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Gut-larynx axis and its contribution to laryngeal immunity. 肠喉轴及其对喉免疫的作用。
IF 4.6 2区 生物学
mSystems Pub Date : 2025-10-07 DOI: 10.1128/msystems.01044-25
Ran An, Elliott Xie, John Binns, Federico E Rey, Christina Kendziorski, Susan L Thibeault
{"title":"Gut-larynx axis and its contribution to laryngeal immunity.","authors":"Ran An, Elliott Xie, John Binns, Federico E Rey, Christina Kendziorski, Susan L Thibeault","doi":"10.1128/msystems.01044-25","DOIUrl":"https://doi.org/10.1128/msystems.01044-25","url":null,"abstract":"<p><p>The larynx is vital for swallowing, breathing, coughing, and voice production, supported by its unique microbial and immunological environment. We hypothesized the existence of a gut-larynx axis, where resident gut and laryngeal microbiota influence immune modulation in the larynx. To test this, conventionally raised, wild-type C57BL/6 J mice were treated with an oral antibiotic regimen to disrupt gut microbiota and compared with untreated controls. Antibiotic treatment significantly disrupted gut microbiota but left laryngeal microbiota largely unaffected. However, antibiotic-treated mice showed notable changes in laryngeal epithelial and immune cells, as well as fibroblasts. Differential gene expression analysis revealed alterations in pathways related to epithelial barrier integrity, immune signaling, and bacterial response. Gene regulatory network analysis identified significant changes in regulons Etv4(+), Irf3(+), Hltf(+), Mga(+), and Nfil3(+). Additionally, cell-cell communication, particularly immune-epithelial interactions, was altered, with integrin-mediated signaling emerging as a key pathway. These findings suggest that gut and laryngeal microbiota may synergistically modulate immune responses, highlighting the importance of gut-larynx interactions in respiratory immunity.</p><p><strong>Importance: </strong>This study investigates the gut-larynx axis, revealing how gut dysbiosis impacts immune responses in the larynx. Although laryngeal microbiota remained stable, significant immunological and cellular changes occurred following gut microbiota disruption. Transcriptomic alterations in epithelial integrity, immune signaling, and cell communication underscore the systemic impact of gut dysbiosis. The identification of integrin-mediated signaling as a key pathway in immune-epithelial interactions emphasizes the complexity of host-microbe dynamics. These findings suggest that gut health plays a critical role in shaping respiratory immunity, providing a foundation for future research into microbiota-driven immune modulation in the upper airway.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0104425"},"PeriodicalIF":4.6,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239225","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}
引用次数: 0
Harnessing machine learning for metagenomic data analysis: trends and applications. 利用机器学习进行宏基因组数据分析:趋势和应用。
IF 4.6 2区 生物学
mSystems Pub Date : 2025-10-07 DOI: 10.1128/msystems.01642-24
Shradha Sharma, Hari Priya Narahari, Karthik Raman
{"title":"Harnessing machine learning for metagenomic data analysis: trends and applications.","authors":"Shradha Sharma, Hari Priya Narahari, Karthik Raman","doi":"10.1128/msystems.01642-24","DOIUrl":"https://doi.org/10.1128/msystems.01642-24","url":null,"abstract":"<p><p>Metagenomic sequencing has revolutionized our understanding of microbial ecosystems by enabling high-resolution profiling of microbes across diverse environments. However, the resulting data are high-dimensional, sparse, and noisy, posing challenges for downstream data analysis. Machine learning (ML) has provided an arsenal of tools to extract meaningful insights from such large and complex data sets. This review surveys the existing state of ML applications in metagenomic data analysis, from traditional supervised and unsupervised learning to time-series modeling, transfer learning, and newer directions such as causal ML and generative models. We highlight certain key challenges and delve into important issues like model interpretability, emphasizing the importance of explainable AI (XAI). We also compare ML with mechanistic models, commenting on their relative advantages, disadvantages, and prospects for synergy. Finally, we preview future directions, such as the incorporation of multi-omics data, synthetic data generation, and Agentic AI systems, highlighting the increasingly prominent role that AI and ML will play in the future of microbiome science.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0164224"},"PeriodicalIF":4.6,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239307","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}
