mSystems最新文献

{"title":"Differential genome organization revealed by comparative topological analysis of <i>Mycobacterium tuberculosis</i> strains H37Rv and H37Ra.","authors":"Mohit Mishra, Ajay Arya, Md Zubbair Malik, Akanksha Mishra, Seyed E Hasnain, Rakesh Bhatnagar, Shandar Ahmad, Rupesh Chaturvedi","doi":"10.1128/msystems.00562-24","DOIUrl":"https://doi.org/10.1128/msystems.00562-24","url":null,"abstract":"<p><p>Recent studies have shown that three-dimensional architecture of bacterial chromatin plays an important role in gene expression regulation. However, genome topological organization in <i>Mycobacterium tuberculosis</i>, the etiologic agent of tuberculosis, remains unknown. On the other hand, the exact mechanism of differential pathogenesis in the canonical strains of <i>M. tuberculosis</i> H37Rv and H37Ra remains poorly understood in terms of their raw sequences. In this context, a detailed contact map from a Hi-C experiment is a candidate for what bridges the gap. Here, we present the first comprehensive report on genome-wide contact maps between regions of H37Rv and H37Ra genomes. We tracked differences between the genome architectures of H37Rv and H37Ra, which could possibly explain the virulence attenuation in H37Ra. We confirm the existence of a differential organization between the two strains most significantly a higher chromosome interaction domain (CID) size in the attenuated H37Ra strain. CID boundaries are also found enriched with highly expressed genes and with higher operon density in H37Rv. Furthermore, most of the differentially expressed PE/PPE genes were present near the CID boundaries in H37Rv and not in H37Ra. We also found a systemic reorganization of CIDs in both virulent H37Rv and avirulent H37Ra strains after hypoxia induction. Collectively, our study proposes a differential genomic topological pattern between H37Rv and H37Ra, which could explain the virulence attenuation in H37Ra.IMPORTANCEGenome organization studies using chromosome conformation capture techniques have proved to be useful in establishing a three-dimensional (3D) landscape of bacterial chromatin. The sequence-based studies failed to unveil the exact mechanism for virulence attenuation in one of the <i>Mycobacterium tuberculosis</i> strains H37Ra. Moreover, as of today, no study investigated the 3D structure of the <i>M. tuberculosis</i> genome and how 3D genome organization affects transcription in <i>M. tuberculosis</i>. We investigated the genome topology in virulent and attenuated strains of <i>M. tuberculosis</i> using Hi-C. Our study demonstrated that virulent and attenuated <i>M. tuberculosis</i> strains exhibit distinct topological features that correlate with higher gene expression of virulence genes in the virulent H37Rv strain.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0056224"},"PeriodicalIF":5.0,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795806","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":"Enzyme-constrained metabolic model of <i>Treponema pallidum</i> identified glycerol-3-phosphate dehydrogenase as an alternate electron sink.","authors":"Nabia Shahreen, Niaz Bahar Chowdhury, Edward Stone, Elle Knobbe, Rajib Saha","doi":"10.1128/msystems.01555-24","DOIUrl":"https://doi.org/10.1128/msystems.01555-24","url":null,"abstract":"<p><p><i>Treponema pallidum</i>, the causative agent of syphilis, poses a significant global health threat. Its strict reliance on host-derived nutrients and difficulties in <i>in vitro</i> cultivation have impeded detailed metabolic characterization. In this study, we present iTP251, the first genome-scale metabolic model of <i>T. pallidum</i>, reconstructed and extensively curated to capture its unique metabolic features. These refinements included the curation of key reactions such as pyrophosphate-dependent phosphorylation and pathways for nucleotide synthesis, amino acid synthesis, and cofactor metabolism. The model demonstrated high predictive accuracy, validated by a MEMOTE score of 92%. To further enhance its predictive capabilities, we developed ec-iTP251, an enzyme-constrained version of iTP251, incorporating enzyme turnover rate and molecular weight information for all reactions having gene-protein-reaction associations. Ec-iTP251 provides detailed insights into protein allocation across carbon sources, showing strong agreement with proteomics data (Pearson's correlation of 0.88) in the central carbon pathway. Moreover, the thermodynamic analysis revealed that lactate uptake serves as an additional ATP-generating strategy to utilize unused proteomes, albeit at the cost of reducing the driving force of the central carbon pathway by 27%. Subsequent analysis identified glycerol-3-phosphate dehydrogenase as an alternative electron sink, compensating for the absence of a conventional electron transport chain while maintaining cellular redox balance. These findings highlight <i>T. pallidum</i>'s metabolic adaptations for survival and redox balance in nutrient-limited, extracellular host environments, providing a foundation for future research into its unique bioenergetics.