mSphere最新文献

{"title":"Integrated bioinformatics analysis of the shared molecular mechanisms between Parkinson's disease and COVID-19.","authors":"Yang Su, Hui Ma, Jiayuan Niu, Dongnan Hou, Liya Li","doi":"10.1128/msphere.00908-25","DOIUrl":"10.1128/msphere.00908-25","url":null,"abstract":"<p><p>To investigate the shared molecular mechanisms between Parkinson's disease (PD) and COVID-19 through integrated bioinformatics analysis and single-cell RNA sequencing (scRNA-seq). We conducted a comprehensive analysis of bulk RNA-seq data from publicly available databases, along with scRNA-seq data from brain tissues of COVID-19 patients. Differential expression analysis identified 725 differentially expressed genes (DEGs) in COVID-19 and 633 in PD samples. A total of 77 overlapping DEGs were identified, highlighting common pathways associated with neuroinflammation and dopaminergic neuron dysfunction. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed significant enrichment in inflammation-related pathways. The protein-protein interaction network analysis identified CHI3L1 as a key gene linking PD and COVID-19. ScRNA-seq analysis revealed a significant increase in CHI3L1-expressing astrocytes in COVID-19 samples, indicating a potential mechanism by which COVID-19 may exacerbate PD symptoms. Furthermore, cell-cell communication analysis revealed enhanced interactions between astrocytes and microglia, excitatory neurons, or oligodendrocytes through signaling molecules such as phosphoprotein 1, CADM1, NCAM1, NRG, and NRXN1, suggesting that astrocytes play a central role in regulating neuronal excitability, synaptic plasticity, and immune responses in the context of COVID-19. These findings suggest a complex interplay between COVID-19 and PD, emphasizing the need for further investigation into the shared pathogenic mechanisms and potential therapeutic targets.IMPORTANCEThis study demonstrates the critical role of neuroinflammation and dopaminergic neuron damage in the shared pathogenesis of COVID-19 and Parkinson's disease. CHI3L1 emerges as a key target, highlighting its potential involvement in modulating neuroinflammatory pathways and synaptic plasticity. The functional significance of CHI3L1, along with its pathological relevance, warrants further investigation through larger studies. Additionally, the active intercellular communication among astrocytes, microglia, and excitatory neurons underscores the profound impact of COVID-19 on neural circuitry. Collectively, these results provide important insights into the mechanisms driving the neurodegenerative consequences of COVID-19, emphasizing the need for continued exploration of therapeutic interventions and the long-term neurological effects of viral infection.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0090825"},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13123704/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147609447","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 <i>Candida albicans NDT80</i> and <i>UME6</i> on biofilm formation and fluconazole susceptibility.","authors":"Katharina Goerlich, Aaron P Mitchell","doi":"10.1128/msphere.00014-26","DOIUrl":"10.1128/msphere.00014-26","url":null,"abstract":"<p><p>The microbiome-associated fungus <i>Candida albicans</i> is an opportunistic pathogen. Virulence traits include its ability to produce biofilm, a surface-associated growth form that persists on mucosae and implanted medical devices. <i>C. albicans</i> clinical isolates vary in ability to produce biofilm and the constituent filamentous cell types. Here, we focus on two transcription factors that promote filamentation and biofilm formation, Ndt80 and Ume6. We address two questions. First, how variable is the impact of Ndt80 among <i>C. albicans</i> strains? Second, what is the genetic interaction between <i>NDT80</i> and <i>UME6</i>? We find that Ndt80 is required for filamentation and biofilm formation in five clinical isolates in addition to the reference strain SC5314, where Ndt80 function has been well established. RNA-sequencing (RNA-seq) data indicate that <i>UME6</i> RNA levels are reduced in an <i>ndt80</i>Δ/Δ mutant, possibly a result of altered <i>RME1</i> and <i>WOR1</i> expression, both of which control <i>UME6</i>. Increased expression of <i>UME6</i> in <i>ndt80</i>Δ/Δ mutants of three strain backgrounds restores filamentation and biofilm formation, though RNA-seq assays indicate that it does not suppress the overall <i>ndt80</i>Δ/Δ gene expression defect. Ndt80 has an additional role in promoting tolerance to the antifungal drug fluconazole, an inhibitor of ergosterol synthesis. This <i>ndt80</i>Δ/Δ phenotype varies considerably among clinical isolates. In three strains tested, increased