mSphere最新文献

{"title":"Sensitive, non-invasive detection of chronic wasting disease in wild and captive white-tailed deer using fecal volatile profiling.","authors":"Amalia Z Berna, Tzvi Y Pollock, Yang Liu, Michelle Gibison, Amritha Mallikarjun, Joey Logan, Cynthia M Otto, Audrey R Odom John","doi":"10.1128/msphere.00351-25","DOIUrl":"10.1128/msphere.00351-25","url":null,"abstract":"<p><p>Chronic wasting disease (CWD) is a universally fatal, transmissible prion disease affecting cervids. Primarily found among deer populations in North America, the disease has spread across the continent and made forays into Europe and Asia as well. Currently, accurate methods for detecting CWD infection require postmortem dissection of the lymph nodes and brainstem of affected animals. New, high-sensitivity methods of identifying CWD in living animals are sorely needed to help curb the spread of this devastating disease in captive and wild deer. Here, we use two-dimensional gas chromatography-mass spectrometry (GCxGC-MS) to detect volatile organic compounds (VOCs) released from feces of white-tailed deer (WTD) for differentiation of the feces of CWD-negative and CWD-positive animals. We report 4 discrete VOCs in captive WTD and 10 discrete VOCs in wild WTD, with which we can discriminate CWD-positive and CWD-negative samples. Additionally, we evaluate the ability to detect biomarkers associated with CWD early during disease progression, by comparing samples from the early stage of infection with samples from the late stage and uninfected WTD. Our data suggest that detection of VOCs from the feces of WTD-both in captive and wild populations-can serve as a highly sensitive and non-invasive technique for identifying CWD infection in living animals.IMPORTANCEChronic wasting disease (CWD) is a deadly, transmissible prion disease of cervids. The spread of CWD is increasing among both wild and captive deer populations; however, the options to detect in living animals are limited. Diagnosing CWD early would allow more effective control over the spread between animals and contamination of the environment. Our research presents a method of determining CWD infection through the detection of disease-associated odor molecules in the feces of affected deer. This methodology lays the foundation for rapid, non-invasive diagnosis of CWD in living white-tailed deer, allowing for the development of tools to enhance control of this devastating disease's spread among both captive and wild populations.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0035125"},"PeriodicalIF":3.1,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874237","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":"YlAaf1-YlAaf2, a bipartite SANT domain-containing complex of transcriptional activator, promotes filamentous growth in the dimorphic yeast <i>Yarrowia lipolytica</i>.","authors":"Meng-Yang Xu, Zhen-Hua Wang, Xiang-Dong Gao","doi":"10.1128/msphere.00403-25","DOIUrl":"10.1128/msphere.00403-25","url":null,"abstract":"<p><p>The yeast-to-filament transition is important for dimorphic fungi to adapt to different environmental conditions. Transcriptional activators that activate downstream target genes in response to environmental stimulations are particularly important for the control of this morphological transition. However, only a limited number of key activators of filamentation have been identified. Here, we report YlAaf1 and YlAaf2, a novel pair of SANT domain-containing transcription factors that promote filamentation in the dimorphic yeast <i>Yarrowia lipolytica</i>. We show that both deletion and co-overexpression of Yl<i>AAF1</i> and Yl<i>AAF2</i> affect filamentation substantially. We also show that YlAaf1 and YlAaf2 interact with each other physically, and the bipartite complex has transcriptional activation activity. In addition, we show that YlAaf1 and YlAaf2 respond to alkaline pH and are upregulated by YlRim101 and Mhy1, two key transcription factors important for alkaline-induced filamentation. Lastly, we show that YlAaf1-YlAaf2 and Mhy1 are direct regulatory targets of each other.IMPORTANCETranscription factors play critical roles in the control of the yeast-to-filament transition in dimorphic fungi. However, many of them contain zinc finger or zinc cluster DNA-binding domains, but not SANT domain, the latter of which is initially identified in nuclear receptor co-repressors and the subunits of many chromatin-remodeling complexes. In this paper, we report two novel SANT domain-containing transcription factors, YlAaf1 and YlAaf2, that promote filamentation in <i>Yarrowia lipolytica</i>. YlAaf1 and YlAaf2 are closely related to <i>Candida albicans</i> Aaf1, which also appears to promote filamentation. YlAaf1 and YlAaf2 are unique in that they are not simply redundant in function but instead form a bipartite transcriptional activator. One subunit, YlAaf2, is highly responsive to environmental stimulation such as alkaline pH, a strong inducer of the yeast-to-filament transition. We identified a crosstalk between YlAaf1-YlAaf2 and Mhy1, the master regulator of filamentation. Our results provide new insights into the regulatory networks that control the yeast-to-filament transition in <i>Y. lipolytica</i>.