</p><p><strong>Importance: </strong>This study advances our understanding of <i>Treponema pallidum</i>, the syphilis-causing pathogen, through the reconstruction of iTP251, the first genome-scale metabolic model for this organism, and its enzyme-constrained version, ec-iTP251. The work addresses the challenges of studying <i>T. pallidum</i>, an extracellular, host-adapted pathogen, due to its strict dependence on host-derived nutrients and challenges in <i>in vitro</i> cultivation. Validated with strong agreement to proteomics data, the model demonstrates high predictive reliability. Key insights include unique metabolic adaptations such as lactate uptake for ATP production and alternative redox-balancing mechanisms. These findings provide a robust framework for future studies aimed at unraveling the pathogen's survival strategies and identifying potential metabolic vulnerabilities.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0155524"},"PeriodicalIF":5.0,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795819","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>Meta</i>Biome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities.","authors":"Javad Aminian-Dehkordi, Andrew Dickson, Amin Valiei, Mohammad R K Mofrad","doi":"10.1128/msystems.01652-24","DOIUrl":"https://doi.org/10.1128/msystems.01652-24","url":null,"abstract":"<p><p>Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies struggle to capture the dynamic metabolic interactions and spatiotemporal variations within MMCs. In this work, we present <i>Meta</i>Biome, a multiscale model integrating agent-based modeling (ABM), finite volume methods, and constraint-based models to explore the metabolic interactions within these communities. Integrating ABM allows for the detailed representation of individual microbial agents each governed by rules that dictate cell growth, division, and interactions with their surroundings. Through a layered approach-encompassing microenvironmental conditions, agent information, and metabolic pathways-we simulated different communities to showcase the potential of the model. Using our <i>in-silico</i> platform, we explored the dynamics and spatiotemporal patterns of MMCs in the proximal small intestine and the cecum, simulating the physiological conditions of the two gut regions. Our findings revealed how specific microbes adapt their metabolic processes based on substrate availability and local environmental conditions, shedding light on spatial metabolite regulation and informing targeted therapies for localized gut diseases. <i>Meta</i>Biome provides a detailed representation of microbial agents and their interactions, surpassing the limitations of traditional grid-based systems. This work marks a significant advancement in microbial ecology, as it offers new insights into predicting and analyzing microbial communities.IMPORTANCEOur study presents a novel multiscale model that combines agent-based modeling, finite volume methods, and genome-scale metabolic models to simulate the complex dynamics of mucosal microbial communities in the gut. This integrated approach allows us to capture spatial and temporal variations in microbial interactions and metabolism that are difficult to study experimentally. Key findings from our model include the following: (i) prediction of metabolic cross-feeding and spatial organization in multi-species communities, (ii) insights into how oxygen gradients and nutrient availability shape community composition in different gut regions, and (iii) identification of spatiallyregulated metabolic pathways and enzymes in <i>E. coli</i>. We believe this work represents a significant advance in computational modeling of microbial communities and provides new insights into the spatial regulation of gut microbiome metabolism. The multiscale modeling approach we have developed could be broadly applicable for studying other complex microbial ecosystems.