mSystems最新文献

{"title":"Global proteomic analysis of <i>Cryptococcus neoformans</i> clinical strains reveals significant differences between latent and lethal infection.","authors":"Jovany J Betancourt, Jason A McAlister, Jesenia M Perez, David B Meya, Stefani N Thomas, Jennifer Geddes-McAlister, Kirsten Nielsen","doi":"10.1128/msystems.00751-25","DOIUrl":"10.1128/msystems.00751-25","url":null,"abstract":"<p><p>To predict the outcomes of disseminated fungal disease, a deeper understanding of host-pathogen interactions at the site of infection is needed to identify targets for clinical intervention and diagnostic development. <i>Cryptococcus neoformans</i> is the causative agent of cryptococcosis, the largest infectious killer of individuals living with HIV. Cryptococcal infection begins in the lungs, and loss of immunological control leads to disseminated central nervous system disease and death. Using advanced mass spectrometry-based proteomic techniques, <i>in vivo</i> infection models, and patient-derived clinical strains, we explored the proteomic profiles of <i>C. neoformans</i> infections related to differences in strain virulence. Our findings reveal that non-lethal latent infection produces a proteomic response that differs significantly from the response caused by lethal infections, and that the proteomic profiles of typical and hypervirulent infections are markedly similar despite differences in time-to-death. Overall, the mouse pulmonary proteomic response in latent infection is defined by enrichment of proteins and pathways involved in extracellular matrix organization, cell adhesion, and structural changes, while the lethal infection is dominated by host defense, translation, and metabolic processes. These results provide clinically relevant information on how infections caused by different <i>Cryptococcus</i> strains may produce significantly different outcomes. We also identified abundant fungal proteins that could be future drug targets in latent and lethal cryptococcal infection.IMPORTANCE<i>Cryptococcus neoformans</i> is a fungal pathogen that causes substantial morbidity and mortality in immunocompromised individuals. The initial infection begins in the lungs after exposure to inhaled spores, after which local immune cells respond by either killing or containing the fungal cells. Immunosuppression weakens the immune system and allows fungal cells in the lungs to escape through the circulatory system and invade the central nervous system and cause fatal disease. However, differences between fungal strains influence the severity of disease manifestation. Our group has previously described genetic differences that contribute to strain-specific disease manifestations. In this study, we expanded our analysis to investigate the proteomic differences between strains of <i>C. neoformans</i> to identify candidate proteins and pathways that contribute to disease manifestation. We found that latent infection differs significantly from lethal disease from both the host and pathogen proteomic perspectives and identified several fungal protein targets for future study.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0075125"},"PeriodicalIF":4.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145138269","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":"Revealing the diversity of commensal corynebacteria from a single human skin site.","authors":"Reyme Herman, Sean Meaden, Michelle Rudden, Robert Cornmell, Holly N Wilkinson, Matthew J Hardman, Anthony J Wilkinson, Barry Murphy, Gavin H Thomas","doi":"10.1128/msystems.00459-25","DOIUrl":"https://doi.org/10.1128/msystems.00459-25","url":null,"abstract":"<p><p>Our understanding of the skin microbiome has significantly advanced with the rise of sequencing technologies. While <i>Corynebacterium</i> species are a major component of the human skin microbiome, research has largely centered on other prevalent genera like <i>Staphylococcus</i> and <i>Cutibacterium</i>. Prior to this study, complete genomes for skin-associated <i>Corynebacterium</i> were limited. For instance, only nine were available for the commonly identified species <i>Corynebacterium tuberculostearicum</i>. In this study, we explored <i>Corynebacterium</i> diversity from a single skin site, the axilla, using selective media to enrich for these bacteria. Long-read whole-genome sequencing and bioinformatic analysis of the enriched isolates provided unprecedented insight into the diversity of this genus at a single body site. The study yielded 215 closed genomes, comprising 30 distinct representative genomes following dereplication. These genomes span seven distinct species, including two new species provisionally named <i>Corynebacterium axilliensis</i> and <i>Corynebacterium jamesii</i>, as well as species not previously linked to the skin. Pangenome analysis of these isolates uncovered potential metabolic differences, antimicrobial resistance genes, novel biosynthetic gene clusters, prophages, and phage defense systems. This study represents the most detailed analysis to date of <i>Corynebacterium</i> from a single skin niche and highlights extensive variation even within a single host. Our culture-based Nanopore sequencing approach has expanded the number of publicly available skin <i>Corynebacterium</i> genomes, providing a valuable resource for future studies investigating the diversity and function of this important skin genus.