mSystems最新文献

{"title":"Phosphite as an engineered niche for <i>Pseudomonas veronii</i> in a synthetic soil bacterial community.","authors":"Clara Bailey, Philip Gwyther, Senka Čaušević, Brandon L Greene, Jan Roelof van der Meer","doi":"10.1128/msystems.00061-25","DOIUrl":"10.1128/msystems.00061-25","url":null,"abstract":"<p><p>Bioaugmentation, the process of soil restoration by introducing microorganisms capable of degrading pollutants, is a promising and cost-effective strategy for environmental remediation. Aromatic hydrocarbons, such as benzene, toluene, ethylbenzene, and <i>p</i>-xylene (BTEX), are highly toxic environmental contaminants that could be transformed to less harmful products through the inoculation of certain organisms capable of BTEX degradation. However, a barrier to successful bioaugmentation is the inoculant's failure to establish within the resident microbial community. In an effort to improve inoculant proliferation, we have investigated phosphite as a phosphorus source for selective nutrient supply. Phosphite is an inaccessible form of phosphorus to organisms that lack the capacity for phosphite oxidation to phosphate. We introduced a phosphite dehydrogenase-coding gene (<i>ptxD</i>) into the genome of the toluene-degrading bacterium <i>Pseudomonas veronii</i> 1YdBTEX2 to couple phosphite metabolism and aromatic hydrocarbon clearance. When inoculated in either soil matrix or liquid soil extract, <i>P. veronii</i> proliferates in a phosphite- and toluene-dependent manner in both growing and stable synthetic soil microbial communities, although the selective effects of phosphite and toluene were not additive in a carbon-limited context. Once toluene is metabolized, <i>P. veronii</i> abundance decays, and the microbial community recovers diversity and abundance resembling the uninoculated controls. Additional members of the microbial community were also enriched in the presence of phosphite, and genomic analysis suggests that these microorganisms utilize an alkaline phosphatase, <i>phoV,</i> for phosphite assimilation.IMPORTANCEBioaugmentation is a promising solution to soil contamination, but its practical application is limited due to poor inoculant establishment in the native soil community. This can often be attributed to low nutrient availability and resource competition with native microorganisms. We proposed the use of phosphite as a selective nutrient source to support the growth of a toluene-degrading bacterium, <i>Pseudomonas veronii</i>, in a model soil system. We engineered a strain of this organism that was capable of using phosphite as a phosphorus source and saw that phosphite application enhanced the abundance of the inoculant sixfold within a synthetic soil community. In this study, we present the first investigation of a phosphite selection system in the soil microbiome and characterize the environmental conditions in which it is effective. By demonstrating the potential of formulated nutritional niches in soil microbiome interventions, we provide significant insights into the field of microbiome engineering.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0006125"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855807","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":"Renal pelvis urobiome dysbiosis is associated with postoperative systemic inflammatory response syndrome after percutaneous nephrolithotomy.","authors":"Qing Wang, Xiaolong Chen, Guanyun Deng, Kunyuan Huang, Senyuan Hong, Kehua Jiang","doi":"10.1128/msystems.00780-25","DOIUrl":"10.1128/msystems.00780-25","url":null,"abstract":"<p><p>Early prediction and diagnosis of systemic inflammatory response syndrome (SIRS) following percutaneous nephrolithotomy (PCNL) are critical. This study aimed to investigate differences in clinical characteristics and the renal pelvis urobiome between patients with and without post-PCNL SIRS to identify potential predictive biomarkers. Patients undergoing unilateral PCNL were categorized into SIRS(+) and SIRS(-) groups based on postoperative SIRS status. Renal pelvis urine samples were collected for 2bRAD-M sequencing to profile the urobiome. Clinical data and urobiome composition were compared between the groups. Logistic regression identified preoperative serum albumin-globulin ratio (AGR) as an independent protective factor and operative time as an independent risk factor for post-PCNL SIRS, with an area under the receiver operating characteristic curve (AUC) of 0.76. Diversity analysis revealed distinctive microbial