mSphere最新文献

{"title":"The hyphae-specific C₂H₂ transcription factor HscA regulates development, stress response, and mycotoxin production in <i>Aspergillus</i> species.","authors":"Ye-Eun Son, Kyu-Hyun Kim, He-Jin Cho, Jae-Hyuk Yu, Hee-Soo Park","doi":"10.1128/msphere.00254-25","DOIUrl":"https://doi.org/10.1128/msphere.00254-25","url":null,"abstract":"<p><p>The zinc cluster family is the largest group of transcription factors involved in regulating fungal growth, morphology, and differentiation in <i>Aspergillus</i> species. In this study, we investigated hyphae-specific zinc cluster transcription factors and characterized a novel hyphae-specific Cys₂His₂ zinc finger transcription factor, designated HscA, in the model fungus <i>Aspergillus nidulans</i> and the toxigenic fungus <i>Aspergillus flavus</i>. Phenotypic analyses demonstrated that HscA is essential for normal asexual and sexual development in <i>A. nidulans</i> and <i>A. flavus</i>. Deletion of <i>hscA</i> resulted in elevated sensitivity to cell wall stress agents and an ion depletion stressor. Moreover, the <i>hscA</i> null mutant exhibited decreased production of sterigmatocystin in <i>A. nidulans</i> and aflatoxin B1 in <i>A. flavus</i>. Conidial production in the kernel was decreased in the Δ<i>hscA</i> strain compared to the control in <i>A. flavus</i>. Overall, these results suggest that HscA plays a pivotal role in fungal development, stress tolerance, and mycotoxin production in <i>Aspergillus</i> species.</p><p><strong>Importance: </strong>Fungal growth and development are closely regulated by a variety of transcription factors. This study identified and characterized a hyphae-specific Cys₂His₂ zinc finger transcription factor in two <i>Aspergillus</i> species. HscA contains a Cys₂His₂ zinc finger domain and plays a crucial role in appropriate fungal development in <i>A. nidulans</i> and <i>A. flavus</i>. Particularly, HscA is involved in stress tolerance in both hyphal and conidial stages. We further demonstrated that HscA acts as a positive regulator of sterigmatocystin production in <i>A. nidulans</i> and is essential for proper aflatoxin B1 production in <i>A. flavus</i>. Additionally, our findings indicate that HscA is crucial for conidial formation in kernel assays, implying that HscA may function as a virulence factor. Overall, these findings enhance our understanding of mycotoxin production and fungal pathogenicity in <i>Aspergillus</i> species.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0025425"},"PeriodicalIF":3.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Host-pathogen interaction profiling of nontypeable <i>Haemophilus influenzae</i> and <i>Moraxella catarrhalis</i> coinfection of bronchial epithelial cells.","authors":"Adonis D'Mello, Timothy F Murphy, Martina Wade, Charmaine Kirkham, Yong Kong, Hervé Tettelin, Melinda M Pettigrew","doi":"10.1128/msphere.00242-25","DOIUrl":"https://doi.org/10.1128/msphere.00242-25","url":null,"abstract":"<p><p>Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory lung disease and the third leading cause of death globally. Nontypeable <i>Haemophilus influenzae</i> (NTHi) and <i>Moraxella catarrhalis</i> (Mcat) are common pathogens in individuals with COPD. Acquisition of NTHi or Mcat can cause acute exacerbations of COPD. NTHi and/or Mcat also persist for months in the lower airways and lead to chronic inflammation. We hypothesized that infection by NTHi or Mcat, singly or during coinfection, requires regulation of specific bacterial and host cell pathways. We investigated this phenomenon using an <i>in vitro</i> cell culture model consisting of lung carcinoma H292 cell lines, infected with NTHi, Mcat, or both species. Samples were fractionated into \"apical fluid,\" containing free-floating bacteria, and adhered/invaded bacteria on or within H292 cells. We used transcriptomic profiling with RNA-seq and various bioinformatic analyses to disentangle host-pathogen interactions in epithelial cell infection from the perspective of each species. Several biological pathways were differentially regulated across all conditions (31, NTHi; 22, Mcat; and 169, human). NTHi transcriptomic profiles differed during mono-infection and coinfection; examples included downregulation of iron-sulfur metabolism (IscR regulon) and differential regulation of quorum sensing in coinfection compared to mono-infection. Mcat was comparatively less affected by the presence of NTHi during coinfection. H292 epithelial cells responded broadly to all infections with distinct responses to mono-infection and coinfection. Enriched host pathways included influenza/interferon/Wnt and proinflammatory responses. These findings suggest common and