</p><p><strong>Importance: </strong>This study uncovers the hidden diversity of <i>Corynebacterium</i>, an important yet often overlooked group of bacteria inhabiting human skin. Focusing on the underarm and using advanced sequencing techniques, we identified over 200 complete bacterial genomes. This collection includes species not previously known to reside on the skin, as well as two entirely new species, highlighting how little is currently known about this cutaneous genus. Most of these bacteria were isolated from a single individual, underscoring the vast microbial diversity that can exist within one person. By closely examining the corynebacterial community at a single site, we begin to uncover the complex relationships within a true microbial ecosystem. These findings deepen our understanding of the skin microbiome and provide a valuable resource for future research into how these microbes affect skin health, hygiene, and disease.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0045925"},"PeriodicalIF":4.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145138238","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":"Clade-specific adaptation and global spread of <i>Staphylococcus aureus</i> ST188 with emergence of a multidrug-resistant MRSA sublineage.","authors":"Deru Lei, Xu Dong, Ting Yang, Ye Jin, Wangxiao Zhou","doi":"10.1128/msystems.00848-25","DOIUrl":"https://doi.org/10.1128/msystems.00848-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Staphylococcus aureus&lt;/i&gt; sequence type (ST) 188 is a globally distributed lineage frequently associated with colonization and bloodstream infection in both humans and animals, yet its evolutionary dynamics and genomic adaptations remain poorly understood. In this study, we conducted a comprehensive genomic analysis of 808 ST188 isolates collected from 24 countries between 2004 and 2023. Phylogenetic reconstruction identified seven clades, with clades I and VII showing independent clonal expansions in China. Frequent cross-regional, international, and cross-host transmission events were observed, supporting the emergence of ST188 as a host-generalist lineage. A distinct methicillin-resistant &lt;i&gt;S. aureus&lt;/i&gt; subclade within clade VI likely emerged from a methicillin-susceptible ancestor through the acquisition of SCC&lt;i&gt;mec&lt;/i&gt; IVa. This event was accompanied by co-acquisition of resistance transposon Tn&lt;i&gt;6636&lt;/i&gt; and fluoroquinolone-resistance mutations, alongside truncation of the adhesion-related gene &lt;i&gt;sraP&lt;/i&gt; and loss of the serine protease genes &lt;i&gt;splDE&lt;/i&gt;. Preliminary phenotypic assays confirmed reduced adhesion and colonization in clade VI isolates. Comparative analysis revealed clade-specific patterns of mobile genetic elements, including vertical inheritance of SaPI1 and SaPI2 in the Chinese subclade of clade VII. In contrast, the novel prophage φST188-1, found exclusively in clade VII isolates, appeared to have been independently acquired. However, accessory genome variation across clades was limited, and the overall population structure was primarily shaped by core genome single-nucleotide polymorphisms. These findings provide a detailed view of the evolution and adaptation of ST188, underscore the role of clade-specific resistance and virulence patterns, and highlight the importance of continued genomic surveillance of this emerging lineage.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;The global emergence of &lt;i&gt;Staphylococcus aureus&lt;/i&gt; ST188 poses new challenges to public health due to its ability to infect both humans and animals and spread across regions and continents. Despite its growing prevalence, little has been known about its evolutionary history and dissemination patterns. In this study, we analyzed 808 ST188 genomes from 24 countries and found evidence of frequent cross-regional and cross-host transmission. Two major clades, showing clear clonal expansion, were dominated by isolates from China. We also identified a newly emerged methicillin-resistant subclade likely derived from a methicillin-susceptible ancestor, characterized by the acquisition of SCC&lt;i&gt;mec&lt;/i&gt; IVa, multiple resistance genes, and fluoroquinolone-resistance mutations. This subclade exhibited reduced adhesion and colonization capacity due to structural loss of key virulence genes. These findings