differences between the two groups. Through differential analysis and random forest, we screened six species, including <i>Sphingomonas paucimobilis</i>, <i>Ralstonia</i> sp000620465, <i>Ralstonia pickettii</i>, <i>Pelomonas puraquae</i>, <i>Comamonas tsuruhatensis</i>, and <i>Lawsonella clevelandensis_A</i>, to build the microbial prediction model, which achieved an AUC of 0.81. The combination of microbial data and clinical factors further improved predictive accuracy, achieving an AUC of 0.94. Functional profiling of the urobiome also demonstrated significant intergroup differences. This is the first study to explore renal pelvis urobiome dysbiosis in post-PCNL SIRS. Both clinical and microbial factors showed strong predictive value, with their combination offering the greatest discriminatory power. This research could pave the way for the early prediction of post-PCNL SIRS.IMPORTANCEGiven the significant morbidity associated with postoperative percutaneous nephrolithotomy (PCNL) systemic inflammatory response syndrome (SIRS), early prediction and diagnosis are crucial for preventing severe complications like sepsis, which can lead to multiple organ dysfunction or death. Our study uniquely explores how renal pelvis urobiome dysbiosis contributes to post-PCNL SIRS. By utilizing the novel 2bRAD-M sequencing, the research identifies key microbial species in the renal pelvis and integrates them with clinical factors like albumin-globulin ratio and operative time. The resulting prediction model, with an impressive area under the curve, significantly outperforms traditional clinical models. This offers a more precise approach to stratify patients at high risk of developing SIRS. This work suggests that microbial imbalances may actively drive SIRS, pointing to the potential to revolutionize the predictive strategies for post-PCNL SIRS.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0078025"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855817","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":"Bacterial alarmone (p)ppGpp mediates the pathogenicity of <i>Clavibacter michiganensis</i> via a dual mechanism that affects both enzyme production and the Tat secretion system.","authors":"Xiaoli Xu, Kaihong Bai, Jia Shi, Chengxuan Yu, Shuang Song, Na Jiang, Jianqiang Li, Laixin Luo","doi":"10.1128/msystems.00135-25","DOIUrl":"10.1128/msystems.00135-25","url":null,"abstract":"<p><p>The gram-positive bacterium <i>Clavibacter michiganensis</i> (Cm) causes bacterial canker of tomato. The infection process of Cm is of considerable interest, and the role of the alarmone guanosine tetraphosphate or pentaphosphate [(p)ppGpp], a global regulator, has been strongly implicated in bacterial survival and pathogenicity. Transcriptome analysis comparing a (p)ppGpp-deficient strain (Δ<i>rel</i>) to the wild-type strain demonstrated that (p)ppGpp down-regulates the expression of many genes encoding ribosomal components and ABC transporter proteins, while up-regulating genes associated with amino acid metabolism, biofilm synthesis, and the production and secretion of cell-wall degrading enzymes. Biochemical assays showed reduced biofilm synthesis and extracellular activity of cell-wall degrading enzymes such as amylase and xylanase. Moreover, the results of microscale thermophoresis and electrophoretic mobility shift assays indicated that (p)ppGpp interacts with the transcription factor Vatr1 to directly suppress expression of the xylanase gene <i>xysB</i>. Meanwhile, amidase reporter assays revealed that xylanase secretion depends on the Tat secretion system, which was significantly inhibited in Δ<i>rel</i>, leading to intracellular accumulation of the xylanase protein. Taken together, these results indicate that (p)ppGpp plays a complex role in the pathogenicity of <i>C. michiganensis</i>, mediating, among other things, not only the production of cell-wall degrading enzymes but also their transport and secretion.</p><p><strong>Importance: </strong>This study reveals the pivotal role of the bacterial alarmone guanosine tetraphosphate and guanosine pentaphosphate in the pathogenicity of <i>Clavibacter michiganensis</i>, a significant plant pathogen. Through the identification of its dual mechanisms in regulating enzyme production and the Tat secretion system, we uncover key insights into bacterial virulence strategies. Our findings not only advance the understanding of bacterial stress response systems but also offer new opportunities for developing targeted interventions to combat plant bacterial diseases, ultimately contributing to agricultural sustainability and food security.