distinct processes involved in NTHi and/or Mcat-induced COPD pathogenesis and have implications for therapeutic intervention.IMPORTANCEChronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide. Bacteria such as nontypeable <i>Haemophilus influenzae</i> (NTHi) and <i>Moraxella catarrhalis</i> (Mcat) can cause exacerbations of COPD, and they can persist in the lungs for months, which increases inflammation. We studied how these bacteria interact with lung cells by infecting a cell culture model with NTHi, Mcat, or both. We used RNA sequencing and bioinformatic analysis to examine how the bacteria and host cells respond. When NTHi and Mcat were present together, they behaved differently than when each was alone. We found that different host biological pathways were activated during infection, including those related to inflammation and immune responses. These results provide insights into how NTHi and Mcat contribute to COPD progression and suggest potential targets for new treatments.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0024225"},"PeriodicalIF":3.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A dynamic barrier: remodeling of the nuclear envelope during closed mitosis in malaria parasites.","authors":"Sabrina Absalon","doi":"10.1128/msphere.00999-24","DOIUrl":"https://doi.org/10.1128/msphere.00999-24","url":null,"abstract":"<p><p><i>Plasmodium falciparum</i>, the protozoan parasite responsible for the most severe form of human malaria, replicates through an unconventional mode of closed mitosis, where the nuclear envelope (NE) remains intact across multiple asynchronous nuclear divisions. This Full Circle minireview illustrates how a decade-long journey-from early electron microscopy observations of nuclear pore dynamics-has evolved into a broader investigation of NE composition, architecture, and regulation across the parasite life cycle. Advances in imaging, including ultrastructure expansion microscopy and cryo-electron tomography, revealed key features such as the bipartite microtubule organizing center, nuclear pore complex rosettes, and specialized NE scaffolds. Structure-guided and proteomic approaches identified divergent SUN-domain proteins, <i>Pf</i>SUN1 and <i>Pf</i>SUN2, as essential for NE integrity, genome stability, and chromatin positioning during schizogony. Hi-C analyses further uncovered species- and stage-specific chromatin organization, linking peripheral heterochromatin clustering to virulence gene regulation and life cycle progression. Despite lacking lamins, <i>Plasmodium</i>'s NE functions as a dynamic architectural hub that bridges chromatin, spindle microtubules, and organelle inheritance. Open questions remain about the full NE proteome, organelle-NE contact sites, and the possibility that mechanical deformation of the nucleus during red blood cell invasion could influence gene expression. These insights not only redefine <i>Plasmodium</i> cell biology but also position NE-associated components as attractive therapeutic targets. By coupling methodological innovation with conceptual inquiry, the study of NE dynamics in <i>Plasmodium</i> offers a powerful model for uncovering general principles of nuclear organization and adaptation in divergent eukaryotes.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0099924"},"PeriodicalIF":3.7,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein-specific immune response elicited by the <i>Shigella sonnei</i> 1790GAHB GMMA-based candidate vaccine in adults with varying exposure to <i>Shigella</i>.","authors":"Arlo Z Randall, Valentino Conti, Usman Nakakana, Xiaowu Liang, Andy A Teng, Antonio Lorenzo Di Pasquale, Melissa Kapulu, Robert Frenck, Odile Launay, Pietro Ferruzzi, Antonella Silvia Sciré, Elisa Marchetti, Christina Obiero, Jozelyn V Pablo, Joshua Edgar, Philip Bejon, Adam D Shandling, Joseph J Campo, Angela Yee, Laura B Martin, Audino Podda, Francesca Micoli","doi":"10.1128/msphere.01057-24","DOIUrl":"10.1128/msphere.01057-24","url":null,"abstract":"<p><p><i>Shigella</i> is a leading cause of diarrheal morbidity and mortality in young children from low- and middle-income countries. Here, we aimed to verify the ability of the generalized modules for membrane antigens (GMMA)-based <i>Shigella sonnei</i> candidate vaccine 1790GAHB to elicit an anti-protein antibody response. Serum samples from previous clinical trials in adults (a dose-escalation study and its extension in France, a vaccine efficacy study after human challenge in the United States, and a study in Kenya) were investigated using pan-proteome microarrays consisting of 3,150 full-length or fragmented <i>Shigella</i> proteins. Pre-/post-vaccination comparisons identified subsets of proteins