provide new insights into the clade-specific adaptation and global spread of ST188 and underscore the need for genomic surveillance of multidrug-resistant &lt;i&gt;","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0084825"},"PeriodicalIF":4.6,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145131422","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":"Targeted assembly recovers high ammonia monooxygenase diversity in mudflat intertides.","authors":"Mengqi Wang, Wen Song, Jiayin Zhou, Mengzhi Ji, Kai Ma, Yan Li, Qichao Tu","doi":"10.1128/msystems.00620-25","DOIUrl":"https://doi.org/10.1128/msystems.00620-25","url":null,"abstract":"<p><p>Microbial communities in the Earth's biosphere mediate various biogeochemical cycling processes that are essential to maintain ecosystem multi-functioning and stability via the functional genes they carry. Although progress is being made, obtaining high-quality sequence data sets for microbial functional genes in complex environments remains challenging, both technically and in terms of computational resources required. In this study, using the <i>amo</i> gene family encoding ammonia monooxygenase as an example, we aimed to recover important microbial functional genes from shotgun metagenomes via targeted assembly. Comparing to conventional assembly approaches such as single-sample and multi-sample assembly, targeted assembly recovered much higher <i>amo</i> gene diversity while requiring substantially less computational resource and shorter running time. In addition, <i>amo</i> genes recovered by targeted assembly were found with fewer chimeras. Meanwhile, more <i>amo</i> operons were recovered. Not only were the commonly known <i>amoABC</i> subunits observed, but also the less commonly found subunits, like <i>amoX</i> and <i>amoE</i>. Notably, the archaeal <i>amoA</i> subunits recovered by targeted assembly represented the most \"super-clades\" for ammonia monooxygenase, including NT-α, NT-γ, NP-γ, NP-ζ, and NP-η, demonstrating the advantage of targeted assembly over conventional approaches. Comparable spatial patterns, such as taxa-area and distance-decay relationships, were also observed for the recovered <i>amo</i> assemblages. This study demonstrated an efficient route to recover microbial functional genes from shotgun metagenomes with minimal computational resource and running time.IMPORTANCEMicrobial communities play critical roles in the Earth's biosphere by mediating various biogeochemical cycles of essential elements and maintaining ecosystem stability and multi-functioning through the functional genes they carry. However, recovering the key functional genes from such complex communities remains challenging. Both advantages and limitations exist for different technologies. In this study, using the <i>amo</i> gene family as an example, we show that targeted assembly enables accurate and rapid recovery of high-quality <i>amo</i> sequences from shotgun metagenomes, consuming minimal computational resources and running time. Compared to conventional full-assembly approaches, the <i>amo</i> sequences recovered by targeted assembly are found with more operons, higher (phylo)genetic diversity, and fewer chimeras. This study provides an efficient alternative route for recovering microbial functional genes, particularly when computational resources are limited.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0062025"},"PeriodicalIF":4.6,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145131369","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":"Beyond microbial exposure and colonization: multisensory shaping of the gut microbiome.","authors":"Jake M Robinson, Martin F Breed","doi":"10.1128/msystems.01107-25","DOIUrl":"https://doi.org/10.1128/msystems.01107-25","url":null,"abstract":"<p><p>Microorganisms play a fundamental role in human health, contributing to digestion, immune regulation, and metabolic processes. While direct colonization by environmental microbes through ingestion, inhalation, and dermal contact has been documented, evidence suggests that multisensory interactions with nature-via visual, auditory, tactile, gustatory, and olfactory stimuli-also influence the gut microbiome through psychophysiological and immune-mediated pathways. Exposure to natural environments can regulate stress and immune responses, activate the parasympathetic nervous system, and modulate the hypothalamic-pituitary-adrenal and gut-brain axes, which in turn may alter gut microbiome composition and function. Furthermore, sensory interactions with nature may induce epigenetic changes that impact immune function and microbiome dynamics over time. Here, we review evidence for nature-based indirect shaping of the human microbiome (including multisensory and exposure-immunoregulation pathways) and suggest that after the early-life critical window of microbiome development (0-3 years), these indirect effects likely have a greater influence on gut microbiome dynamics than direct colonization by environmental microbiota (e.g., ingested directly from the air). However, this concept remains to be comprehensively tested. Therefore, understanding the relative contributions of direct microbial colonization versus indirect effects-such as multisensory stimulation and immune modulation-demands more integrated, transdisciplinary research. Integrating these insights into public health strategies, urban design, and nature-based interventions could promote microbiome eubiosis, ultimately improving human (and non-human animal) well-being in an era of increasing environmental and health challenges.