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0013525"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455917/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144775833","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":"Impact of study design, contamination, and data characteristics on results and interpretation of microbiome studies.","authors":"Jose Agudelo, Aaron W Miller","doi":"10.1128/msystems.00408-25","DOIUrl":"10.1128/msystems.00408-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Advances in high-throughput molecular techniques have enabled microbiome studies in low-biomass environments, which pose unique challenges due to contamination risks. While best-practice guidelines can reduce contamination by over 90%, the impact of residual contamination and data set variability on statistical outcomes remains understudied. Here, we quantitatively assessed how study design factors influence microbiome analyses using simulated and real-world data sets. Alpha diversity was affected by sample number and community dissimilarity, but not by the number of unique taxa. Beta diversity was influenced primarily by unique taxa and group dissimilarity, with a marginal effect of sample number. The number of differentially abundant taxa depended on the number of unique taxa but was also influenced by sample number, depending on thealgorithm. Notably, contamination had a marginal impact on weighted beta diversity but altered the number of differentially abundant taxa when at least 10 contaminants were present, with a greater effect as contamination increased. Findings closely mirrored results from seven real-world low-biomass data sets. Overall, group dissimilarity and the number of unique taxa were the primary drivers of statistical outcomes. The DESeq2 algorithm outperformed ANCOM-BC when exposed to stochastically distributed contamination, but algorithms were equivocal under contamination weighted toward one group. In all cases, the rate of false positives in differential abundance analyses was &lt;15%. Importantly, in both simulated and real-world data, contamination rarely impacts whether microbiome differences were detected but did affect the number of differentially abundant taxa. Thus, when validated protocols with internal negative controls are used, residual contamination minimally impacts statistical outcomes. Alpha diversity was affected by sample number and community dissimilarity, but not by the number of unique taxa. Beta diversity was influenced primarily by unique taxa and group dissimilarity, with a marginal effect of sample number. The number of differentially abundant taxa depended on the number of unique taxa but was also influenced by sample number, depending on the algorithm. Notably, contamination had a marginal impact on weighted beta diversity but altered the number of differentially abundant taxa when at least 10 contaminants were present, with a greater effect as contamination increased. Findings closely mirrored results from seven real-world low-biomass data sets. Overall, group dissimilarity and the number of unique taxa were the primary drivers of statistical outcomes. The DESeq2 algorithm outperformed ANCOM-BC when exposed to stochastically distributed contamination, but algorithms were equivocal under contamination weighted toward one group. In all cases, the rate of false positives in differential abundance analyses was &lt;15%. Importantly, in both simulated and real-world data, contamination rarely whether m","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0040825"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12456016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789588","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":"Integrated insights into gut microbiota and metabolomic landscape in breast cancer patients undergoing adjuvant endocrine therapy.","authors":"Taha Majid Mahmood Sheikh, Fen Yao, Zhenyan Liu, Muhammad Shafiq, Jilong Wu, Areeba Khalid, Qingdong Xie, Xiaoyang Jiao, Weitao Shen","doi":"10.1128/msystems.00879-25","DOIUrl":"10.1128/msystems.00879-25","url":null,"abstract":"<p><p>Gut microbiota and systemic metabolites are critical for breast cancer progression and therapeutic response. This study investigated gut microbiota and metabolic profiles of breast cancer patients before and after adjuvant endocrine therapy (AET). Using 16S rRNA sequencing and untargeted metabolomics, we