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0165224"},"PeriodicalIF":5.0,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780567","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":"Novel selenoprotein neighborhoods suggest specialized biochemical processes.","authors":"Daniel H Haft, Igor Tolstoy","doi":"10.1128/msystems.01417-24","DOIUrl":"https://doi.org/10.1128/msystems.01417-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Prokaryotic genomes encode selenoproteins sparsely, roughly one protein per 5,000. Finding novel selenoprotein families can expose unknown biological processes that are enabled, or at least enhanced, by having a selenium atom replace a sulfur atom in some cysteine residues. Here, we report the discovery of 18 novel selenoprotein families or second selenocysteine sites in previously unrecognized extensions of protein translations. Most of these families had some confounding factors-too small a family, too few selenoproteins in the family, selenocysteine (U) too close to one end, a skew toward understudied or uncultured lineages, and consequently were missed previously. Discoveries were triggered by observations during the ongoing construction of protein family models for the National Center for Biotechnology Information's RefSeq and Prokaryotic Gene Annotation Pipeline or made by targeted searches for novel selenoproteins in the vicinity of known ones, rather than by any broadly applied genome mining method. Unrelated families TsoA, TsoB, TsoC, and TsoX are adjacent in &lt;i&gt;tso&lt;/i&gt; (three selenoprotein operon) loci in the bacterial phylum &lt;i&gt;Thermodesulfobacteriota&lt;/i&gt;. TrsS (third radical SAM selenoprotein) occurs strictly in the context of a molybdopterin-dependent aldehyde oxidoreductase. A short carboxy-terminal motif, U-X-X-stop (UXX-star), occurs in selenoproteins with various architectures, usually providing the second U in the protein. The multiple new selenocysteine insertion sites, selenoprotein families, and selenium-dependent operons we curated manually suggest that many more proteins and pathways remain to be discovered; once improved computational methods are applied comprehensively to the latest collections of microbial genomes and metagenomes, they may reveal surprising new biochemical processes.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Next-generation DNA sequencing and assembly of metagenome-assembled genomes (MAGs) for uncultured species of various microbiomes adds a vast \"dark matter\" of hard-to-decipher protein sequences. Selenoproteins, optimized by natural selection to encode selenocysteine where cysteine might have been encoded much more easily, carry a strong clue to their function-some specialized aspect of binding or catalysis. Operons with multiple adjacent, but otherwise unrelated, selenoproteins should provide even more vivid information. In this study, efforts in protein family construction and curation, aimed at improving the PGAP genome annotation pipeline, generated multiple novel selenoprotein-containing genomic contexts that may lead to the future characterization of several systems of proteins. Past observations suggest roles in the metabolic handling of trace elements (mercury, tungsten, arsenic, etc.) or of organic compounds refractory to simpler enzymatic pathways. In addition, the work significantly expands the truth set of validated selenoproteins, which should aid future, more automated genome mining effort","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0141724"},"PeriodicalIF":5.0,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143753619","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":"Honeybees fed D-galactose exhibit aging signs with changes in gut microbiota and metabolism.","authors":"Guanzhou Zhou, Jiabin Hu, Mengqi Xu, Yiyuan Li, Ruqi Chang, Jiaqi Zeng, Wanyue Dan, Lihua Peng, Zikai Wang, Gang Sun, Fei Pan, Yunsheng Yang","doi":"10.1128/msystems.01487-24","DOIUrl":"https://doi.org/10.1128/msystems.01487-24","url":null,"abstract":"<p><p>Honeybees (<i>Apis mellifera</i>), as social insects, exhibit complex social behaviors and cognitive functions. The short lifespan and stable gut microorganisms of honeybees provide certain availability as a rapid and high-flux animal model for aging research. This study explored the effect of D-galactose, a common aging inducer, on honeybees and investigated the associated effects and mechanisms, with particular focus on the potential protective role of sodium butyrate. Experimental cohorts were established as follows: conventional (CV) group, D-galactose-treated (DG) group, and sodium butyrate-treated (SB) group. The CV group was fed sucrose solution; the DG group was fed D-galactose solution; and the SB group was fed D-galactose and sodium butyrate solution. A comprehensive assessment was conducted on day 15 post-treatment, including survival analysis, starvation test, motor, learning and memory ability tests, malondialdehyde test, and Smurf test. Potential mechanisms through the microbiome and metabolome were investigated. Compared to the honeybees from the CV group, those in the DG group showed a shortened lifespan, a weaker energy storage ability, impaired motor, learning, and