that were highly immunoreactive and largely overlapped across all trials; the T3SS lipochaperone family protein (expressed on GMMA) was the most reactive in all studies. Responses to several microarray antigens correlated well with <i>S. sonnei</i> LPS serum IgG antibody levels. Overall, we confirmed the ability of GMMA to elicit an anti-protein IgG/IgA response; however, no association with protection against shigellosis was identified. In the challenge study, IgG response to seven antigens (IpaC, IpaB, IpaA, IpaD, IpaH, IpgC, and MxiD; not expressed on GMMA) was associated with a decreased risk of shigellosis. These antigens were observed to also have high IgG responses at baseline in individuals naturally exposed to <i>Shigella</i> and could constitute targets for future vaccine development.IMPORTANCE<i>Shigella</i> remains a major cause of diarrheal disease, especially in children aged under 5 years from low-to-middle-income countries. No vaccine against shigellosis is yet widely available despite the high public health need. An ideal vaccine would provide protection against the most prevalent species, <i>Shigella flexneri</i> and <i>Shigella sonnei</i>; therefore, it could be relevant to identify common antigens. We developed a microarray containing 3,150 full-length or fragmented proteins selected across <i>Shigella</i> species. Sera collected in four clinical trials conducted in three countries of varying endemicity to evaluate a <i>S. sonnei</i> GMMA-based candidate vaccine were tested against these proteins. We identified several <i>Shigella</i> proteins (IpaC, IpaB, IpaA, IpaD, IpaH, IpgC, MxiD) that induced robust antibody response following experimental challenge or natural infection. These proteins correlated with a reduced risk of shigellosis after the <i>S. sonnei</i> challenge. We found no apparent role for anti-GMMA proteins' IgG or IgA response in protection against shigellosis.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0105724"},"PeriodicalIF":3.7,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019830","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":"Host-specific microbiome-rumination interactions shape methane-yield phenotypes in dairy cattle.","authors":"Alejandro Castaneda, Nagaraju Indugu, Kathryn Lenker, Kapil Narayan, Sarah Rassler, Joseph Bender, Linda Baker, Ojas Purandare, David Chai, Xin Zhao, Dipti Pitta","doi":"10.1128/msphere.00090-25","DOIUrl":"10.1128/msphere.00090-25","url":null,"abstract":"<p><p>Enteric methane emissions (EMEs) negatively impact both the environment and livestock efficiency. Given the proposed link between CH₄ yield and the rumination time (RT) phenotype, we hypothesize that this connection is mediated by the gut microbiome. This study investigated the RT-microbiome-EME connection using rumination-bolus, fecal, and rumen microbiomes as non-invasive proxies for identifying low-EME cows. High-RT cows ruminated 94 minutes longer per day (20%) and exhibited 26% lower EME than low-RT cows, confirming a strong RT-CH₄-yield association. Microbial analysis revealed conserved methanogen diversity across the rumen, bolus, and fecal microbiomes, though functional differences were evident. High-RT cows had a greater abundance of <i>Methanosphaera stadtmanae</i>, suggesting an increased potential for methylotrophic methanogenesis, whereas low-RT cows exhibited higher <i>Methanobrevibacter</i> YE315 abundance, indicative of CO₂-utilizing methanogenesis. Additionally, high-RT cows showed increased alternative hydrogen sinks, supported by upregulated genes encoding fumarate reductase, sulfate reductase, nitrate reductase, and ammonia-forming nitrite reductase, thereby reducing hydrogen availability for methanogenesis. Metabolically, high-RT cows had higher propionate concentrations and were enriched with rapid-fermenting bacteria (<i>Prevotella</i>, <i>Sharpea</i>, <i>Veillonellaceae</i>, and <i>Succinivibrionaceae</i>), whereas low-RT cows exhibited higher acetate concentrations with elevated acetate-producing pathways, reflecting differences in energy partitioning mechanisms. This study establishes RT as a microbiome-linked, non-invasive screening tool for identifying low-EME cows. The observed microbial and metabolic shifts in high-RT cows suggest that RT-based selection could enhance methane mitigation, rumen efficiency, and climate-smart livestock production. Leveraging RT-associated microbial profiles offers a scalable and cost-effective approach to reducing EME in cattle.