identified significant disruptions in microbial diversity and metabolic pathways. Alpha diversity was reduced in pre-AET patients, with partial restoration observed post-AET. Key genera, such as <i>Bifidobacterium</i> and <i>Coprococcus</i>, were enriched in pre-AET patients, whereas <i>Proteus</i> and <i>Methylobacterium</i> were enriched in post-AET patients. Metabolomic analysis revealed significant reductions in the levels of vitamin B6 metabolites in both the pre-AET and post-AET groups compared to those in the healthy control (HC) group, indicating potential nutrient deficiencies or metabolic stress. Elevated cholesterol and estrogen metabolite levels in pre-AET patients reflect dysregulated lipid and hormone metabolism, with post-AET decreases in estrogen metabolites, confirming therapeutic efficacy. Correlation analysis revealed that <i>Klebsiella_724518</i> was positively correlated with estrogen and vitamin B6 metabolites, whereas <i>Proteus</i>, <i>Methylobacterium</i>, <i>Treponema_D</i>, and <i>Holdemanella</i> were negatively correlated with cholesterol. Receiver operating characteristic (ROC) curve analysis identified estriol (area under the curve [AUC] = 1.000) as a strong diagnostic biomarker for distinguishing HCs from pre-AET patients, whereas cholesterol (AUC = 0.880) and estradiol-17β (AUC = 0.870) were highly effective in monitoring the therapeutic response to AET. This study highlights the role of gut microbiota and its metabolic byproducts in breast cancer development and treatment outcomes. It also reveals promising microbial and metabolite signatures for non-invasive cancer detection, tracking progression, and monitoring treatment response.IMPORTANCEBreast cancer progression and treatment response remain challenging to predict and monitor effectively. Our findings demonstrate the dual role of the gut microbiota and its metabolic products in influencing both. Strong correlations between specific microbial taxa and key metabolites provide new mechanistic insights into the influence of gut microbes on therapeutic outcomes during endocrine therapy. Importantly, we identified high-performance biomarkers, with estriol showing perfect diagnostic accuracy (AUC = 1.000) and cholesterol effectively monitoring treatment response (AUC = 0.880), highlighting their potential for non-invasive clinical applications. This study provides a foundation for applying gut microbiome research to develop clinical tools that could improve breast cancer management.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0087925"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455969/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855801","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":"Unexplored viral diversity in Siberian cranes and wild geese: metagenomic insights from a global wintering haven.","authors":"Jing Gao, Weijie Han, Xiaojie Jiang, Yuan Xi, Yue Chen, Shiyin Huang, Xiaofeng Huang, Yang Zhang, Tianxiang Zhang, Manyu Zhang, Wen Zhang, Bin Ni","doi":"10.1128/msystems.00756-25","DOIUrl":"10.1128/msystems.00756-25","url":null,"abstract":"<p><p>Migratory birds are critical global carriers and vectors of various viruses, potentially driving the mutation and transmission of novel pathogens, especially zoonotic viruses. Despite advancements in sequencing technologies, the viral diversity in wintering Siberian cranes (<i>Leucogeranus leucogeranus</i>) and wild geese (<i>Anser</i> spp.) remains poorly understood. In this study, we conducted a viral metagenomic survey of fecal samples from 320 Siberian cranes and wild geese wintering in Poyang Lake, China. Through this approach, we identified 183 novel viruses associated with known and putative vertebrate-infecting viruses, including a novel coronavirus, parvoviruses, picornaviruses, picobirnaviruses, anelloviruses, and CRESS-DNA viruses. Furthermore, we detected evidence of cross-species transmission and identified viruses with zoonotic potential, such as picobirnaviruses and picornaviruses. These findings highlight the significant public health risks posed by migratory birds and provide new insights into the viral diversity within these populations, contributing to a better understanding of their role in viral evolution and transmission.IMPORTANCEUnderstanding the diversity of enteroviruses in Siberian cranes and geese is essential for biodiversity conservation and ecosystem stability. As migratory birds, these species play key roles in ecological networks while carrying intestinal viruses that may spread along migration routes, which could pose potential risks to wildlife, poultry, and human health. This study systematically analyzed enterovirus diversity and the genetic characteristics of novel viruses in wintering Siberian cranes and geese at Poyang Lake using metagenomic sequencing. We identified viral sequences distantly related to known viruses and those with potential cross-species transmission risks. These findings highlight the diversity of migratory bird viruses and their public health implications, providing data to evaluate transmission risks and monitor emerging threats, supporting strategies for wildlife conservation and disease prevention.