expression of <i>UME6</i> in <i>ndt80</i>Δ/Δ mutants enhances their susceptibility to fluconazole. Therefore, our results show an unexpected relationship between Ume6 expression and azole drug sensitivity. To our knowledge, Ume6 has previously been understood to function only in filamentation, biofilm formation, and related processes.IMPORTANCEOur focus is the fungal pathogen <i>Candida albicans</i>. Two traits, biofilm/hypha formation and azole resistance, are major drivers of its infection ability. We examine the roles of two biofilm transcriptional regulators, Ndt80 and Ume6, in several <i>C. albicans</i> clinical isolates. Prior studies in one strain background (SC5314) indicated that Ndt80 controls both biofilm/hypha formation and azole drug susceptibility and that Ume6 controls biofilm/hypha formation. The four new findings here are that (i) Ndt80 effects on fluconazole sensitivity vary considerably with strain background; (ii) Ndt80 is required for filamentation and biofilm formation in multiple clinical isolates; (iii) the Ndt80 target Ume6 contributes to Ndt80 control of filamentation and biofilm formation in multiple clinical isolates; and (iv) Ume6 influences fluconazole vulnerability, the first Ume6 function to our knowledge that is unrelated to filamentation.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0001426"},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13123709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147531268","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":"Pathological phimosis is associated with foreskin immune cell infiltration but not microbiota composition.","authors":"Rachel Penney, Lane B Buchanan, Jorge Rojas-Vargas, Jeff Lin, Yazan Khan, Jacob Davidson, Claire A Wilson, Vera Tai, Thatiane A Russo, Thomas J Hope, Hannah Wilcox, Bern Monari, Jacques Ravel, Kait F Al, Sumit Dave, Peter Zhan Tao Wang, Jeremy P Burton, Jessica L Prodger","doi":"10.1128/msphere.00725-25","DOIUrl":"10.1128/msphere.00725-25","url":null,"abstract":"<p><p>The penile microbiota has been implicated in genital inflammation and increased risk of HIV, HPV, HSV-2, and female-partner bacterial vaginosis in adult males, yet its development during childhood and potential role in pediatric foreskin pathologies remain unknown. We characterized the coronal sulcus microbiota of 75 pediatric males (median age 8.5 years; 43% with pathological phimosis) before and after circumcision and compared these profiles to 56 uncircumcised adult men. Pediatric penile microbiota were highly diverse, dominated by strict and facultative anaerobes, and loosely structured compared to adults, who exhibited two distinct, ecologically organized communities. Circumcision markedly reduced anaerobic taxa and increased <i>Corynebacterium</i> and <i>Staphylococcus</i>. Pathological phimosis (the inability to retract the foreskin due to scarring) was associated with increased densities of CD3+ T cells, CD4+ cells, and CD11c+ dendritic cells, suggesting an adaptive immune mechanism; however, pathological phimosis was not associated with microbiota composition. Nonetheless, <i>Mobiluncus</i> was negatively correlated with CD11c+ dendritic cells, while <i>Campylobacter</i> and <i>Peptoniphilus</i> were negatively correlated with CD56+ NK cells, suggesting microbe-immune interactions. Our data suggest pathologic phimosis is driven by adaptive immune responses but not by specific bacteria; the pathology may be driven by differences in host responses to bacteria or by other stimuli, such as fungal antigens. Our data also demonstrate that the transition to adulthood is accompanied by reorganization of penile communities into structured types previously linked to infection risk, highlighting puberty as a potential window for interventions that promote protective adult microbiota and improve lifelong sexual and reproductive health.</p><p><strong>Importance: </strong>The human penis hosts complex bacterial communities that can influence inflammation, infection risk, and sexual health, but little is known about how these communities form early in life or whether they contribute to childhood foreskin inflammatory disorders. We combined 16S rRNA sequencing with quantitative microscopy to investigate the penile microbiota in boys and its relationship to pathological phimosis, a common condition marked by foreskin scarring. We found that phimosis is associated with infiltration of T cells and dendritic cells, indicating an adaptive immune process, but with no associations with specific bacteria. We also show that penile microbiota reorganize during puberty into structured community types previously linked to HIV and sexually transmitted infection risk. These findings suggest that childhood pathologic phimosis is mediated by adaptive immune responses rather than driven by specific bacterial communities and identify puberty as a critical period for shaping adult penile microbiota, with implications for lifelong genital health.