-04021-4","DOIUrl":"https://doi.org/10.1186/s12866-025-04021-4","url":null,"abstract":"<p><p>Antibiograms are statistics on bacterial spectrum and resistance rates. It is of importance to regularly monitor the trends in antimicrobial resistance within the institution through the periodic cumulative resistance to provide the effective empiric antibiotic selection, enhanced infection control interventions, and containment strategies. Antimicrobial stewardship interventions improve quality and quantity of prescribing antimicrobial in ICUs without compromising any patient outcomes. The aim of this study was to develop a local unit-specific antibiogram for the Intensive Care Units based on the susceptibility rates of antimicrobials. Facility- based cross sectional study was done among ICU patients of a Tertiary hospital, Khartoum. Data were collected from the record of microbiology Laboratory from August-2021 to September-2022. Results were presented as tables and figures, Chi- square test was used to assess associations between variables, results were statistically significant when p < 0.05. Gram negative bacteria comprised 32% of the samples and only 4% of the samples had Gram positive bacteria, the remaining samples had no growth. Klebsiella spp. were the most prevalent 14.4% (44/306). The lowest susceptibility to antimicrobials were documented for Acinetobacter spp. and Klebsiella spp. Regarding Pseudomonas aeruginosa, it was susceptible to Meropenem but resistant to Pip/Tazo and Aminoglycosides. Gram positive bacteria, all were susceptible to Vancomycin and low Methicillin-resistant Staphylococcus aureus prevalence was observed. The antibiogram revealed high prevalence of Gram negative bacteria with low antimicrobials-susceptibility; especially Klebsiella spp. Low prevalence was recorded for MRSA and the most prevalent Gram positive bacteria were E. faecalis. This antibiogram of ICU can provide a reference for all future ICU antibiograms which will give a clear picture of the antimicrobial susceptibility pattern among ICU patients. Clinical trial number Not applicable.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"290"},"PeriodicalIF":4.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12076941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144076075","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":"Utilization of agro-industrial wastes and by-products by Bacillus subtilis for the biogenic synthesis and In-Depth characterization and cytotoxicity assessment of silver nanoparticles.","authors":"Basma T Abd-Elhalim, Salma H Mohamed, Badawi A Othman, Mohammed N Abou Seada","doi":"10.1186/s12866-025-03998-2","DOIUrl":"https://doi.org/10.1186/s12866-025-03998-2","url":null,"abstract":"<p><p>Silver nanoparticles (AgNPs) have garnered significant attention due to their diverse applications in nanotechnology, biomedicine, and environmental science. This study explores the biogenic synthesis of AgNPs utilizing various agro-industrial wastes by Bacillus subtilis AMD2024 as a sustainable and eco-friendly alternative to conventional chemical synthesis methods. We evaluated a range of agro-industrial by-products, including blackstrap sugarcane molasses, sugar beet waste, and arish cheese whey, for their potential in AgNPs production. Comprehensive characterization techniques-such as X-ray diffraction (XRD), atomic absorption spectroscopy (AAS), dynamic light scattering (DLS), UV-visible spectroscopy, high-resolution scanning electron microscopy (HR-SEM), zeta potential analysis, and Fourier transform infrared spectroscopy (FTIR)-were employed to assess the properties of the synthesized nanoparticles. The DLS and UV-visible study findings were obtained at a particle size of 15.63 nm and a surface plasmon resonance (SPR) of 0.593 at 450 nm, respectively. The time course showed the maximum concentration of AgNPs after 48 h at 1.535 mg/L. The preliminary findings suggest that the size of the synthesized AgNPs was effectively reduced to as low as 4.849 nm when using blackstrap sugarcane molasses. The cytotoxicity assessment revealed a half-maximum inhibitory concentration (IC₅₀) of 200 mg/mL against normal kidney epithelial cell lines, indicating the potential for safe applications in infection control and water treatment. This study highlights the applicability of agro-industrial waste valorization in nanoparticle synthesis, showcasing its promise for developing effective antimicrobial agents in various sectors.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"291"},"PeriodicalIF":4.