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0110725"},"PeriodicalIF":4.6,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145131460","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":"Ecophysiology and niche differentiation of three genera of polyphosphate-accumulating bacteria in a full-scale wastewater treatment plant.","authors":"Z Kondrotaite, J Petersen, C Singleton, M Peces, F Petriglieri, T B N Jensen, M Sereika, A O H Daugberg, M Wagner, M K D Dueholm, P H Nielsen","doi":"10.1128/msystems.00322-25","DOIUrl":"10.1128/msystems.00322-25","url":null,"abstract":"<p><p>Polyphosphate-accumulating organisms (PAOs) are the main bacteria responsible for phosphorus removal and recovery in full-scale wastewater treatment plants (WWTPs). They encompass members of the genera <i>Candidatus</i> Accumulibacter, <i>Azonexus</i> (formerly <i>Dechloromonas</i>), and <i>Candidatus</i> Phosphoribacter (formerly <i>Tetrasphaera</i>), with most studies focusing on <i>Ca</i>. Accumulibacter, primarily using lab-scale enrichment cultures. Although members from the three genera often co-exist in full-scale WWTPs, the metabolic capabilities and traits that determine the niche differentiation of the specific species are still unknown. We retrieved 214 high-quality metagenome-assembled genomes from a full-scale plant with phosphorus removal and examined the polyphosphate-related metabolic pathways using genome-resolved metatranscriptomics in the different process tanks <i>in situ</i> and by using short-term incubations <i>ex situ</i>. We observed the co-existence of nine uncultured PAO species from the three genera with clear niche differentiation in the utilization of different carbon sources and involvement in the denitrification process. Additionally, we observed several physiological differences among species of the same genus, indicating variations in niche specialization. This suggests that biological P removal and other processes in full-scale WWTPs are carried out by a complex and diverse PAO community that together ensures stable plant performance.IMPORTANCEThe current understanding of the ecology and physiology of polyphosphate-accumulating organisms (PAOs) is mostly based on <i>Candidatus</i> Accumulibacter, primarily studied in enriched lab-scale studies. Recent taxonomic reclassification revealed that the most studied <i>Ca</i>. Accumulibacter species are either not present or present in low abundance in full-scale wastewater treatment plants (WWTPs). This raises concerns that knowledge from lab-scale studies may not apply to species in full-scale plants. Additionally, the indication of a distinct PAO physiology in <i>Candidatus</i> Phosphoribacter compared to <i>Ca</i>. Accumulibacter and the other abundant PAO <i>Ca</i>. Azonexus poses further questions about the accuracy of the current PAO model. Here, we show that in full-scale plant species from <i>Ca</i>. Accumulibacter, <i>Ca</i>. Azonexus, and <i>Ca</i>. Phosphoribacter always co-exist, and they have distinct niche separations in terms of carbon source utilization and the use of electron acceptors. This co-existence and metabolic diversity indicate that a complex microbial community is crucial for efficient phosphorus removal in full-scale WWTPs.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0032225"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855713","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":"Repeated measures of decaying wood reveal the success and influence of fungal wood endophytes.","authors":"Yanmei Zhang, Zhuobing Peng, Zewei Song, Jonathan S Schilling","doi":"10.1128/msystems.00382-25","DOIUrl":"10.1128/msystems.00382-25","url":null,"abstract":"<p><p>Predicting wood decomposition is challenging due to complex successional dynamics among decomposers that colonize and defend wood territory. This starts with saprotrophic fungi that reside latently in healthy wood until trees senesce, but these \"endophytes\" are rarely considered an endogenous wood trait that might improve predictions for decomposition rates or fates. Here, we used repeated measures to track the decomposition of paper birch (<i>Betula papyrifera</i>) and red pine (<i>Pinus resinosa</i>), assessing wood properties and