</p><p><strong>Importance: </strong>Methane emissions from livestock contribute to climate change and reduce animal efficiency. This study reveals that cows with longer rumination times (chewing cud for an extra 94 minutes daily) produce 26% less methane than cows with shorter rumination times. The gut microbiome plays a key role-low-methane cows host microbial communities that produce less methane while efficiently utilizing hydrogen for energy conservation in the rumen. By analyzing rumination sensor data and/or in combination with microbial profiles from rumen or fecal samples, farmers can non-invasively identify and select cows that naturally emit less methane. This scalable, cost-effective strategy offers a practical solution for reducing livestock's environmental footprint while enhancing efficiency and advancing climate-smart agriculture.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0009025"},"PeriodicalIF":3.7,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108071/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143983287","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":"Deep mutational scanning and CRISPR-engineered viruses: tools for evolutionary and functional genomics studies.","authors":"Mercedes Paz, Gonzalo Moratorio","doi":"10.1128/msphere.00508-24","DOIUrl":"10.1128/msphere.00508-24","url":null,"abstract":"<p><p>Recent advancements in synthetic biology and sequencing technologies have revolutionized the ability to manipulate viral genomes with unparalleled precision. This review focuses on two powerful methodologies: deep mutational scanning and CRISPR-based genome editing, that enable comprehensive mutagenesis and detailed functional characterization of viral proteins. These approaches have significantly deepened our understanding of the molecular determinants driving viral evolution and adaptation. Furthermore, we discuss how these advances provide transformative insights for future vaccine development and therapeutic strategies.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0050824"},"PeriodicalIF":3.7,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108059/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144034317","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":"Functional implications of respiratory syncytial virus F sequence variability: a comparative analysis using contemporary RSV isolates.","authors":"Kim Stobbelaar, Lotte Jacobs, Francisco I Serrano-Cano, Axelle Fransen, Winke Van der Gucht, Annemieke Smet, Benedicte Y De Winter, Paul Cos, Winnok de Vos, Kim Van Hoorenbeeck, Stijn Verhulst, Peter L Delputte","doi":"10.1128/msphere.00860-24","DOIUrl":"10.1128/msphere.00860-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Respiratory syncytial virus (RSV) remains a major global health issue. Therapeutic options are limited, but new prophylactics, all targeting the fusion (F) glycoprotein, were recently licensed. Although F sequence variation is limited, it is unclear if and how this variability translates to phenotypical differences. We analyzed full F sequences of 105 contemporary RSV isolates, gathered from children presenting with acute lower respiratory tract infections. Based on F antigenic site variation, 20 isolates were selected for functional characterization. Although RSV F diversity is generally low, the overall mean pairwise distance between RSV-A strains is higher than RSV-B (0.014 vs 0.008, &lt;i&gt;P&lt;/i&gt; &lt; 0.001). Sequence variability in the known monoclonal antibody (mAb)-binding sites seems insufficient to explain the divergent and often subgroup-dependent sensitivity to mAb neutralization. Despite comparable growth rates, mean syncytium size was higher (mean 61.68 [SD 24.51] vs 31.72 [SD 11.64], &lt;i&gt;P&lt;/i&gt; &lt; 0.001), and mean syncytium frequency was lower (mean 25.37 [SD 9.20] vs 47.85 [11.52], &lt;i&gt;P&lt;/i&gt; &lt; 0.001) in RSV-A strains. For all isolates, higher temperatures were associated with increased inactivation, although some RSV-A isolates displayed manifestly higher stability. Genomic and phenotypic variability among our contemporary RSV isolates was limited, with noticeable exceptions. The availability of new prophylactics targeting RSV F corroborates the importance of continued RSV surveillance to identify changes in the F sequence, including mutations that reduce mAb efficacy or lead to escape mutants. Surveillance should include both sequencing data and an evaluation of sensitivity to prophylactic antibodies, using contemporary clinical isolates.IMPORTANCERespiratory syncytial virus (RSV) is a major cause of respiratory infections in young children worldwide. Recent progress has led to new ways to prevent serious RSV-associated disease. The virus's fusion (F) protein is a key focus for vaccine development because it helps the virus enter host cells and is well conserved across different virus strains. However, it is