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12080011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144076033","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":"Effects of dietary Bacillus velezensis Y01 supplementation on growth performance, immune function, and cecal microbiota of 1 to 42 days Langya chickens.","authors":"Lumin Yu, Lingling Zhang, Shanpeng Zhang, Yuzhong Zhao, Zhihao Bi, Junye Xu, Hongcheng Fu, Xinglin Zhang","doi":"10.1186/s12866-025-04008-1","DOIUrl":"10.1186/s12866-025-04008-1","url":null,"abstract":"<p><p>Bacillus velezensis (B. velezensis) has gained increasing recognition as a probiotic for improving animal growth performance and intestinal health. However, whether B. velezensis affects growth performance, immune function, and cecal microbiota in Chinese local breeds of chickens remains unclear. In this study, a total of 180 one-day-old healthy male Langya chicks were randomly divided into 3 treatment groups with 5 replicates per group and 12 chicks each replicate. Langya chicks were fed with a corn-soybean-based diet as the control group (CON), and 2 other groups were fed the same basal diet supplemented with 50 mg/kg aureomycin or 2.0 × 10⁹ CFU/kg B. velezensis Y01 as the antibiotic-treated group (ANT) and the B. velezensis-treated group (BVT), respectively, for 42 days. Dietary supplementation with B. velezensis Y01 resulted in a 7.01% increase in the final body weight, a 7.27% increase in weight gain (WG), and a 7.24% increase in average daily gain (ADG) in Langya chickens at 42 days of age in the BVT group when compared to the CON group (p < 0.05). Meantime, the final body weight was increased by 5.88%, WG by 6.18%, and ADG by 6.19% in the BVT group when compared to the ANT group (p < 0.05). The BVT group with B. velezensis Y01 resulted in a 26.80% decrease in lactate dehydrogenase (LDH), a 52.92% decrease in uric acid (UA), a 20.70% decrease in cholesterol (CH), and a 40.84% decrease in urea when compared to the CON group (p < 0.05). Furthermore, the serum immunoglobulin G (IgG) levels were increased by 36.09%, IgM by 56.08%, and interleukin-2 (IL-2) by 32.83% in the BVT group in comparison to the CON group (p < 0.05), but IL-1, IL-6, and tumor necrosis factor-α (TNF-α) levels had no changes (p > 0.05). Notably, B. velezensis Y01 enriched the abundance of Firmicutes and Bacteroidetes, resulting in the production of certain beneficial metabolites that play pivotal roles in reducing the abundance of harmful bacteria. This, in turn, decreases the virulence genes and antibiotic resistance genes in the cecal microbial communities, ultimately enhancing immunity and metabolism in Langya chickens. Collectively, these results are encouraging and suggesting that B. velezensis Y01 may be an effective alternative of antibiotic growth promoters for improving chickens' growth performance and intestinal health in poultry production.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"288"},"PeriodicalIF":4.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12070716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143977216","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":"Drug resistant Klebsiella pneumoniae from patients and hospital effluent: a correlation?","authors":"Naledi S Masalane, Linda A Bester, Arshad Ismail, Sabiha Y Essack, Joshua Mbanga","doi":"10.1186/s12866-025-03987-5","DOIUrl":"https://doi.org/10.1186/s12866-025-03987-5","url":null,"abstract":"<p><strong>Background: </strong>The application of wastewater-based epidemiology has gained traction as a cost effective tool in antimicrobial resistance (AMR) surveillance with studies showing a correlation between the presence of resistant bacteria from hospital sewage and patients. This study compared Klebsiella pneumoniae from patients and hospital effluent in terms of antibiotic resistance patterns, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and phylogenomic relationships.</p><p><strong>Results: </strong>Pooled effluent samples were collected from the final effluent point of a regional hospital and K. pneumoniae isolates were identified on selective media. Clinical isolates were also collected from the same hospital. Antimicrobial susceptibility testing (AST) was performed using the VITEK® 2 system. DNA was extracted prior to whole genome sequencing (WGS). The resistome, mobilome, and phylogenetic lineages of sequenced isolates were assessed using bioinformatics analysis. A total of 10 randomly selected presumptive and 10 clinical K. pneumoniae constituted the sample and were subjected to AST. Total resistance was observed in the clinical samples to cefuroxime, cefotaxime, piperacillin/tazobactam, gentamicin, tobramycin and trimethoprim/sulfamethoxazole. The effluent isolates exhibited total susceptibility to most antibiotics but showed resistance to amoxicillin/clavulanic acid and piperacillin/tazobactam (100%), and tigecycline (10%). The effluent isolates did not exhibit a diverse resistome, while the clinical isolates harboured genes conferring resistance to aminoglycoside (aph(6)-Id, aph(3'')-Ib, aac(6')-Ib-cr, aadA16), ß-lactam (bla_SVH group, bla_OXA group, bla_TEM group), and fluoroquinolone (oqxA, oqxB) antibiotics. Only class 1 integrons were identified. Phylogenetic analysis revealed that effluent isolates from this study were not closely related to the clinical isolates.</p><p><strong>Conclusion: </strong>This study showed no correlation between the resistance profiles of the clinical and effluent isolates. The relationship between AMR in hospital effluent and clinical resistance may depend on the antimicrobial agents and bacterial species studied.