microbial succession over 5 years in a northern forest (Minnesota, USA). We compared fungi and bacteria present in sound wood (endophytes) versus those arriving as external colonizers, and we used relevant treatments to vary accessibility for colonizers (ground contact versus aboveground; bark off versus bark on). Over 5 years, accessibility treatments had a significant effect on decay rates and fungal community succession. Wood rot type was unanimously white rot (lignin-degrading fungi), but fungal dominance was treatment-specific. Most dominant fungi could be traced to operational taxonomic units (OTUs) present as endophytes in sound wood, suggesting that treatments affected endophyte competition more than external colonizer success, even in ground contact. Although fungal communities lost diversity (Shannon index) as certain taxa became dominant, bacterial communities converged irrespective of treatment, without notable co-occurrence with fungi and without losing diversity, suggesting a decoupled dynamic. The results imply a strategic benefit for saprotrophic fungi to colonize trees as endophytes, and they support including fungal endophytes along with predictors of their competitive success as \"plant\" traits to improve predictive models.IMPORTANCEEstablishing this persistence and influence for endophytic saprotrophs has not been possible without repeated measures in a long-term study. We believe our findings are significant for two key reasons. First, they link community succession to a \"trait\" in wood that may be more predictable-governed by the living tree as the \"gate-keeper\"-compared with predicting assembly history for external colonizers. Second, they highlight a new avenue toward developing a predictable trait for wood decomposition that could improve Earth Systems modeling, which has historically been challenged in predicting carbon sequestered/released by wood, where most of Earth's aboveground biotic carbon resides.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0038225"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Lactobacillus crispatus</i>-derived nCEV vesicles promote cutaneous wound healing and inhibit HPV16 infection.","authors":"Ke Peng, Xiaoting Chen, Yulin Zhang, Lina Liu, Qingye Huang, Shujuan Du, Caixia Zhu, Yuyan Wang, Fang Wei, Shujun Gao, Qiliang Cai","doi":"10.1128/msystems.00683-25","DOIUrl":"10.1128/msystems.00683-25","url":null,"abstract":"<p><p>Cervical cancer (CC) is a common gynecological malignancy, primarily associated with persistent infection by high-risk human papillomavirus (HPV). The vaginal microbiota, dominated by <i>Lactobacillus</i> species, plays a critical role in maintaining a healthy vaginocervical microenvironment. However, the influence of <i>Lactobacillus</i> on the pathogenesis and treatment of CC remains underexplored. Here, we report that the optimized 60-80 nm size dominant of extracellular vesicles from various <i>Lactobacillus</i> species (nLEVs) significantly affects cutaneous wound healing and HPV infection. Specifically, nCEVs <i>from Lactobacillus crispatus</i> demonstrate superior efficacy compared to nIEVs from <i>Lactobacillus iners</i> in promoting cell migration, angiogenesis, and wound healing via macrophage M2 polarization and blocking intravaginal HPV16 infection. Moreover, metabolic profiling revealed that D-lactate may be key to the functions of nCEVs. Altogether, our findings uncover a novel nCEV/D-lactate-mediated mechanism that promotes homeostasis and offers potential new approaches for the prevention and treatment of CC.</p><p><strong>Importance: </strong>This study identifies <i>Lactobacillus crispatus</i>-derived vesicles (nCEVs) as crucial for cervicovaginal homeostasis, functioning through promoting wound healing via macrophage polarization and blocking HPV infection, and delivering D-lactate-a key bioactive component. These insights advance microbiome-based female healthcare interventions.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0068325"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics analysis reveals the genetic basis for rapid CO₂ utilization in the acetogenic bacterium <i>Sporomusa sphaeroides</i> KIAC.","authors":"Jiyun Bae, Donghwi Lee, Chanho Park, Hyunwoo Jung, Minkyu Huh, Seulgi Kang, Ye Jin Gwak, Hyo Jung Lee, You-Jung Jung, Hyeokjun Yoon, Moonsuk Hur, Sangrak Jin, Suhyung Cho, Byung-Kwan Cho","doi":"10.1128/msystems.00451-25","DOIUrl":"10.1128/msystems.00451-25","url":null,"abstract":"<p><p><i>Sporomusa sphaeroides</i> KIAC is a novel acetogen isolated from cattle feces that exhibits rapid CO₂ utilization. To investigate the molecular basis of this phenotype, we performed a comprehensive multi-omics analysis, including Genome-seq, RNA-seq, dRNA-seq, and Term-seq, to map its transcriptome architecture. We identified 2,158 transcription start sites and 2,275 transcript 3' ends, enabling high-resolution reconstruction of the transcriptional