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0075625"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12456024/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961826","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":"Calprotectin protects <i>Staphylococcus aureus</i> in coculture with <i>Pseudomonas aeruginosa</i> by attenuating quorum sensing and decreasing the production of pseudomonal antimicrobials.","authors":"Wei H Lee, Amanda G Oglesby, Elizabeth M Nolan","doi":"10.1128/msystems.00576-25","DOIUrl":"10.1128/msystems.00576-25","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> and <i>Staphylococcus aureus</i> cause debilitating polymicrobial infections in diverse patient populations. Studies of these bacterial pathogens in coculture have shown that environmental variables, including Fe availability and the host-defense protein calprotectin (CP), impact coculture dynamics. To decipher how CP modulates interactions between <i>P. aeruginosa</i> and <i>S. aureus</i>, we employed dual-species RNA-seq to examine the transcriptional responses of both pathogens in coculture to CP treatment and metal depletion. Analysis of these responses revealed that, for both <i>P. aeruginosa</i> and <i>S. aureus</i>, CP treatment not only induced gene expression changes consistent with single- and multi-metal starvation responses but also induced gene expression changes that were not observed under metal limitation. For <i>P. aeruginosa</i>, CP treatment induced gene expression changes pointing to a shift in chorismate flux away from alkylquinolone and phenazine biosynthesis and toward folate biosynthesis. These observations were consistent with decreased production of alkylquinolones by <i>P. aeruginosa</i>, including the potent anti-staphylococcal alkylquinolone N-oxides. CP treatment altered the levels of two quorum-sensing molecules, 3-oxo-C₁₂-homoserine lactone and C₄-homoserine lactone, produced by <i>P. aeruginosa</i>. In addition, CP treatment enhanced the ability of <i>S. aureus</i> to mount Fe-starvation responses and caused <i>S. aureus</i> to express host virulence genes. This analysis illuminated the physiological consequences of CP treatment that extend beyond metal starvation and impact interspecies interactions. Our findings provide a working model in which CP effectively disarms <i>P. aeruginosa</i> by inhibiting the production of anti-staphylococcal factors and boosts the ability of <i>S. aureus</i> to protect itself from attack.IMPORTANCEThe innate immune protein calprotectin (CP) defends the host against bacterial pathogens by sequestering multiple essential nutrient metal ions at infection sites. In addition to this role in nutritional immunity, CP promotes the survival of <i>Staphylococcus aureus</i> in coculture with <i>Pseudomonas aeruginosa</i>, an effect that is independent of its metal-sequestering function. In this work, we sought to understand how CP modulates this interspecies interaction by evaluating the transcriptional responses of <i>P. aeruginosa</i> and <i>S. aureus</i> to CP and metal limitation in cocultures. Our study revealed that CP attenuates the ability of <i>P. aeruginosa</i> to attack <i>S. aureus</i> with anti-staphylococcal factors and enhances the capacity of <i>S. aureus</i> to withstand this assault, effects that are not recapitulated by metal limitation. This work provides a new understanding of how CP modulates microbial interactions that are relevant to human health.