unclear if small differences in the F protein sequence could affect how the virus behaves &lt;i&gt;in vitro&lt;/i&gt;. In this study, we, therefore, analyzed 105 RSV samples from children under two who presented with respiratory infections. We selected 20 samples (12 RSV-A and 8 RSV-B) for functional testing, based on their F protein sequences. Phenotypic differences between clinical isolates and reference strains, such as virus stability at 4°C and susceptibility to monoclonal antibody neutralization, highlight the importance of using viruses isolated from recent clinical samples. Although significant functional differences were observed in traits related to the F protein, both between the RSV subgroups and within, the underlying molecular mechanisms remain unclear. Ongoing monitoring of RSV is critical to ensure current and future vaccines re","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0086024"},"PeriodicalIF":3.7,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144025690","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":"Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.","authors":"Stephanie N Majernik, Larry Beaver, Patrick H Bradley","doi":"10.1128/msphere.00857-24","DOIUrl":"10.1128/msphere.00857-24","url":null,"abstract":"<p><p>Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which, in turn, are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the <i>Lachnospiraceae</i> and then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as <i>Veillonella</i> and <i>Haemophilus</i>, unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the <i>Lachnospira eligens</i> pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.IMPORTANCEMetagenome-assembled genomes, or MAGs, can be constructed without pure cultures of microbes. Large-scale efforts to build MAGs have yielded more complete pangenomes (i.e., sets of all genes found in one species). Pangenomes allow us to measure strain variation in gene content, which can strongly affect phenotype. However, because MAGs come from mixed communities, they can contaminate pangenomes with unrelated DNA; how much this impacts downstream analyses has not been studied. Using a metagenomic study of gut microbes in cirrhosis as our test case, we investigate how contamination affects analyses of microbial gene content. Surprisingly, even small, typical amounts of MAG contamination (<5%) result in disproportionately high levels of false positive associations (38%). Fortunately, we show that most contaminants can be automatically flagged and provide a simple method for doing so. Furthermore, applying this method reveals a new association between cirrhosis and gut microbial motility.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0085724"},"PeriodicalIF":3.7,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033204","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":"TIMP1 secretion induced by <i>Toxoplasma</i> effector GRA24 via p38 MAPK signaling promotes non-disruptive parasite translocation across polarized brain endothelial monolayers.","authors":"Elena Afanaseva, Antonio Barragan","doi":"10.1128/msphere.00102-25","DOIUrl":"10.1128/msphere.00102-25","url":null,"abstract":"<p><p>The protozoan <i>Toxoplasma gondii</i> first crosses the intestinal wall and then the blood-brain barrier (BBB) to establish chronic, latent infections in humans and other warm-blooded vertebrates. However, the molecular mechanisms underlying this stealthy colonization remain poorly understood. In this study, we investigated the passage of <i>T. gondii</i> tachyzoites across polarized monolayers of murine brain endothelial cells (bEnd.3) and human intestinal cells (Caco-2). We found that exposure to live <i>T. gondii</i> tachyzoites, but not to tachyzoite lysate or lipopolysaccharide, induced elevated transcription and secretion of tissue inhibitor of metalloproteinases 1 (TIMP1), a pleiotropic protein linked to BBB maintenance. Recombinant TIMP1 consistently increased <i>T. gondii</i> transmigration across monolayers, while pharmacological inhibition of matrix metalloproteinases (MMPs) non-significantly impacted transmigration. Through a combined approach of pharmacological inhibition and mutant <i>T. gondii</i> lines, we identified the MYR translocon-associated effector GRA24 and host cell p38 mitogen-activated protein kinase (MAPK) signaling as key mediators of <i>Timp1</i> induction. Moreover, despite <i>T. gondii</i> transmigration, cell polarization and barrier integrity were preserved, suggesting a non-disruptive passage of tachyzoites with minimal or transient barrier dysregulation. These findings reveal a role for GRA24-p38 MAPK signalling and TIMP1's MMP-independent effects in facilitating