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0072525"},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13123712/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147513079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A heterologous marker-free selection approach for CRISPR/Cas9-based gene editing in the malaria parasite <i>Plasmodium falciparum</i>.","authors":"Eilidh Carrington, Daniel Ballmer, Igor Niederwieser, Basil T Thommen, Nicolas M B Brancucci, Till S Voss","doi":"10.1128/msphere.00884-25","DOIUrl":"10.1128/msphere.00884-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;CRISPR/Cas9-based gene editing of the malaria parasite &lt;i&gt;Plasmodium falciparum&lt;/i&gt; has emerged as a transformative tool for advancing functional studies on parasite biology and identifying new therapeutic targets. Currently applied CRISPR/Cas9 methodologies depend on a limited set of heterologous drug resistance markers for the selection of transgenic parasites, which restricts the potential for iterative genetic modifications. Here, we developed a heterologous marker-free CRISPR/Cas9 gene editing strategy (CRISPR/Cas9&lt;sup&gt;pyrR&lt;/sup&gt;) for &lt;i&gt;P. falciparum&lt;/i&gt; based on the simultaneous editing of a gene of interest and introduction of pyrimethamine (PYR) resistance-conferring mutations into the dihydrofolate reductase-thymidylate synthase (&lt;i&gt;pfdhfr-ts&lt;/i&gt;) gene. By providing a &lt;i&gt;pfdhfr&lt;sup&gt;pyrR&lt;/sup&gt;&lt;/i&gt; donor sequence and the Cas9 expression cassette on separate plasmids, CRISPR/Cas9&lt;sup&gt;pyrR&lt;/sup&gt; ensures that only parasites acquiring both plasmids survive under PYR pressure. As a proof of principle, we applied CRISPR/Cas9&lt;sup&gt;pyrR&lt;/sup&gt; to generate two transgenic parasite lines expressing GFP-tagged versions of the putative nuclear envelope protein PfGEX1 and nuclear pore protein PfNUP116, respectively. We show that PfGEX1-GFP marks the nuclear envelope specifically in gametocytes, but not in asexual blood stage parasites. Similarly, and against previous reports, we find PfNUP116-GFP expression is undetectable in asexual parasites but instead localizes to a distinct perinuclear region in early gametocytes. These results suggest dynamic compositional changes of the nuclear periphery during sexual differentiation. We further demonstrate sequential genetic engineering of the PfNUP116-GFP-expressing line using the human &lt;i&gt;dhfr&lt;/i&gt; drug resistance marker combined with WR99210-based selection by additionally tagging PfAP2-G, the master transcriptional regulator of sexual commitment, and the nuclear pore protein PfNUP313. Hence, CRISPR/Cas9&lt;sup&gt;pyrR&lt;/sup&gt; provides a versatile and effective new method that enhances and complements the current genetic toolkit for malaria research.IMPORTANCEMalaria tropica, which is caused by the unicellular parasite &lt;i&gt;Plasmodium falciparum&lt;/i&gt;, is one of the most devastating infectious diseases worldwide. The development of urgently needed effective vaccines and new antimalarial drugs with novel modes of action requires a profound understanding of parasite biology. CRISPR/Cas9-based genome engineering is beyond doubt the most important experimental approach to study the function and essentiality of parasite proteins and to identify and validate new vaccine and drug targets. In this study, we developed and successfully applied a modified CRISPR/Cas9 strategy, termed CRISPR/Cas9&lt;sup&gt;pyrR&lt;/sup&gt;, that avoids the use of a heterologous drug resistance marker for the selection of genetically modified parasites. CRISPR/Cas9&lt;sup&gt;pyrR&lt;/sup&gt; thus complements the CRISPR/Cas9 toolbox available for gene editing in &lt;i&gt;P. fa","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0088425"},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13123713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147513813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.","authors":"Kunal Dixit, Susheel Bhanu Busi, Anam Ahmed, Avinash Kshirsagar, Christian Jäger, Alka Singh, Varun Shah, Sunil D Saroj, Vineet Ahuja, Paul Wilmes, Yogesh Shouche, Govind Makharia, Dhiraj Dhotre","doi":"10.1128/msphere.00856-25","DOIUrl":"10.1128/msphere.00856-25","url":null,"abstract":"<p><p>Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as <i>Methanobrevibacter filiformis</i>, <i>Methanobrevibacter boviskoreani</i>, <i>Methanosphaera stadtmanae</i>, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.