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0040325"},"PeriodicalIF":3.1,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874238","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":"Insect-associated bacterial communities across an anthropogenic landscape.","authors":"Elina Hanhimäki, Susanna Linna, Camila Souza Beraldo, Mikael Englund, Uxue Rezola, Pedro Cardoso, Rose Thorogood, Marjo Saastamoinen, Anne Duplouy","doi":"10.1128/msphere.00320-25","DOIUrl":"10.1128/msphere.00320-25","url":null,"abstract":"<p><p>Anthropogenic activities induce drastic changes in land use that are at least partly responsible for the ongoing global patterns of macro-biodiversity erosion. These habitat changes also impact the fitness of the resilient species, through direct effects on diet and/or indirect environmental effects. Although microbial communities associated with species can crucially influence a diverse set of their host's biological functions, studies on how microbial communities associated with wild species respond to habitat degradation remain scarce. We use metacommunities of two sympatric herbivorous insect species specialized in feeding on <i>Plantago lanceolata</i> that occurs across a network of natural meadows, pastures, and roadsides, as a model system to test the hypothesis that habitat degradation can also impact their associated microbial communities. The Glanville fritillary butterfly, <i>Melitaea cinxia</i>, and the weevil <i>Mecinus pascuorum</i> were sampled from local meadow habitats affected by various levels of disturbance (e.g., roads, agricultural fields, and buildings). The two species carry very distinct microbiota, either highly diverse and transient for the butterfly or dominated by a few resident bacterial symbionts for the weevil. Spatial characteristics of the focal habitat patch, namely the area of the meadow or the location of the meadow, explained the largest proportion of the variation in microbial community composition in both species, but these effects were significant only in the weevil. In contrast to our prediction, despite a minor increase in bacterial diversity along the gradient of habitat degradation, the overall composition of the microbiota was unchanged across habitats in both host species. Overall, local environmental characteristics other than habitat degradation explain the microbial associations in the two herbivorous insects of this system.</p><p><strong>Importance: </strong>This research dives into the impact of habitat degradation on bacterial communities associated with wild herbivorous insect species, utilizing the ecologically relevant and well-characterized fragmented landscape of the Åland Islands, Finland. This study is crucial as habitat degradation driven by anthropogenic activities (i.e., land use change and habitat fragment size) poses a growing threat to global biodiversity. Indeed, as microbial partners play a pivotal role in the ecology and adaptation of their host species to their environment, there is a pressing need to comprehend how the host-associated microbial diversity responds to their host environmental changes to evaluate their contribution to the escalating patterns of biodiversity erosion globally. However, despite extensive research on the impact of habitat degradation on macro-species, the effects on microbial communities remain an understudied aspect of species ecology.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0032025"},"PeriodicalIF":3.1,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482173/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144962442","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 insights into <i>Streptomyces</i> isolates containing both clavulanic acid-like and carbapenem biosynthetic gene clusters.","authors":"Kapil Tahlan, Arshad Ali Shaikh, Jingyu Liu, Kajal Gupta, Nader AbuSara, Santosh Kumar Srivastava, Adau Deng, Ayla Rouah, Madelyn Joan Swackhamer","doi":"10.1128/msphere.00188-25","DOIUrl":"10.1128/msphere.00188-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;β-Lactam antibiotics and β-lactamase inhibitor combinations are essential for combating antimicrobial resistance, with many β-lactams, including clavulanic acid (CA), themselves being products of specialized metabolic pathways in bacteria. CA is a potent β-lactamase inhibitor, and in known producers such as &lt;i&gt;Streptomyces clavuligerus&lt;/i&gt;, it