引用次数: 0
Characterizing Staphylococcus aureus genomic epidemiology with multilevel genome typing. 多水平基因组分型表征金黄色葡萄球菌基因组流行病学。
IF 4.6 2区 生物学
mSystems Pub Date : 2025-10-02 DOI: 10.1128/msystems.00935-25
Michael Payne, Liam Cheney, Sandeep Kaur, Genevieve McKew, Ruiting Lan
{"title":"Characterizing <i>Staphylococcus aureus</i> genomic epidemiology with multilevel genome typing.","authors":"Michael Payne, Liam Cheney, Sandeep Kaur, Genevieve McKew, Ruiting Lan","doi":"10.1128/msystems.00935-25","DOIUrl":"https://doi.org/10.1128/msystems.00935-25","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> is a major source of both hospital- and community-acquired infections worldwide. Advances in whole-genome sequencing (WGS) technologies have recently generated large volumes of <i>S. aureus</i> WGS data. The timely classification of <i>S. aureus</i> WGS data using genomic typing technologies has the potential to describe detailed genomic epidemiology at large and small scales. In this study, a multilevel genome typing (MGT) scheme, consisting of eight levels of multilocus sequence typing (MLST) schemes of increasing resolution, was developed for <i>S. aureus</i> and was used to analyze 50,481 publicly available genomes. The application of MGT to <i>S. aureus</i> epidemiology was shown in three case studies. First, the population structure of the globally disseminated MLST sequence type 8 (ST8) was described by MGT2 and compared with <i>Spa</i> typing. Second, MGT was used to characterize MLST ST8-USA300 isolates that colonized multiple body sites in the same patient. Finally, the MGT was used to describe the transmission of MLST ST239-SCC<i>mec</i> III throughout a single hospital. MGT STs were able to describe both isolates that had spread between wards and those that had colonized different reservoirs within a ward. <i>S. aureus</i> MGT describes <i>S. aureus</i> genomic epidemiology at multiple resolutions ranging from the global spread to local/individual scale using stable and standardized ST assignments. The <i>S. aureus</i> MGT database (https://mgtdb.unsw.edu.au/staphylococcus) is capable of tracking new and existing clones to facilitate the design of new strategies to reduce the global health burden of <i>S. aureus</i> infections.</p><p><strong>Importance: </strong><i>Staphylococcus aureus</i> causes both hospital- and community-acquired infections worldwide. Methicillin-resistant <i>S. aureus</i> is best known and has spread across the globe. Whole-genome sequencing (WGS) can type strains at the highest resolution. To enable best use of WGS data for surveillance of <i>S. aureus</i>, this study developed a multilevel genome typing (MGT) scheme that provides a publicly available, standardized, flexible, and easily communicated system to describe <i>S. aureus</i> strains. MGT has eight typing levels that provide progressively higher resolution. Each of these levels allows subtypes to be accurately identified and tracked. We show that MGT can be used to track well-known <i>S. aureus</i> strains at low resolution while simultaneously being able to track outbreaks in hospital settings at high resolution. The <i>S. aureus</i> MGT will facilitate the use of genomic data for surveillance without the need for bioinformatic expertise, improving efforts to control this important pathogen and prevent infections.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0093525"},"PeriodicalIF":4.6,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206706","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}
引用次数: 0
Genome-resolved insights into the bacterial phylum WOR-3: hydrogenotrophic metabolism and unique carbon fixation via archaeal form III RuBisCO. 基因组解析细菌门WOR-3:氢营养代谢和独特的碳固定通过古细菌形式III RuBisCO。
IF 4.6 2区 生物学
mSystems Pub Date : 2025-10-02 DOI: 10.1128/msystems.01178-25
Jianxiong Zeng, Wenzhe Hu, Licao Chang, Zhengshuang Hua, Geng Wu, Yun Fang, Guowei Wang, Chunqiao Xiao, Jun Liu