the translocation of <i>T. gondii</i> across restrictive biological barriers.IMPORTANCEThe parasite <i>Toxoplasma gondii</i>, which is globally widespread, colonizes the brains of humans and other warm-blooded animals. To do so, it first crosses the gut wall before entering the brain via the bloodstream. However, the mechanisms by which <i>Toxoplasma</i> overcomes the body's restrictive biological barriers remain largely unknown. In this study, we used cellular models of the gut and brain barriers to investigate how the parasite passes through. We found that <i>Toxoplasma</i> induces cells to secrete TIMP1, a multifunctional protein that reduces inflammation and is linked to blood-brain barrier protection. Surprisingly, TIMP1 also facilitated <i>Toxoplasma</i>'s passage across cellular barriers. This elevated TIMP1 production and secretion by host cells was triggered by a secreted <i>Toxoplasma</i> effector protein (GRA24) and mediated through host cell signaling pathways (p38 MAPK). These findings suggest that <i>Toxoplasma</i> manipulates host cells to produce factors that aid its colonization while suppressing inflammation.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0010225"},"PeriodicalIF":3.7,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108053/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144030091","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":"Sodium butyrate inhibits the expression of virulence factors in <i>Vibrio cholerae</i> by targeting ToxT protein.","authors":"Sushmita Kundu, Suman Das, Priyanka Maitra, Prolay Halder, Hemanta Koley, Asish K Mukhopadhyay, Shin-Ichi Miyoshi, Shanta Dutta, Nabendu Sekhar Chatterjee, Sushmita Bhattacharya","doi":"10.1128/msphere.00824-24","DOIUrl":"10.1128/msphere.00824-24","url":null,"abstract":"<p><p>Cholera, a diarrheal disease caused by the gram-negative bacterium <i>Vibrio cholerae</i>, remains a global health threat in developing countries due to its high transmissibility and increased antibiotic resistance. There is a pressing need for alternative strategies, with an emphasis on anti-virulent approaches to alter the outcome of bacterial infections, given the increase in antimicrobial-resistant strains. <i>V. cholerae</i> causes cholera by secreting virulence factors in the intestinal epithelial cells. These virulence factors facilitate bacterial colonization and cholera toxin production during infection. Here, we demonstrate that sodium butyrate (SB), a small molecule, had no effect on bacterial viability but was effective in suppressing the virulence attributes of <i>V. cholerae</i>. The production of cholera toxin (CT) was significantly reduced in a standard <i>V. cholerae</i> El Tor strain and two clinical isolates when grown in the presence of SB. Analysis of mRNA and protein levels further revealed that SB reduced the expression of the ToxT-dependent virulence genes like <i>tcpA</i> and <i>ctxAB</i>. DNA-protein interaction assays, conducted at cellular (ChIP) and <i>in vitro</i> conditions (EMSA), indicated that SB weakens the binding between ToxT and its downstream promoter DNA, likely by blocking DNA binding. Furthermore, the anti-virulence efficacy of SB was confirmed in animal models. These findings suggest that SB could be developed as an anti-virulence agent against <i>V. cholerae,</i> serving as a potential alternative to conventional antibiotics or as an adjunctive therapy to combat cholera.</p><p><strong>Importance: </strong>The world has been facing an upsurge in cholera cases since 2021, a similar trend continuing into 2022, with over 29 countries reporting cholera outbreaks (World Health Organization, 16 December 2022, Disease Outbreak News, Cholera-global situation). Treatment of cholera involves oral rehydration therapy coupled with antibiotics to reduce the duration of the illness. However, in recent years, indiscriminate use of antibiotics has contributed to the emergence of antibiotic-resistant strains. In this study, we have addressed the problem of antibiotic resistance by targeting virulence factors. Screening various compounds using <i>in silico</i> methods led to the identification of a small molecule, SB, that inhibits the virulence cascade in <i>V. cholerae</i>. We demonstrated that (i) SB intervened in ToxT protein-DNA binding and subsequently affected the expression of ToxT-regulated virulence genes (<i>ctxAB</i> and <i>tcpA</i>) and (ii) SB is a potential therapeutic candidate for the development of a novel antimicrobial agent.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0082424"},"PeriodicalIF":3.7,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143982405","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}