</p><p><strong>Importance: </strong>Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0085625"},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13123714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147574923","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":"Rapid identification of COVID wastewater surges in the absence of case data.","authors":"Victoria I Verhoeve, Joshua Lambert, Amy Jones, Timothy Driscoll","doi":"10.1128/msphere.00652-25","DOIUrl":"10.1128/msphere.00652-25","url":null,"abstract":"<p><p>Genetic testing of community wastewater (wastewater surveillance) is a valuable tool for following trends in the abundance of SARS-CoV-2 and other infectious disease pathogens over time. Wastewater surveillance is increasingly important in the absence of corresponding epidemiological data, particularly for infectious diseases with limited timely data on clinical case incidences. Due to the inherent noise in wastewater data, a single sample is not sufficient to identify a sustained trend in the abundance of a target. This challenge is magnified in resource-limited settings where samples may be collected only once or twice per week. In this work, we collected 24-h composite samples of wastewater daily from a single facility for nearly 4 years. We use this high-frequency data set to describe a method for identifying trends in SARS-CoV-2 abundance in wastewater based on a variety of collection frequencies. Our results indicate that collecting two 24-h composites per week for 2 weeks is sufficient to accurately identify a SARS-CoV-2 surge. We conclude that low-frequency wastewater sampling performs reasonably well in identifying trends in a timely fashion.IMPORTANCEWastewater surveillance is increasingly being used to track trends in infectious disease targets such as SARS-CoV-2, often in the absence of widespread clinical data. In order to interpret the results of wastewater surveillance appropriately in these contexts, it is important to understand how to identify a surge in abundance in time to provoke appropriate downstream responses. This information can be used to adjust collection strategies to optimize target surveillance, particularly in resource-limited settings.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0065225"},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13123706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147593305","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":"Planning for the future of the American Society for Microbiology's Health Unit by the Council on Microbial Sciences.","authors":"Austin J Fox, Andrea M Prinzi, Nancy W Wamburu, Nicholas M Moore, Michael M Lieberman, Kileen Shier, Nancy L Haigwood","doi":"10.1128/msphere.00633-25","DOIUrl":"10.1128/msphere.00633-25","url":null,"abstract":"<p><p>In February and March 2025, the American Society for Microbiology (ASM)'s Council on Microbial Sciences (COMS) hosted a series of virtual retreats to integrate the communities of Clinical Infections and Vaccines (CIV) and Clinical and Public Health Microbiology (CPHM) under the umbrella of the new scientific unit ASM Health. Representatives from these two communities invited experts and ASM members to reflect on the current state of the science, identify challenges hindering scientific advancements, and propose recommendations for overcoming these challenges. Sessions focused on progress in (i) vaccines, therapeutics, diagnostics, and global pathogen surveillance; (ii) improving data integration and cross-agency sharing; (iii) supporting the microbial health workforce; and (iv) gaining public support and confidence in microbiology. Four major recommendations emerged for ASM Health. First, increased support for microbiological science is crucial to ensure the advancement of vaccines, therapeutics, diagnostics, and global pathogen surveillance to mitigate infectious disease threats. Second, enhancement of data integration and sharing in real-time via information systems will facilitate a deeper understanding of disease epidemiology. Third, modern approaches to recruitment, career path, and profession awareness, and dynamic training programs are necessary to achieve microbial workforce balance. Fourth, microbiologists will benefit from outreach training and resources designed to restore public trust in an environment that questions science and evidence-based approaches. ASM is uniquely positioned to take a pivotal leadership role to develop these concepts into specific programs, as well as to enhance partnerships across the spectrum to innovate in funding, both for scientific research and public health.