memory abilities, reduced weight, increased oxidation, and a disrupted gut barrier. These phenotypic changes were associated with microbial dysbiosis characterized by <i>Lactobacillus</i> enrichment and diminished butyrate levels. Notably, sodium butyrate supplementation extended the honeybees' lifespan and improved their learning and memory abilities damaged by D-galactose. Our findings establish honeybees as a valuable model system for aging research and highlight the crucial role of butyrate metabolism in senescence regulation.IMPORTANCEThis study presents a novel approach to investigating aging processes by establishing a D-galactose-induced aging model in honeybees. Our findings demonstrate that butyrate supplementation effectively attenuates D-galactose-induced senescence phenotypes, suggesting its potential as a therapeutic intervention for age-related decline. This research provides a unique model system for aging studies and highlights the significant role of butyrate in modulating senescence progression. The results contribute to our understanding of the molecular mechanisms underlying aging and offer new insights into potential anti-aging strategies.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0148724"},"PeriodicalIF":5.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730634","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":"Unveiling the role of phages in shaping the periodontal microbial ecosystem.","authors":"Fangfang Yao, Jiajun He, Raphael Nyaruaba, Hongping Wei, Yuhong Li","doi":"10.1128/msystems.00201-25","DOIUrl":"https://doi.org/10.1128/msystems.00201-25","url":null,"abstract":"<p><p>The oral microbiome comprises various species and plays a crucial role in maintaining the oral ecosystem and host health. Phages are an important component of the periodontal microbiome, yet our understanding of periodontal phages remains limited. Here, we investigated oral periodontal phages using various advanced bioinformatics tools based on genomes of key periodontitis pathogens. Prophages were found to encode various auxiliary genes that potentially enhance host survival and pathogenicity, including genes involved in carbohydrate metabolism, antibiotic resistance, and immune modulation. We observed cross-species transmission among prophages with a complex network of phage-bacteria interactions. Our findings suggest that prophages play a crucial role in shaping the periodontal microbial ecosystem, influencing microbial community dynamics and the progression of periodontitis.IMPORTANCEIn the context of periodontitis, the ecological dynamics of the microbiome are largely driven by interactions between bacteria and their phages. While the impact of prophages on regulating oral pathogens has been increasingly recognized, their role in modulating periodontal disease remains underexplored. This study reveals that prophages within key periodontitis pathogens contribute significantly to virulence factor dissemination, antibiotic resistance, and host metabolism. By influencing the metabolic capabilities and survival strategies of their bacterial hosts, prophages may act as critical regulators of microbial communities in the oral cavity. Understanding these prophage-mediated interactions is essential not only for unraveling the mechanisms of periodontal disease progression but also for developing innovative therapeutic approaches that target the microbial ecosystem at the genetic level. These insights emphasize the need for more comprehensive studies on the ecological risks posed by prophages in shaping microbial pathogenicity and resistance.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0020125"},"PeriodicalIF":5.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729523","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":"Rumen microbiota regulates IMF deposition in Xizang sheep by activating the <i>PPARγ</i> transcription factor: a rumen-muscle axis perspective.","authors":"Cheng Pan, Junru Pan, Yangzong Zhaxi, Haiyan Li, Zhenzhen Zhang, Feng Guan, Jiacuo Jinmei, Zhaxi Baijiu, Sangzhu Baima, Quzhu Yixi, Tianzeng Song, Wangsheng Zhao","doi":"10.1128/msystems.01557-24","DOIUrl":"https://doi.org/10.1128/msystems.01557-24","url":null,"abstract":"<p><p>The interaction between microbiota and muscle by the rumen-muscle axis and its impact on sheep meat flavor has received little attention. This study selected Xizang sheep under summer and autumn grazing conditions as models for different rumen bacteria and intramuscular fat (IMF) to attempt to address the current research gap. Specifically, the deposition characteristics of IMF and the expression of lipid metabolism genes in Xizang sheep were determined; 16S rDNA sequencing technology and gas chromatography were