{"title":"Genome-resolved insights into the bacterial phylum WOR-3: hydrogenotrophic metabolism and unique carbon fixation via archaeal form III RuBisCO.","authors":"Jianxiong Zeng, Wenzhe Hu, Licao Chang, Zhengshuang Hua, Geng Wu, Yun Fang, Guowei Wang, Chunqiao Xiao, Jun Liu","doi":"10.1128/msystems.01178-25","DOIUrl":"https://doi.org/10.1128/msystems.01178-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The WOR-3 phylum is widely distributed in various environments, including hot springs, marine ecosystems, and hydrothermal vents, yet its ecological roles and metabolic capabilities remain poorly understood. In this study, we analyzed 181 medium- to high-quality metagenome-assembled genomes, including 59 newly reconstructed from environmental samples and 122 retrieved from public databases. Phylogenetic analyses resolved the WOR-3 lineage into four subgroups (subgroup 1-4). Metabolic reconstruction revealed significant divergence of the carbon, sulfur, nitrogen, and hydrogen metabolism pathways among the different subgroups. Subgroup 1 was characterized by fermentative metabolism involving formate and ethanol and uniquely exhibited potential for carbon fixation via the Calvin cycle, as indicated by the presence of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) gene. Notably, WOR-3 RuBisCO is phylogenetically affiliated with archaeal form III, although the carbon fixation pathway follows the canonical bacterial Calvin cycle-a feature of potential evolutionary significance. Subgroup 3 exhibits metabolic versatility, including genes for dissimilatory sulfate reduction, sulfur oxidation, partial denitrification, and fatty acid degradation. In addition, all subgroups harbored key components of hydrogen metabolism, including widespread NiFe hydrogenases, supporting H&lt;sub&gt;2&lt;/sub&gt;-dependent electron transfer and energy conservation. Within the WOR-3 lineage, the coexistence of two respiratory enzyme systems-the Rnf complex and the oxidative phosphorylation respiratory chain-indicates distinct anaerobic and aerobic metabolic lifestyles, respectively. Collectively, this study expands the genomic framework for the WOR-3 phylum and provides novel insights into the metabolic versatility and ecological functions of this previously uncharacterized lineage in biogeochemical cycles of carbon, nitrogen, and sulfur.IMPORTANCEThe WOR-3 phylum represents a widespread but poorly understood bacterial lineage inhabiting diverse various environments. By integrating 181 metagenome-assembled genomes, including 59 newly reconstructed, this study provides the most comprehensive genomic framework to date for WOR-3. Phylogenomic and metabolic reconstruction revealed four distinct subgroups with divergent capacities for carbon, sulfur, and nitrogen metabolism. Notably, subgroup 1 encodes a complete Calvin-Benson-Bassham cycle featuring an archaeal-type form III ribulose-1,5-bisphosphate carboxylase/oxygenase, suggesting an unusual evolutionary trajectory for carbon fixation in this lineage. Subgroup 3 exhibits versatile metabolic potential, including dissimilatory sulfur metabolism, partial denitrification, and fatty acid degradation, highlighting its possible roles in multiple biogeochemical processes. These findings not only expand the taxonomic and functional landscape of the WOR-3 phylum but also offer key insights into its ecological roles in global elemen","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0117825"},"PeriodicalIF":4.6,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206728","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}
引用次数: 0
Effects of matric vs osmotic potential changes on Variovorax beijingensis transcription. 基质电位和渗透电位变化对北京杂交蟹转录的影响。
IF 4.6 2区 生物学
mSystems Pub Date : 2025-10-02 DOI: 10.1128/msystems.00924-25
Jiwoo Kim, Bjorn Shockey, Kirsten S Hofmockel, Xiaodong Gao, Caroline A Masiello, Jonathan J Silberg
{"title":"Effects of matric vs osmotic potential changes on <i>Variovorax beijingensis</i> transcription.","authors":"Jiwoo Kim, Bjorn Shockey, Kirsten S Hofmockel, Xiaodong Gao, Caroline A Masiello, Jonathan J Silberg","doi":"10.1128/msystems.00924-25","DOIUrl":"https://doi.org/10.1128/msystems.00924-25","url":null,"abstract":"<p><p>Soil water potential, which regulates microbe-available water, is controlled by osmotic and matric potential, which both become more negative as soils dry. While both parameters can independently alter water potential, the genetic mechanisms underlying microbial responses to both are unknown, with potentially different mechanisms available for microbes to respond to these hydrological parameters. To explore microbial responses to matric vs osmotic potential shifts independently, we evaluated the growth and transcription of <i>Variovorax beijingensis</i> in soils and liquid cultures of varying water potential. We found that this microbe respires in dilute minimal medium (-240 ± 104 kPa), in liquid medium containing sucrose (-1,323 ± 21 kPa), and in matrices that span a similar pressure range (-183 ± 55 and -1,393 ± 200 kPa). We show that the global gene expression patterns vary significantly across these four conditions, even when the matric potential and osmotic pressure are set to similar values. However, 68% of the differentially expressed genes (DEGs) observed when transitioning osmotic pressure in liquid medium