is co-produced with the β-lactam antibiotic cephamycin C, and their biosynthetic gene clusters (BGCs) are always located adjacent on the chromosome. However, CA-like BGCs have also been identified in other bacteria, often without an accompanying cephamycin C BGC. Similarly, carbapenem BGCs (a subclass of β-lactams), such as those responsible for producing MM 4550, a member of the olivanic acid complex with both antibiotic and β-lactamase inhibitory properties, are also found in &lt;i&gt;Streptomyces&lt;/i&gt; species. This study investigated antimicrobial and β-lactamase inhibitory activity production in &lt;i&gt;Streptomyces pratensis&lt;/i&gt; and 10 environmental &lt;i&gt;Streptomyces&lt;/i&gt; isolates (JAC strains) containing CA-like and MM 4550-like BGCs but lacking cephamycin C BGCs. While the examined isolates do not produce CA, they synthesize predicted monocyclic β-lactam precursors of CA, which potentially represent a previously unrecognized, primordial form of β-lactamase inhibitor. Several JAC isolates also exhibited both β-lactamase inhibitory and β-lactam antibiotic activities, indicating that the carbapenem BGC is active in these strains. Gene disruption analysis confirmed that MM 4550-like carbapenem BGCs contribute to both antimicrobial and β-lactamase inhibitory activities, whereas CA-like clavam BGCs only contribute to β-lactamase inhibition. The findings also suggest that both β-lactam BGC types co-occur in nature more frequently than previously recognized, possibly with functional significance and potential applications in the discovery of novel antibiotic-inhibitor combinations.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;The global rise of antimicrobial resistance calls for innovative strategies to preserve the efficacy of existing antibiotics and identify new therapeutic agents. This study explores naturally occurring β-lactamase inhibitors and antibiotics beyond well-characterized systems. Investigation of clavulanic acid (CA)-like and MM 4550-like biosynthetic gene clusters (BGCs) in &lt;i&gt;Streptomyces pratensis&lt;/i&gt; and related environmental isolates revealed a broader occurrence of monocyclic β-lactam precursors and dual-function carbapenems in nature. These findings offer new insights into β-lactam co-production and further indicate that unlinked β-lactam BGCs may have functional significance. The study also highlights the importance of exploring silent counterparts of known BGCs as potential sources of bioactive metabolites, enhancing our understanding of β-lactam BGC diversity and evolution. Notably, it identifies β-lactamase inhibitor and antibiotic-producing strains, opening new avenues for discovering antibiotic-in","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0018825"},"PeriodicalIF":3.1,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144962461","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":"Potential for prolonged replication of common acute respiratory viruses in air-liquid interface cultures of primary human airway cells.","authors":"Miyuki Kawase, Reiko Suwa, Satoko Sugimoto, Masatoshi Kakizaki, Yohei Kume, Hisao Okabe, Sakurako Norito, Makoto Ujike, Hayato Go, Mitsuaki Hosoya, Koichi Hashimoto, Kazuya Shirato","doi":"10.1128/msphere.00422-25","DOIUrl":"10.1128/msphere.00422-25","url":null,"abstract":"<p><p>A previous study provides clinical evidence that extended respiratory virus detection can occur in healthy pediatric individuals. However, it remains unclear how long respiratory viruses can survive in the human respiratory tissue. In this study, the replication potential of common respiratory viruses was evaluated using air-liquid interface (ALI) cultures of primary human respiratory epithelial cells. The findings demonstrate that most respiratory viruses can replicate for approximately 100 days in ALI cultures, with some showing prolonged replication for up to 150-200 days. In contrast, influenza and respiratory DNA viruses showed shorter replication periods likely due to virus-induced cell death. Even during the late phase, some samples continued to support viral replication in re-infection experiments, indicating sustained viral viability. ALI cultures, which lack effector immune cells, did not exhibit apparent type I interferon responses during long-term replication, except for transient IFNβ secretion in the early phase of infection, suggesting a state of tolerance that allows prolonged viral replication. Furthermore, genetic analysis revealed that viruses replicating for more than 50-60 days developed genetic variations, indicating an increased risk of mutations during prolonged infection. These results suggest that common respiratory viruses can remain detectable in human respiratory tissues for extended periods. However, transmission within 50-60 days may be preferable to reduce the risk of generating genetic variants. This concern is particularly relevant in immunocompromised individuals, where prolonged infections may facilitate viral evolution and contribute to the emergence of novel variants.