used to study the rumen microbiota and its metabolic products, short-chain fatty acids (SCFAs); RNA sequencing was used to identify the transcriptome of the rumen epithelium. Based on the above results, we proposed the hypothesis that the flavor of Xizang sheep meat is regulated by the microbiota-rumen-muscle axis. SCFAs produced in the rumen of Xizang sheep are absorbed by the rumen epithelium under the regulation of the solute carrier family genes (<i>SLC</i>). SCFAs can directly reach muscle tissue through the circulatory system and then activate the expression of the peroxisome proliferator-activated receptor Gamma (<i>PPARγ</i>) gene through the rumen-muscle axis. The expression of fat synthesis genes carnitine palmitoyltransferase II (<i>CPT2</i>), fatty acid synthase (<i>FAS</i>), patatin-like phospholipase domain-containing 2 (<i>PNPLA2</i>), and stearoyl-CoA desaturase 1 (<i>SCD1</i>) is correspondingly upregulated, promoting the deposition of IMF in Xizang sheep and thus affecting its flavor. This study introduces the theory of the microbiota-rumen-muscle axis into the research of the flavor of ruminant animal food, comprehensively elucidating the regulatory mechanism of the flavor of Xizang sheep meat.IMPORTANCEOur study employed a multi-omics approach to reveal how the rumen microbiota regulate muscle lipid metabolism in Xizang sheep through the activation of the <i>PPARγ</i> transcription factor. Importantly, by developing models of Xizang sheep with varying rumen microbial communities and muscle fatty acid profiles, we established the critical role of the microbiota-rumen-muscle axis in determining the flavor of Xizang sheep meat. This finding suggests that modulating the composition of the microbial community could serve as a strategy to improve the flavor of ruminant-derived food products. These insights provide valuable understanding of the complex interactions between rumen bacteria and mutton flavor, offering new approaches for research in this field.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0155724"},"PeriodicalIF":5.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730786","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":"Phages-bacteria interactions underlying the dynamics of polyhydroxyalkanoate-producing mixed microbial cultures via meta-omics study.","authors":"Jian Yao, Yan Zeng, Xia Hong, Meng Wang, Quan Zhang, Yating Chen, Min Gou, Zi-Yuan Xia, Yue-Qin Tang","doi":"10.1128/msystems.00200-25","DOIUrl":"https://doi.org/10.1128/msystems.00200-25","url":null,"abstract":"<p><p>The dynamics of the structure of polyhydroxyalkanoate-producing mixed microbial cultures (PHA-MMCs) during enrichment and maintenance is an unsolved problem. The effect of phages has been proposed as a cause of dynamic changes in community structure, but evidence is lacking. To address this question, five PHA-MMCs were enriched, and biological samples were sampled temporally to study the interactions between phage and bacterial members by combining metagenomics and metatranscriptomics. A total of 963 metagenome-assembled genomes (MAGs) and 4,294 phage operational taxonomic units (pOTUs) were assembled from bulk metagenomic data. The dynamic changes in the structure of phage and bacterial communities were remarkably consistent. Structural equation modeling analysis showed that phages could infect and lyse dominant species to vacate ecological niches for other species, resulting in a community succession state in which dominant species alternated. Seven key auxiliary metabolic genes (AMGs), <i>phaC</i>, <i>fadJ</i>, <i>acs</i>, <i>ackA</i>, <i>phbB</i>, <i>acdAB,</i> and <i>fadD</i>, potentially contributing to PHA synthesis were identified from phage sequences. Importantly, these AMGs were transcribed, indicating that they were in an active expression state. The meta-analysis provides the first catalog of phages in PHA-MMCs and the AMGs they carry, as well as how they affect the dynamic changes in bacterial communities. This study provides a reference for subsequent studies on understanding and regulating the microbial community structure of open microbial systems.IMPORTANCEThe synthesis of biodegradable plastic PHA from organic waste through mixed microbial cultures (PHA-MMCs), at extremely low cost, has the potential for expanded production. However, the dynamics of dominant species in PHA-MMCs are poorly understood. Our results demonstrate for the first time the impact of phages on the structure of bacterial communities in the PHA-MMCs. There are complex interactions between the PHA producers (e.g., <i>Azomonas</i>, <i>Paracoccus</i>, and <i>Thauera</i>) and phages (e.g., Casadabanvirus and unclassified Hendrixvirinae). Phage communities can regulate the activity and structure of bacterial communities. In addition, the AMGs related to PHA synthesis may hitchhike during phage-host infection cycles, enabling their dissemination across bacterial communities, and phages may act as a critical genetic reservoir for bacterial members, facilitating access to PHA synthesis-related functional traits. This study highlights the impact of phages on bacterial community structure, suggesting that phages have the potential to be used as a tool for better controlling the microbial community structure of PHA-MMCs.