from -240 to -1,323 kPa were also observed when transitioning matric potential from -183 to -1,393 kPa. As osmotic and matric potential approached the plant wilting point, both presented DEGs implicated in amino acid, betaine, and energy metabolism, as well as plant-growth promotion. While a large overlap was observed in the <i>Variovorax</i> transcriptional response to shifts in both osmotic and matric potential, the responses were not identical, with matric potential shifts leading to 2.55-fold more genes exhibiting differential expression.IMPORTANCEIt remains hard to establish how changes in soil water properties affect microbial behaviors that regulate soil health, and the energy with which soil water is held is likely a holistic control on at least some of those microbial behaviors. This energy is controlled by parameters associated with soil salinity (osmotic potential) and texture (matric potential), which both alter bioavailable water by contributing to total soil water potential. To investigate how the transcription of a soil microbe changes when the microbe-available water is altered either by changing soil texture or by changing osmolyte concentrations, we varied osmotic and matric potential individually and performed RNA sequencing. We observe differences in the transcriptome across all conditions analyzed. However, a large set of genes presented similar gene expression changes when osmotic and matric potential approached the plant wilting point, suggesting that these transcriptional changes are independent of the mechanism that alters soil water potential.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0092425"},"PeriodicalIF":4.6,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206723","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}
引用次数: 0
Farmed oyster mortality follows consistent Vibrio community reorganization. 养殖牡蛎死亡率随弧菌群落重组而持续上升。
IF 4.6 2区 生物学
mSystems Pub Date : 2025-10-02 DOI: 10.1128/msystems.01078-25
Steph Smith, Mark Ciesielski, Thomas Clerkin, Tal Ben-Horin, Rachel T Noble
{"title":"Farmed oyster mortality follows consistent Vibrio community reorganization.","authors":"Steph Smith, Mark Ciesielski, Thomas Clerkin, Tal Ben-Horin, Rachel T Noble","doi":"10.1128/msystems.01078-25","DOIUrl":"https://doi.org/10.1128/msystems.01078-25","url":null,"abstract":"<p><p>Mortality events in marine bivalves cause substantial economic losses in aquaculture, yet the microbial dynamics underlying these events remain poorly characterized. Here, we investigated succession patterns in oyster-associated Vibrio communities during mortality events by sampling eastern oysters (<i>Crassostrea virginica</i>) at a North Carolina commercial farm that has experienced repeated, unexplained mortality events. Through whole-genome sequencing of 110 Vibrio isolates from 26 oysters sampled across mortality events in two consecutive years, we identified six conserved phylogenetic clades with distinct temporal associations. <i>Vibrio mediterranei</i> and a clade of resident vibrios consistently dominated the initial cultured community at the onset of mortality. However, <i>V. mediterranei</i> was absent as mortality progressed, coinciding with increased abundance of <i>V. harveyi</i>, <i>V. alginolyticus</i>, <i>V. diabolicus</i>, and <i>V. agarivorans</i>. Comparative genomic analysis revealed that initial isolates were enriched in pathways associated with host colonization and complex carbon metabolism, while isolates from elevated mortality showed enrichment in virulence mechanisms and adaptation to degraded host tissues. Temporal separation between genetically distinct clades suggests microbial competition shapes community assembly during mortality events that ultimately reached >85% mortality in both years. This predictable succession from commensal to potentially pathogenic Vibrio species provides genome-level insight into microbial community dynamics during oyster mortality. The consistent loss of <i>V. mediterranei</i> prior to severe mortality suggests this species could serve as a bioindicator for early warning systems to mitigate economic losses in shellfish aquaculture.IMPORTANCEMortality events in aquaculture systems represent complex host-microbe-environment interactions that challenge our ability to predict and prevent disease. By characterizing succession patterns in oyster-associated Vibrio communities at whole-genome resolution, we reveal a consistent transition from metabolically versatile species associated with healthy oysters to functionally distinct Vibrio taxa enriched in virulence factors and tissue degradation pathways as mortality progresses. This genome-level evidence for predictable community reorganization suggests that monitoring commensal Vibrio populations, particularly the presence or absence of <i>Vibrio mediterranei</i>, could provide earlier warning of impending disease compared to tracking only known pathogens. This shift in monitoring approach could advance aquaculture disease management while expanding our fundamental understanding of how microbial community transitions contribute to host health and disease progression.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0107825"},"PeriodicalIF":4.6,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206779","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}