</p><p><strong>Importance: </strong>This study demonstrates that most common respiratory viruses, excluding influenza and DNA viruses, can replicate and produce infectious progeny for an average of up to 100 days in air-liquid interface (ALI) cultures of primary human respiratory epithelial cells without obvious innate immune responses. These findings imply that extended viral replication may occur in human hosts, potentially supported by the slow turnover of the respiratory epithelium. Notably, replication beyond 50-60 days was associated with the accumulation of genetic variations, suggesting a potential mechanism for the emergence of novel variants. To mitigate this risk, limiting transmission to within 50-60 days may be preferable. This issue is particularly relevant in immunocompromised individuals, where prolonged infection may promote viral evolution. Together, these findings provide insight into the replication dynamics of respiratory viruses in human tissue and highlight the importance of limiting long-term replication to prevent the emergence of new variants.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0042225"},"PeriodicalIF":3.1,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144962420","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":"Viral apoptotic mimicry and the role of phosphatidylserine receptors.","authors":"Melinda A Brindley, Michael A Pisciotta","doi":"10.1128/msphere.00089-25","DOIUrl":"https://doi.org/10.1128/msphere.00089-25","url":null,"abstract":"<p><p>In our 2021 mSphere of Influence article (M. A. Brindley, mSphere 6:e00034-21, 2021, https://doi.org/10.1128/mSphere.00034-21), we discussed the concept of viral apoptotic mimicry and how the seminal study by Mercer and Helenius proposed a new paradigm in how viruses can gain entry into cells (J. Mercer and A. Helenius, Science 320:531-535, 2008, https://doi.org/10.1126/science.1155164). Building on the observation that enveloped viral lipids can mediate viral entry, subsequent studies have expanded these observations and further defined the lipids that can initiate infection, the cellular receptors involved, as well as started to explore how viruses obtain their membrane and potentially alter the lipid environment to enhance infection. Exploring the role viral apoptotic mimicry plays in the host has proven more difficult, as many of the receptors that interact with viral lipids also play key roles in immune signaling. This Full Circle review summarizes the lipids and receptors that are involved with viral apoptotic mimicry, the viruses that use them, as well as examines the studies that attempt to explore the role apoptotic mimicry plays in a host.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0008925"},"PeriodicalIF":3.1,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145186325","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 genetic strategy to allow detection of F-actin by phalloidin staining in diverse fungi.","authors":"Alison C E Wirshing, Cristina Colino-Palomino, Analeigha V Colarusso, Mario Pinar, Daniel J Lew","doi":"10.1128/msphere.00517-25","DOIUrl":"10.1128/msphere.00517-25","url":null,"abstract":"<p><p>Actin is highly conserved across eukaryotes. This versatile protein builds cytoskeletal networks central to diverse cellular processes, including cell division and cell motility. The most potent and broadly used reagents to detect polymerized actin distribution in fixed cells are fluorescently conjugated derivatives of the basidiomycete-derived toxin, phalloidin. However, despite its conservation, actin in many ascomycete fungi fails to bind phalloidin. Here, we trace the failure to bind phalloidin to a single amino acid change in a phalloidin-binding residue in actin. Reverting this change in the fungi <i>Aureobasidium pullulans</i> and <i>Aspergillus nidulans</i> by introducing the point mutation <i>act1^V75I</i> at the native <i>ACT1</i> locus confers phalloidin binding while retaining actin function. This strategy should enable characterization of F-actin in a wider range of fungi.IMPORTANCEHigh-resolution tools to visualize filamentous actin networks are critical to the investigation of organisms' cell biology. The gold standard tool is fluorescent phalloidin, a mushroom toxin. However, several fungi have actin that fails to stain with phalloidin. Here, we describe a way to reverse that failure, rendering the invisible actin visible.