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0063325"},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13123707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147468433","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":"Within-patient evolution of <i>Pseudomonas aeruginosa</i> populations during antimicrobial treatment.","authors":"Giuseppe Fleres, Ellen G Kline, Kevin M Squires, Tyler Tate, Hannah M Creager, Ryan K Shields, Daria Van Tyne","doi":"10.1128/msphere.00656-25","DOIUrl":"10.1128/msphere.00656-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Multidrug-resistant (MDR) &lt;i&gt;Pseudomonas aeruginosa&lt;/i&gt; infections pose a major challenge to effective treatment. Understanding genomic adaptations during antimicrobial therapy in patients infected with this pathogen is crucial for preventing therapeutic failure. Here, we investigated the population diversity and evolution of &lt;i&gt;P. aeruginosa&lt;/i&gt; collected longitudinally from six patients who evolved multidrug-resistant infections. Serial clinical &lt;i&gt;P. aeruginosa&lt;/i&gt; single-colony isolates (&lt;i&gt;n&lt;/i&gt; = 63) and culture-enriched metagenomic population samples (&lt;i&gt;n&lt;/i&gt; = 39) were collected and subjected to whole-genome sequencing. The resulting data were used to characterize and compare the species composition, multi-locus sequence types (STs), and resistance-associated mutations present within each sample type. Single-colony isolate sequencing showed that each patient was infected with a single &lt;i&gt;P. aeruginosa&lt;/i&gt; strain that accumulated mutations and became increasingly more antibiotic-resistant over time. Mutations in genes associated with β-lactam resistance, including &lt;i&gt;ampC, ftsI&lt;/i&gt;, and &lt;i&gt;mexR,&lt;/i&gt; arose over time and corresponded with changes in antimicrobial susceptibility in single-colony isolates. Species profiling of culture-enriched metagenomic populations revealed that all samples contained &lt;i&gt;P. aeruginosa&lt;/i&gt;, but also additional gram-negative pathogens. Metagenomic analysis of culture-enriched populations identified resistance-associated mutations at low frequency, many of which were not identified in single-colony isolates from the same sample. In some cases, resistance-associated mutations initially detected at low frequency rose to fixation after antimicrobial treatment. Overall, this study shows that population-based metagenomic sequencing effectively captures the within-patient genomic diversity of &lt;i&gt;P. aeruginosa&lt;/i&gt; during antimicrobial therapy and could aid the detection and interpretation of resistance-associated mutations in this pathogen.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;&lt;i&gt;Pseudomonas aeruginosa&lt;/i&gt; infections are notoriously difficult to treat and are associated with high rates of morbidity and mortality. While the genetic basis of resistance in &lt;i&gt;P. aeruginosa&lt;/i&gt; is well documented &lt;i&gt;in vitro&lt;/i&gt;, less is known about how resistance evolves within patients during antibiotic therapy. Standard approaches based on analysis of clonal isolates may miss within-patient diversity, potentially overlooking low-frequency mutations that contribute to treatment failure. In this study, we compared single-colony isolate whole-genome sequencing with culture-enriched metagenomic sequencing to monitor the evolution of &lt;i&gt;P. aeruginosa&lt;/i&gt; populations in patients receiving antibiotic therapy. The culture-enriched metagenomic approach enabled the detection of emerging resistance mutations, such as low-frequency variants in &lt;i&gt;ampC&lt;/i&gt; and &lt;i&gt;ftsI&lt;/i&gt;, before these variants rose to fixation. It also revealed genetically res","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0065625"},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13123702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147468416","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":"Two new factors modulating <i>Bacillus subtilis</i> spore resistance and germination.","authors":"William J Bannon, Dejalee Padilla, Dhruv Suryadevara, Faith Ye, George Korza, James Wicander, Peter Setlow","doi":"10.1128/msphere.00741-25","DOIUrl":"10.1128/msphere.00741-25","url":null,"abstract":"<p><p>New effectors of spore properties have been identified in two <i>Bacillus subtilis</i> strains-bacillithiol, the major low-molecular-weight thiol in <i>B. subtilis</i>, and sporulene, a multi-ring compound synthesized from curcumene in spores' outer layers. The absence of either bacillithiol or sporulene caused faster germination of spores of one wild-type <i>B. subtilis</i> strain, PS832, with two germinant receptors (GR)-dependent germinants, L-valine for the GerA GR, and the AGFK mixture for the cooperative action