引用次数: 0
Exo-metabolome profiling of soybean endophytes: a road map of antagonism against Fusarium oxysporum. 大豆内生菌的外显代谢组分析:对尖孢镰刀菌拮抗的路线图。
IF 4.6 2区 生物学
mSystems Pub Date : 2025-10-01 DOI: 10.1128/msystems.00927-25
H Tariq, C Viau, S Subramanian, A Geitmann, D L Smith
{"title":"Exo-metabolome profiling of soybean endophytes: a road map of antagonism against <i>Fusarium oxysporum</i>.","authors":"H Tariq, C Viau, S Subramanian, A Geitmann, D L Smith","doi":"10.1128/msystems.00927-25","DOIUrl":"https://doi.org/10.1128/msystems.00927-25","url":null,"abstract":"<p><p>Soybean is one of the world's most valuable agricultural crops. The phytopathogen <i>Fusarium oxysporum</i> compromises the growth of soybean and decreases its yield. Controlling this pathogen with fungicides is environmentally harmful. As with other species, soybean plants are associated with beneficial bacterial communities that contribute to plant health. Based on 16S rRNA sequencing, the present study identifies three important bacterial strains from this community: <i>Bacillus</i>-HT1, <i>Bacillus</i>-HT2, and <i>Bacillus</i>-HT3. Screening of these bacteria against <i>F. oxysporum</i> of soybean showed that <i>Bacillus-</i>HT1 and <i>Bacillus-</i>HT2 are antagonistic against this pathogen. The overall changes in fungal structure caused by biocontrol bacteria were visualized using scanning electron microscopy. An untargeted metabolomics approach based on liquid chromatography-tandem mass spectrometry was employed to uncover the bacterial secondary metabolites underlying this antagonistic activity. Based on MS2 fragmentation analysis and annotation, <i>Bacillus-</i>HT1 and <i>Bacillus</i>-HT2 potentially produce significant amounts of putative antifungal compounds, whereas <i>Bacillus</i>-HT3 lacks these. This absence of relevant metabolites correlates with this strain's inability to inhibit <i>F. oxysporum</i> fungal growth. Among the putative antifungal metabolites produced by <i>Bacillus-</i>HT1 and <i>Bacillus</i>-HT2 are bacillibactin and surfactin C. <i>Bacillus</i>-HT1 also produces significant amounts of fusidic acid and kynurenine, while <i>Bacillus-</i>HT2 produces significant amounts of putative antifungal fatty acids. These findings suggest that <i>Bacillus</i>-HT1 and <i>Bacillus-</i>HT2 have the potential to be developed into effective biocontrol agents, reducing chemical fungicides in crop cultivation, improving plant health and yield, thus contributing to the protection of biodiversity and soil health in the long term.</p><p><strong>Importance: </strong>Modern agricultural practices depend heavily on synthetic fertilizers and pesticides, which are major contributors to greenhouse gas emissions, groundwater pollution, and disruptions in agroecosystem dynamics. These challenges underscore the pressing need for sustainable alternatives that maintain crop productivity while minimizing environmental impact. Here, we investigate the use of antifungal-producing biocontrol agents as a microbial-based strategy to suppress pathogenic fungi in soybean cultivation. By harnessing the metabolic capabilities of beneficial microbes, this approach offers a promising path toward environmentally responsible crop protection, with implications for future food security and sustainable agricultural systems.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0092725"},"PeriodicalIF":4.6,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200211","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}
引用次数: 0
Metabolic response of a chemolithoautotrophic archaeon to carbon limitation. 一种化化石自养古菌对碳限制的代谢反应。
IF 4.6 2区 生物学
mSystems Pub Date : 2025-09-30 DOI: 10.1128/msystems.00732-25
Logan H Hodgskiss, Melina Kerou, Zhen-Hao Luo, Barbara Bayer, Andreas Maier, Wolfram Weckwerth, Thomas Nägele, Christa Schleper