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0051725"},"PeriodicalIF":3.1,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145186329","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":"Kinetic characterization of RNA synthesis catalyzed by the model hyperthermophilic archaeon <i>Thermococcus kodakarensis</i> RNA polymerase.","authors":"Stephanie L Cooper Horton, Thomas J Santangelo, Aaron L Lucius, David A Schneider","doi":"10.1128/msphere.00319-25","DOIUrl":"https://doi.org/10.1128/msphere.00319-25","url":null,"abstract":"<p><p>At the broadest level of taxonomy, living organisms are divided into the domains Archaea, Bacteria, and Eukarya. Despite the significant differences in cellular organization, metabolic processes, and native environments between the prokaryotic Bacteria and Archaea compared to eukaryotes, the essential biological process of RNA synthesis is generally conserved across all domains. Archaea are the progenitors of Eukarya, and the homology of the singular archaeal RNA polymerase (RNAP) and eukaryotic RNA polymerases-particularly eukaryotic RNAP II (Pol II)-highlights the common evolutionary ancestry that resulted in the modern division of transcription activities between at least three distinct eukaryotic RNAPs. While detailed kinetic evaluations of the activities of bacteria and eukaryotic RNAPs have revealed both universal and significant differences in kinetic elongation schemes, identical comparisons to archaeal-derived RNAPs have largely been absent. Here, we characterize the elongation properties of <i>Thermococcus kodakarensis</i> (<i>T. k</i>.) RNAP, a model hyperthermophilic archaeon, and compare these properties to previously characterized bacterial and eukaryotic RNAPs. We demonstrate that <i>T. k</i>. RNAP forms transcription elongation complexes even more stable than Pol II at ambient temperatures, and remarkably stable complexes at high temperatures, wherein this archaeon thrives. We surprisingly observed no significant impact of NTP concentration on the rate of nucleotide addition by the archaeal RNAP at multiple temperatures that uniquely distinguishes the archaeal RNAP from bacterial and eukaryotic RNAPs. Our results reveal how distinct regulatory strategies can be employed for the archaeal RNAP despite the overall highly conserved structure and cellular functions of multi-subunit RNAPs.</p><p><strong>Importance: </strong>Accurate and timely regulation of gene expression is critical for survival under dynamic conditions in all living organisms. Control of transcription initiation and elongation rates is a key parameter for cellular fitness, and determination of the conserved and unique regulatory strategies that control RNA polymerase activities is of paramount importance. How RNA synthesis is catalyzed by archaeal RNA polymerases provides insight into unique and conserved regulatory strategies for survival at the limits of life.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0031925"},"PeriodicalIF":3.1,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145150218","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":"Microbiome signatures of <i>Clostridioides difficile</i> toxin production and toxin gene presence: a shotgun metagenomic approach.","authors":"Jiye Kwon, Maria A Correa, Yong Kong, William Pelletiers, Martina Wade, Danyel Olson, Melinda M Pettigrew","doi":"10.1128/msphere.00435-25","DOIUrl":"https://doi.org/10.1128/msphere.00435-25","url":null,"abstract":"<p><p><i>Clostridioides difficile</i> is an opportunistic gastrointestinal pathogen capable of asymptomatic colonization and causes diseases ranging from diarrhea to pseudomembranous colitis. Accurate diagnosis of <i>C. difficile</i> infection (CDI) is challenging and critical for treatment and control. We hypothesized that gut microbiome profiles could help distinguish <i>C. difficile</i> colonized patients with diarrhea from those with true CDI. We analyzed 172 stool samples from individuals who tested glutamate dehydrogenase positive for <i>C. difficile</i>. Participants were categorized by toxin status (i.e., toxin positive or negative) and then further classified into three toxin groups based on the production of toxin, and if not produced, whether the <i>C. difficile</i> strain carried toxin-encoding genes. We examined associations between patient characteristics, prior antibiotics exposure, microbiome community structure and function, and toxin categories. Thirty-five percent of toxin-negative participants received antibiotics despite not meeting the criteria for true CDI. <i>Enterococcus</i> species were abundant in all groups. The relative abundance of <i>E. faecalis</i> was higher among individuals with prior antibiotics exposure. Alpha and beta diversity did not differ by toxin group. After controlling for prior antibiotics exposure and previous CDI episode, the abundance of <i>Akkermansia muciniphila, Flavonifractor plautii</i>, and <i>Bifidobacterium adolescentis</i> distinguished individuals