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0057625"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144993113","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":"Impact of seasonal variation on the oral and nasopharyngeal microbiome in school-aged children: the school MicroBE initiative.","authors":"Juan Castro-Severyn, Nicolás Pacheco, Guillermo Valdivia, Gabriel I Krüger, Coral Pardo-Esté, Francisco Remonsellez, Aldo Gaggero, Gloria Arriagada, Fernando Valiente-Echeverria, Jorge Olivares-Pacheco, Jorge H Valdes, Claudia P Saavedra","doi":"10.1128/msystems.00467-25","DOIUrl":"10.1128/msystems.00467-25","url":null,"abstract":"<p><p>The \"School MicroBE\" initiative explores how the built environment impacts microbial communities in school-aged children by examining temporal dynamics and shifts in nasopharyngeal and oral microbiomes. This longitudinal study involved 119 children aged 4 to 13 at a public school, with nasopharyngeal and oral samples collected in autumn, winter, and spring of 2023. Using 16S rRNA gene sequencing, we assessed microbial composition through alpha and beta diversity analyses, characterized microbial assemblages, and evaluated the relative abundance of key taxa. Significant seasonal variations were observed, with an increase in alpha diversity from autumn to spring in nasopharyngeal samples. Beta diversity analyses did not reveal distinct clustering patterns based on collection months. Hierarchical clustering identified four major microbiome groups with characteristic taxonomic distribution, and co-occurrence network analysis suggested both synergistic and competitive interactions among taxa. Longitudinal transition analysis between microbiome clusters revealed dynamic changes over time, providing a baseline of microbiome states in the tested children. These findings highlight the importance of microbial community shifts in the environment by providing direct measures on microbiome stability and diversity in children, providing insights into how microbial communities respond to environmental fluctuations, including potential pathogen exposures. Understanding these temporal changes will improve the development of targeted public health strategies to assess and manage potential infectious disease outbreaks and the emergence of antimicrobial resistance in school settings.IMPORTANCEThe \"School MicroBE\" initiative enhances our understanding of pediatric microbiome dynamics by revealing temporal and compositional shifts, thus establishing basal studies on a sentinel school contributing to the understanding of pediatric microbiome and its associated health issues.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0046725"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799583","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":"<i>Populus simonii × Populus nigra</i> overexpressing <i>PsnWRKY70</i> recruits phyllosphere bacterial strains that inhibit <i>Alternaria alternata</i>.","authors":"Wei Wang, Weixiong Wang, Jing Jiang, Xiangdong Bai, Kun Chen, Xiaoyue Zhang, Jingya Yang, Di Wu, Ben Niu, Guifeng Liu","doi":"10.1128/msystems.01765-24","DOIUrl":"10.1128/msystems.01765-24","url":null,"abstract":"<p><p>WRKY transcription factors have been implicated in the regulation of disease resistance associated with plant immune responses, which has crucial implications for defense responses against stress in plants. The role played by the <i>PsnWRKY70</i> gene of <i>Populus</i> (<i>Populus simonii</i> × <i>P. nigra</i>) in triggering the mechanism between the phyllosphere microbiome and plant defense against foliar pathogens remains unclear. Molecular ecological network analysis demonstrated that the stability and complexity of the phyllosphere bacterial community of <i>Populus</i> were influenced by <i>Alternaria alternata</i> infection. Specifically, compared to the wild-type line, the <i>PsnWRKY70</i>-overexpressing (OE) line had a higher average clustering coefficient and modularity. Furthermore, metabolomic analysis revealed that 19 differential metabolites were significantly enriched in the leaves of the OE line. Among these metabolites, coumarin compounds, such as fraxetin-8-O-glucoside (fraxin) and scopoletin-7-O-glucoside (scopolin), significantly promoted the proliferation of the genera <i>Methylobacterium</i> and <i>Achromobacter</i> with resistance to <i>A. alternata</i>. Additionally, these genera also served as connectors in the molecular ecological network of the phyllosphere microbiome of the OE line. Thus, we concluded that the <i>PsnWRKY70</i> gene enhanced the stability, complexity, and core taxa cooperation of the phyllosphere microbial network in <i>Populus</i> and regulated the biosynthesis of fraxin and scopolin to recruit beneficial bacteria controlling <i>A. alternata</i> infection. These findings provide valuable insights into the ability of resistant plant genotypes to