of the GerB and GerK GRs, as well as the GR-independent germinant dodecylamine. However, these effects on PS832 spore germination were due to the presence of the antibiotic marker used to replace the genes for bacillithiol or sporulene synthesis. The absence of bacillithiol also caused reduced spore resistance to wet heat but not to hydrogen peroxide or UV radiation, while sporulenes' absence had no effect on spore wet heat resistance, but reduced spore resistance to hydrogen peroxide as found previously (T. Bosak, R. M. Losick, and A. Pearson, Proc Natl Acad Sci USA 105:6725-6729, 2008, https://doi.org/10.1073/pnas.0800199105) and to UV radiation, but the presence of the antibiotic markers in these mutant strains was not responsible for these effects. Notably, spores lacking sporulene were much whiter than wild-type (wt) spores, suggesting that sporulene and its precursor curcumene contribute to spore pigmentation that can absorb UV, thus reducing spores' UV resistance. Analyses of reasons for the effects of bacillithiol's or sporulene's absence on spore resistance, specifically core water content and/or altered spore inner membrane (IM) permeability, found no major differences from values in wt spores. However, other analyses showed that sporulene's absence led to slight changes in spore IM fluidity.</p><p><strong>Importance: </strong>The work in this paper has identified two new factors, bacillithiol and sporulene, as modulators of the resistance and germination of spores of two <i>Bacillus subtilis</i> strains, and by extension, probably spores of other Bacillota. Since spores of some species can give rise to cells that can cause food spoilage and/or disease, new knowledge about spore resistance and germination could have applied utility.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0074125"},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13123705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147574945","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":"YWHAZ downregulated innate immune responses to RNA viruses by inhibiting the IRF3 signaling pathway.","authors":"Shasha Li, Jinyuan Han, Hefei Wang, Jixia Hou, Linhao Wang, Zhengyang Hou, Yaxin Zhang, Xueer Dou, Jingying Xie, Huixia Li, Xiangrong Li, Ruofei Feng","doi":"10.1128/msphere.00038-26","DOIUrl":"10.1128/msphere.00038-26","url":null,"abstract":"<p><p>Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta polypeptide (YWHAZ) is a member of the YWHA/14-3-3 family. YWHAZ is highly conserved in mammalian cells and generally mediates signal transduction through direct interactions with target proteins. YWHAZ has been reported as a crucial regulator of tumor immunity, inflammation, and apoptosis pathways. However, the precise role of YWHAZ in regulating host antiviral immune responses is not fully understood. Here, our study revealed that YWHAZ negatively regulated type 1 interferon (type 1 IFN) production in response to RNA viruses. Overexpression of YWHAZ inhibited type 1 IFN production triggered by RNA viruses, whereas knockout of YWHAZ increased type 1 IFN production. Mechanistically, YWHAZ interacted with IRF3 and suppressed the nuclear translocation of IRF3 by directly inhibiting IRF3 phosphorylation-dependent dimerization and disrupting the KPNA3-IRF3 interaction. Our findings demonstrated that YWHAZ played a crucial role in regulating IRF3-mediated type 1 IFN production.</p><p><strong>Importance: </strong>The activation of IRF3 induced by RIG-I-like receptors is pivotal for type 1 interferon (IFN) production in antiviral immunity. Virus infection leads to type 1 IFN production through inducing the dimerization and subsequent nuclear translocation of IRF3. Following its activation, IRF3 must be tightly regulated to prevent a dysregulated or excessive immune response. Here, we first found that YWHAZ, a member of the 14-3-3 protein family, is a negative regulator of type 1 IFN production by targeting IRF3 signaling. YWHAZ is bound to IRF3 to inhibit the formation of the TBK1-IRF3 complex, the phosphorylation and dimerization of IRF3, as well as the subsequent nuclear translocation. YWHAZ also impeded the KPNA3-IRF3 interaction by binding to KPNA3, thereby inhibiting IRF3 nuclear translocation. The aa 124-184 in YWHAZ was critical for YWHAZ-mediated suppression of type 1 IFNs. These findings reveal the mechanism by which YWHAZ promotes RNA virus replication, thereby advancing our understanding of how YWHAZ mediates innate immune responses.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0003826"},"PeriodicalIF":3.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13123716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147609472","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}