with toxin-positive <i>C. difficile. C. difficile</i> abundance did not differentiate participants with true CDI from those who were colonized. We identified associations between the gut microbiome and <i>C. difficile</i> toxin gene presence and toxin production. These results highlight the potential for microbiome-informed diagnostics to improve CDI accuracy and guide treatment decisions.IMPORTANCE<i>Clostridioides difficile</i> colonizes humans and causes diarrhea in community and hospital settings. <i>C. difficile</i> infection (CDI) is a toxin-mediated disease, and its diagnosis is challenging. The goal of this study was to determine whether differences in the gut microbiome could help distinguish between colonized individuals and those with CDI. We examined stool samples and data from 172 individuals categorized into three groups based on the detection of toxin and, if not detected, whether toxin-encoding genes were present in the <i>C. difficile</i> strain. We identified bacteria, such as <i>Enterococcus faecalis</i>, that were more abundant in people who had used antibiotics. While the diversity of the gut microbiome did not differ by toxin group, specific gut bacteria, antibiotic resistance genes, and metabolic pathways were associated with toxin group. Our findings suggest that considering the full gut microbiome and factors like past antibiotic use could help improve the diagnosis and treatment of CDI.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0043525"},"PeriodicalIF":3.1,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145138187","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":"<i>Candida albicans</i> Hxk1 influences expression of metabolic- and virulence-related genes.","authors":"Stefanie Wijnants, Dimitrios Sofras, Wouter Van Genechten, Rudy Vergauwen, Ashley Valle Arevalo, Deepika Gunasekaran, Craig L Ennis, Sabrina Jenull, Karl Kuchler, Clarissa J Nobile, Patrick Van Dijck","doi":"10.1128/msphere.00395-25","DOIUrl":"https://doi.org/10.1128/msphere.00395-25","url":null,"abstract":"<p><p>The Hxk1 protein of <i>Candida albicans</i> phosphorylates N-acetylglucosamine (GlcNAc) which is necessary for various cellular functions, including energy production and chitin synthesis. Further, this protein also regulates morphogenesis independently of its role in GlcNAc catabolism. When <i>HXK1</i> is deleted, cells are hyperfilamentous on serum-containing medium. Furthermore, Hxk1 translocates to the nucleus in the presence of glucose. To gain a broad understanding of the effect of Hxk1 on gene expression in <i>C. albicans</i>, we performed genome-wide transcriptional profiling of the <i>hxk1</i> mutant strain by RNA-Seq. The analysis of these RNA-Seq data showed that Hxk1 affects gene expression in both a carbon source-dependent and -independent manner. However, the effect on gene expression occurs via an indirect mechanism, as genome-wide CUT&RUN binding experiments demonstrated that Hxk1 does not bind to the upstream intergenic regions of the differentially expressed genes. Deletion of <i>HXK1</i> not only resulted in differences in gene expression of genes present in the GlcNAc and galactose regulons, but also in glucose transporter genes, including <i>HGT13</i>. Hxk1 also negatively influences the expression of virulence-associated genes, including <i>HWP1</i>, <i>BRG1</i>, and <i>UME6</i>. Consequently, an <i>hxk1</i> mutant strain showed higher toxicity toward gut epithelial cells compared to the WT strain. Furthermore, the <i>hxk1</i> mutant strain had higher expression levels of <i>SOD4</i> and <i>SOD5</i> and showed higher resistance toward H₂O₂. These findings highlight the multiple functions of Hxk1 in different cellular processes.IMPORTANCE<i>Candida albicans</i> is a fungus that lives in the human body but does not cause any harm in healthy individuals. However, when the immune system is weakened, <i>C. albicans</i> can spread via the bloodstream all over the body and can lead to severe illness and even death. To infect the human body, multiple proteins hold distinct functions. Hxk1 is one of these proteins. This protein is involved in N-acetylglucosamine (GlcNAc) phosphorylation, as well as hyphae formation and glucose transport. To obtain a complete view of the processes regulated by Hxk1, we performed an RNA-Seq experiment. These data revealed that Hxk1 influences the regulation of genes involved in metabolic and virulence-related processes, such as GlcNAc metabolism, sterol metabolism, and oxidative stress resistance. These findings are important to better understand how <i>C. albicans</i> adapted itself to infect the host.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0039525"},"PeriodicalIF":3.1,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145138172","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}