drive the assembly of the phyllosphere microbiome, advancing our understanding of defense against pathogens using the biocontrol phyllosphere microbial community.IMPORTANCEPoplar leaf blight caused by <i>Alternaria alternata</i>, a common disease in Northeast China, can cause abnormal abscission of poplar leaves and even lead to plant death in severe cases. WRKY transcription factors have been implicated in the regulation of disease resistance associated with plant immune responses to secondary metabolism via a complicated gene network. However, little is known about how the metabolites regulated by the <i>PsnWRKY70</i> gene trigger changes in the phyllosphere microbiome, leading to increased resistance to foliar pathogens. Here, the <i>PsnWRKY70</i> overexpressing line of <i>Populus</i> (<i>Populus simonii</i> × <i>P. nigra</i>) exhibited increased coumarin synthesis in the leaves, triggering changes in microbial species central in phyllosphere microbial networks and leading to increased resistance to <i>A. alternata</i> infection. This study provides insights into the role of the <i>PsnWRKY70</i> gene in triggering the resistance mechanism to <i>A</i>. <i>alternata</i> in <i>Populus</i>.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0176524"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855710","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":"Systematic evaluation of phenotypic variations induced by prophages in a clinical isolate of <i>Pseudomonas aeruginosa</i>.","authors":"Xiaoyu Li, Yang Tao, Bingrui Sui, DanDan Li, Lili Wang, Yumin Hou, Yongping Xu, Bijie Hu, Na Li, Demeng Tan","doi":"10.1128/msystems.00428-25","DOIUrl":"10.1128/msystems.00428-25","url":null,"abstract":"<p><p>With the rise of antibiotic resistance, nosocomial infections caused by <i>Pseudomonas aeruginosa</i> present a significant challenge to healthcare systems. Prophages integrated into bacterial chromosomes play a key role in generating phenotypic and genotypic diversity, influencing bacterial pathogenicity and complicating antimicrobial treatment strategies. Recent advances in high-throughput sequencing have facilitated the precise localization of prophages within bacterial genomes. However, the mechanisms by which prophages influence host phenotypes remain poorly understood, particularly in clinical polylysogens. In this study, we conducted a comprehensive investigation of prophages predicted in the clinical <i>P. aeruginosa</i> isolate ZS-PA-05 in the absence of an external trigger, focusing on their contribution to bacterial phenotype through the use of prophage deletion mutants. Our findings indicate that ZS-PA-05 harbors both active and cryptic prophages, each exhibiting unique spontaneous induction rates. Notably, the absence of certain prophages significantly affects bacterial growth, motility, biofilm formation, antibiotic susceptibility, and phage proliferation, as well as virulence. Intriguingly, the deletion of prophage Y significantly increased pyocyanin production, enhancing interspecies competition and cell line survival, despite impaired bacterial growth. This underscores the complexity of prophage-host interactions and emphasizes the role of prophages in bacterial adaptation, with far-reaching implications for antimicrobial therapies and beyond.IMPORTANCEUpon infecting a bacterial host, phages can follow one of two developmental pathways: the lytic or lysogenic cycle. In the lysogenic state, prophages remain dormant, integrating into the bacterial genome and being vertically transmitted through binary fission. These prophages profoundly influence bacterial phenotypic and genetic diversity and contribute to the structuring of microbial communities. Here, we systematically assess the beneficial and detrimental impacts of prophage carriage in the clinical multilysogen <i>Pseudomonas aeruginosa</i> strain ZS-PA-05. Our results reveal marked variation in spontaneous induction frequencies among co-resident prophages and demonstrate prophage-driven phenotypic heterogeneity. By uncovering key aspects of prophage-host interactions, this study highlights the critical role of prophages in shaping the behavior of clinical isolates, particularly in the context of antimicrobial interventions such as antibiotic and phage therapies.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0042825"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12456005/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855819","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}