{"title":"Metabolic response of a chemolithoautotrophic archaeon to carbon limitation.","authors":"Logan H Hodgskiss, Melina Kerou, Zhen-Hao Luo, Barbara Bayer, Andreas Maier, Wolfram Weckwerth, Thomas Nägele, Christa Schleper","doi":"10.1128/msystems.00732-25","DOIUrl":"https://doi.org/10.1128/msystems.00732-25","url":null,"abstract":"<p><p>The ubiquitously distributed ammonia-oxidizing archaea generate energy from ammonia and build cell mass from inorganic carbon sources, thereby contributing to both the global nitrogen and carbon cycles. However, little is known about the regulation of their predicted core carbon metabolism. A thermodynamic model for <i>Nitrososphaera viennensis</i> was developed to estimate the consumption of inorganic carbon in relation to ammonia consumed for energy and was tested experimentally by growing cells in carbon-limited and excess conditions. A combined proteomic and metabolomic approach to the experimental conditions revealed distinct metabolic adaptation depending on the amount of carbon supplied, either in a catalase or pyruvate background as a reactive oxygen species scavenger. Integration of protein and metabolite dynamics revealed a cellular strategy under carbon limitation to maintain a pool of amino acids and an upregulation of proteins necessary for translation initiation to stay primed for protein synthesis. The combination of modeling and functional genomics fills gaps in the understanding of the central metabolism and its regulation in a chemolithoautotrophic, ammonia-oxidizing archaeon, even in the absence of available genetic tools.IMPORTANCELittle is known about the regulation of carbon metabolism within ammonia-oxidizing archaea (AOA), a widespread clade that plays a critical role in the global nitrogen cycle while also fixing inorganic carbon. To address this missing knowledge, the soil AOA <i>Nitrososphaera viennensis</i> was subjected to various levels of inorganic carbon and analyzed via a systems biology approach to better understand how its core metabolism is regulated. The results demonstrate a strong dependence on the carbon fixation cycle and highlight key connection points between the core metabolic pathways. The analysis additionally revealed tight control on translational processes and elucidated unique cellular responses when the organism was exposed to either exogenous catalase or pyruvate to relieve oxidative stress from reactive oxygen species. The presented data highlight metabolic responses of <i>N. viennensis</i> and provide a better understanding of how the organism, and likely other AOA, respond to various environmental conditions.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0073225"},"PeriodicalIF":4.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191895","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}
引用次数: 0
Comprehensive characterization of gastrointestinal microbiota dysbiosis in patients with refractory Helicobacter pylori infection. 难治性幽门螺杆菌感染患者胃肠道菌群失调的综合表征。
IF 4.6 2区 生物学
mSystems Pub Date : 2025-09-30 DOI: 10.1128/msystems.01090-25
Yu Li, Xinbo Xu, Chao Peng, Yichen Liu, Nonghua Lu, Yin Zhu, Cong He
{"title":"Comprehensive characterization of gastrointestinal microbiota dysbiosis in patients with refractory <i>Helicobacter pylori</i> infection.","authors":"Yu Li, Xinbo Xu, Chao Peng, Yichen Liu, Nonghua Lu, Yin Zhu, Cong He","doi":"10.1128/msystems.01090-25","DOIUrl":"https://doi.org/10.1128/msystems.01090-25","url":null,"abstract":"<p><p>While repeated <i>Helicobacter pylori</i> eradication attempts are increasingly common due to antimicrobial resistance, the compounding effects of multiple antibiotic courses on gastrointestinal microbiota remain unquantified. We enrolled 32 treatment-naïve patients and 84 patients with refractory <i>H. pylori</i> infections, defined as failure of at least two prior eradication attempts. Antibiotic susceptibility testing was conducted for refractory <i>H. pylori</i> isolates to assess resistance patterns. Gastric mucosal biopsies and fecal samples were obtained for 16S rRNA gene sequencing. Antimicrobial susceptibility testing revealed resistance rates of 96.55% to metronidazole, 77.59% to clarithromycin, 56.90% to levofloxacin, 5.17% to rifampicin, 1.72% to tetracycline, and 0% to amoxicillin and furazolidone. The rates of dual drug and multidrug resistance were 27.59% and 55.17%, respectively. Refractory patients exhibited significant gastric microbiota restructuring, marked by reduced alpha diversity. The refractory group had higher concentrations of pathogens like <i>Pseudomonas</i> and <i>Burkholderia</i> and lower relative abundances of beneficial bacteria, including <i>Bifidobacterium</i>, <i>Blautia</i>, and <i>Roseburia</i>. Levofloxacin-resistant individuals exhibited an amplified abundance of pathogenic <i>Veillonella</i>. The gastric microbial diversity was