landscape and associated regulatory features. This analysis uncovered key <i>cis</i>-regulatory elements and an expanded regulatory role for the alternative sigma factor SigH in controlling acetogenesis-related genes. Notably, KIAC harbors nine functionally diverse hydrogenases-a greater diversity than observed in other acetogens-likely contributing to its rapid CO₂ utilization. Heterologous expression of KIAC-derived hydrogenases in <i>Eubacterium limosum</i> led to doubled H₂ and CO₂ consumption rates, increased growth rates, and notably, the first reported butyrate production under energy-limited H₂/CO₂ conditions. These improvements stem from enhanced H₂ oxidation, which supplies additional reducing equivalents for growth and biochemical production. Our findings provide critical insights into the genetic basis for rapid autotrophic growth in acetogens. The discovery of the expanded regulatory role of SigH and the energetic advantages of diverse hydrogenases offers new strategies for enhanced CO₂ bioconversion of acetogens.IMPORTANCEAcetogens offer a promising solution for sustainable CO₂ bioconversion into multicarbon biochemicals through the Wood-Ljungdahl pathway, the most energy-efficient carbon fixation route known in nature. However, an incomplete understanding of their metabolism and regulatory systems has limited metabolic engineering efforts to achieve superior CO₂ fixation efficiency. In this study, we investigated <i>Sporomusa sphaeroides</i> KIAC, a newly isolated acetogen with rapid CO₂ utilization, to uncover the molecular mechanisms underlying its superior performance. By revealing an expanded regulatory role for an alternative sigma factor and a highly diverse set of hydrogenases, our findings provide a foundation for engineering acetogens with enhanced CO₂ conversion efficiency under energy-limited conditions.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0045125"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12456013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789589","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":"Metabolic potentials of the gut microbes in Antarctic krill (<i>Euphausia superba</i>).","authors":"ZhanFei Wei, Lihui Meng, Sheng Du, Fang Wang, Aijun Jiang, Rui Lu, Kaiqiang Liu, Xinliang Wang, Qingchang Xu, Xiuxia Mu, Liang Meng, ChangWei Shao","doi":"10.1128/msystems.00377-25","DOIUrl":"10.1128/msystems.00377-25","url":null,"abstract":"<p><p>Antarctic krill (<i>Euphausia superba</i>) plays crucial roles in the Southern Ocean biological system, yet the ecological functions of their gut microbiota remain poorly understood. The study investigated the composition and diversity of the gut microbiota in <i>E. superba</i> using 16S rRNA gene sequencing, revealing a highly diverse and tissue-specific microbiota. Further investigation through direct metagenomics and culture-enriched metagenomics identified 12 metagenome-assembled genomes (MAGs), which might represent novel species based on their phylogenetic positions, average nucleotide identity (ANI), average amino acid identity (AAI), and relative evolutionary divergence (RED) values. These MAGs were grouped into two distinct clusters according to their completeness of metabolic modules. Although MAGs in cluster 2 showed lower read relative abundance compared to those in cluster 1, they exhibited a greater number of amino acid synthesis modules. The synthesis of glutathione, heme, ubiquinone, vitamins, and betaine by MAGs suggested potential roles in enhancing survival of <i>E. superba</i> in extreme environment. Moreover, the functional genes in the 12 MAGs had abundant transcripts indicating they exhibited high metabolic activity in the <i>E. superba</i> gut microbiota. These findings shed new light on the metabolic contributions of gut microbiota in <i>E. superba</i>.IMPORTANCEThis study provided a comprehensive characterization of the gut microbiome of <i>Euphausia superba</i>, revealing its diverse and functionally distinct microbial community. Furthermore, 12 metagenome-assembled genomes (MAGs) representing novel species were successfully identified. The metabolic analysis demonstrated that these microbes contribute to host nutrient acquisition by synthesizing essential amino acids and vitamins. The identification of antioxidant and osmoregulatory compound synthesis modules suggested that gut microbiota might facilitate the survival of <i>E. superba</i> in the harsh Antarctic environment. Those findings elucidated the host-microbe interactions in polar marine ecosystems and provided new insights into microbial contributions to host nutrient cycling and environmental adaptation in the Southern Ocean.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0037725"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12456004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144794937","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}