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"284"},"PeriodicalIF":4.0,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066053/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143981016","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":"The repressor PrtR1 and the global H-NS-like regulators MvaT and MvaV enable the fine-tuning of R-tailocin expression in Pseudomonas protegens.","authors":"Clara Margot Heiman, Hammam Antar, Florian Fournes, Christoph Keel, Jordan Vacheron","doi":"10.1186/s12866-025-03983-9","DOIUrl":"https://doi.org/10.1186/s12866-025-03983-9","url":null,"abstract":"<p><strong>Background: </strong>Bacteria rely on an arsenal of weapons to challenge their opponents in highly competitive environments. To specifically counter closely related bacteria, specialized weapons with a narrow activity spectrum are deployed, particularly contractile phage tail-like particles or R-tailocins. Their production leads to the lysis of the producing cells, indicating that their expression must be carefully orchestrated so that only a small percentage of cells produce R-tailocins for the benefit of the entire population.</p><p><strong>Results: </strong>In this study, we set out to better understand how the production of these phage tail-like weapons is regulated in environmental pseudomonads using the competitive plant root colonizer and environmental model strain Pseudomonas protegens CHA0. Using an RNA sequencing (RNA-seq) approach, we found that genes involved in DNA repair, particularly the SOS response program, are upregulated following exposure of the pseudomonad to the DNA-damaging agents mitomycin C and hydrogen peroxide, while genes involved in cell division and primary metabolism are downregulated. The R-tailocin and prophage gene clusters were also upregulated in response to these DNA damaging agents. By combining reverse genetics, transcriptional reporters and chromatin immunoprecipitation sequencing (ChIP-seq), we show that the R-tailocin locus-specific LexA-like regulator PrtR1 represses R-tailocin gene expression by binding directly to the promoter region of the cluster, while the histone-like nucleoid structuring (H-NS) proteins MvaT and MvaV act as master regulators that indirectly regulate R-tailocin cluster expression.</p><p><strong>Conclusion: </strong>Our results suggest that at least these three regulators operate in concert to ensure tight control of R-tailocin expression and cell lytic release in environmental Pseudomonas protegens strains.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"286"},"PeriodicalIF":4.0,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143973778","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":"Microbial diversity and ecological roles of halophilic microorganisms in Dingbian (Shaanxi, China) saline-alkali soils and salt lakes.","authors":"Yue Ding, Juntao Ke, Tao Hong, Aodi Zhang, Xue Wu, Xinran Jiang, Shilong Shao, Ming Gong, Shengda Zhao, Liang Shen, Shaoxing Chen","doi":"10.1186/s12866-025-03997-3","DOIUrl":"https://doi.org/10.1186/s12866-025-03997-3","url":null,"abstract":"<p><p>Halophilic microorganisms abound in numerous hypersaline environments, such as salt lakes, salt mines, solar salterns, and salted seafood. In the northwest of Dingbian county (Shaanxi province, China), there exists a belt of hypersaline habitats extending from the west to the north consisting of saline-alkali soil and salt lakes. Theoretically, such a hypersaline environment has a high probability of containing abundant halophilic archaea communities. Nevertheless, there is nearly no systematic research on halophilic archaea in this area. Here, we employed a combination of culture-dependent and culture-independent methods to analyze the collected samples. The high-throughput sequencing results of the archaeal 16S rRNA gene indicated that the richness of halophilic archaea in saline-alkali soils was significantly higher than that in salt lakes. In saline-alkali soils, the Natronomonas genus of archaea was more predominant compared to other genera, while in salt lakes, the Halonotius, Halorubrum, and Haloarcula genera of archaea had relatively higher abundances. However, the dominant families of halophilic archaea in both environments were mainly Haloferacaceae (30.96-72%), Halomicrobiaceae (17-53.19%) and Nanosalinaceae (1-19.08%). Based on the outcomes of pure culture experiments, a total of 26 genera and 98 strains were identified. Among the identified halophilic microorganisms, the predominant species were Halorubrum and Fodinibius, accounting for 33.67% and 13.27%, respectively. The remainder were mostly low-abundance groups within the community, and 22 potential novel taxa were discovered. Additionally, metagenomic technology was employed in our research. The analysis results demonstrated that the microorganisms in this area possess metabolic pathways capable of degrading various pollutants such as atrazine, methane, and dioxins, suggesting that some microorganisms in this area play a positive role in environmental remediation. This study roughly reveals the diversity composition and dominant species of halophilic archaea in these hypersaline environments and provides a scientific basis for the possible ecological functions of microorganisms in this area during long-term survival. It also offers scientific evidence for the development and utilization of halophilic microbial resources and ecological protection.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"287"},"PeriodicalIF":4.0,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143980369","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}