higher in clarithromycin-resistant patients, with the enrichment of <i>Micromonospora</i>. Compared with the single-resistant group, pathogens, such as <i>Veillonella</i> and <i>Peptostreptococcus</i>, were increased in the multidrug-resistant group. We also observed perturbations of gut microbiota in refractory <i>H. pylori</i>-infected patients, with the predominance of <i>Streptococcus</i> and depletion of <i>Bacteroides</i>. Our findings establish that refractory <i>H. pylori</i> infection induces a disruption of gastrointestinal microbiota, highlighting the importance of optimizing first-line regimens to prevent retreatment cycles and the potential benefit of microbiota-modulating strategies in refractory <i>H. pylori</i> management.IMPORTANCEPrevious research has demonstrated that <i>H. pylori</i> eradication therapies can transiently alter gut microbiota. However, the long-term consequences of repeated antibiotic treatments in refractory infections remain unexplored. In this study, we link failed eradication attempts to persistent gastrointestinal dysbiosis, characterized by increased <i>Pseudomonas</i> and antibiotic-resistant <i>Veillonella</i>, alongside depletion of beneficial bacteria. In addition, we also demonstrate distinct gastric microbiota structure in patients with different antibiotic resistance patterns. Our findings showed distinct microbial dysbiosis after repeated eradication attempts, highlighting the need to explore microbiota-modulating approaches in future clinical trials.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0109025"},"PeriodicalIF":4.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191935","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}
引用次数: 0
Genome-scale metabolic modeling of Ruminiclostridium cellulolyticum: a microbial cell factory for valorization of lignocellulosic biomass. 纤维素分解反刍杆菌的基因组尺度代谢模型:木质纤维素生物质增殖的微生物细胞工厂。
IF 4.6 2区 生物学
mSystems Pub Date : 2025-09-30 DOI: 10.1128/msystems.00960-25
Idun Burgos, Ove Øyås, Stéphanie Perret, Henri-Pierre Fierobe, Daniel Machado
{"title":"Genome-scale metabolic modeling of <i>Ruminiclostridium cellulolyticum</i>: a microbial cell factory for valorization of lignocellulosic biomass.","authors":"Idun Burgos, Ove Øyås, Stéphanie Perret, Henri-Pierre Fierobe, Daniel Machado","doi":"10.1128/msystems.00960-25","DOIUrl":"https://doi.org/10.1128/msystems.00960-25","url":null,"abstract":"<p><p>The development of sustainable biotechnological processes requires a transition from the traditional fermentation of refined substrates toward the valorization of waste materials such as lignocellulosic biomass. Although these so-called recalcitrant substrates cannot be degraded by model industrial organisms, they can be degraded by microbial consortia through a process of anaerobic digestion, where different community members are able to break down polysaccharides of varied complexity. Among these microbes, <i>Ruminiclostridium cellulolyticum</i> stands out as a promising candidate for fermentation of lignocellulose due to its ability to degrade both cellulose and hemicellulose. In this work, we present an updated genome-scale metabolic model for <i>R. cellulolyticum</i> strain H10. The model was manually curated with experimental data, and the pathways for degradation of cellulose and hemicellulose (arabinoxylan and xyloglucan) were reconstructed and annotated with full detail. The model enables the simulation of the fermentation profile of lignocellulosic materials of various compositions, facilitating the use of this organism as a potential workhorse for sustainable biotechnology, and it provides a valuable template for the reconstruction and optimization of lignocellulose degradation pathways in related organisms.</p><p><strong>Importance: </strong>In this work, we present a manually curated genome-scale metabolic model for <i>Ruminiclostridium cellulolyticum</i>, one of the few species known to fully degrade cellulose and hemicellulose. The model was extensively curated with experimental data obtained from the literature, covering approximately 25 years of research on this organism. We use this model to simulate the fermentation of mixed lignocellulosic polysaccharides and observe a good agreement with experimental data. This organism is therefore a promising microbial cell factory for sustainable transformation of lignocellulosic residues into valuable industrial products.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0096025"},"PeriodicalIF":4.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191930","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}
引用次数: 0
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