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0020025"},"PeriodicalIF":5.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730665","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":"Global dissemination of conjugative virulence plasmids co-harboring hypervirulence and multidrug resistance genes in <i>Klebsiella pneumoniae</i>.","authors":"Qi Xu, Ruanyang Sun, Xiaoxuan Liu, Heng Heng, Xuemei Yang, Miaomiao Xie, Chen Yang, Lianwei Ye, Edward Wai-Chi Chan, Rong Zhang, Sheng Chen","doi":"10.1128/msystems.01675-24","DOIUrl":"https://doi.org/10.1128/msystems.01675-24","url":null,"abstract":"<p><p>Carbapenem-resistant hypervirulent <i>Klebsiella pneumoniae</i> (CR-hv<i>Kp</i>) has led to a high mortality rate in the clinical setting and garnered significant attention in the clinical and scientific communities. It is still not clear which major mechanisms mediate the rapid evolution of hv<i>Kp</i> in clinical settings since the plasmid-encoding hypervirulence phenotype is considered non-conjugative. In this study, we revealed a conjugative plasmid, p16HN200-Vir, encoding virulence-associated <i>iuc</i> operon (<i>iucABCDiutA</i>) and resulting in a hypervirulent phenotype. <i>In silico</i> analysis of <i>Kp</i> strains from NCBI predicted a total of 94 p16HN200-Vir-like conjugative virulence plasmids. These sequences were identified in 19 sequence types (STs) of the host with significant geographical variations in distribution across countries and continents. Notably, ST11 was predominant in China, while ST147 and ST395 were prominent in the United Kingdom and Russia, respectively. These plasmids could be categorized into seven lineages, some of which formed distinct geographical clusters in China and the UK, while others exhibited a hybrid population. Importantly, most of the plasmids carried different carbapenemases, including <i>bl</i>a_NDM-1/5 (lineage 6 and 7), and <i>bla</i>_OXA-48/232 (lineage 2 and 5). Specifically, plasmids recovered from the United Kingdom and Russia were lineage-specific, with <i>bla</i>_NDM-1 present in lineage 6 and <i>bla</i>_NDM-5 in lineage 7. Our data suggest that this type of conjugative plasmids has spread around the world and contributed significantly to the current rapid evolution of CR-hv<i>Kp</i> in clinical settings. Further surveillance of these types of conjugative plasmids in clinical <i>Kp</i> is warranted.</p><p><strong>Importance: </strong>In this study, we found that the conjugative virulence plasmids containing carbapenem resistance genes could be conjugated to <i>Klebsiella</i> strains, enabling them to express antibiotic resistance and hypervirulence-associated phenotypes simultaneously. More importantly, we observed that the global dissemination of this type of multidrug resistance and hypervirulence conjugative plasmid is lineage specific. The UMAP projection revealed that the regional variations were correlated with ST types and serotypes, which poses a global threat of the CR-hv<i>Kp</i> infection worldwide.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0167524"},"PeriodicalIF":5.0,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700957","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":"ArtSymbioCyc, a metabolic network database collection dedicated to arthropod symbioses: a case study, the tripartite cooperation in <i>Sipha maydis</i>.","authors":"Patrice Baa-Puyoulet, Léo Gerlin, Nicolas Parisot, Sergio Peignier, François Renoz, Federica Calevro, Hubert Charles","doi":"10.1128/msystems.00140-25","DOIUrl":"https://doi.org/10.1128/msystems.00140-25","url":null,"abstract":"<p><p>Most arthropods live in close association with bacteria. The genomes of associated partners have co-evolved, creating situations of interdependence that are complex to decipher despite the availability of their complete sequences. We developed ArtSymbioCyc, a metabolism-oriented database collection gathering genomic resources for arthropods and their associated bacteria. ArtSymbioCyc uses the powerful tools of the BioCyc community to produce high-quality annotations and to analyze and compare metabolic networks on a genome-wide scale. We used ArtSymbioCyc to study the case of the tripartite symbiosis of the cereal aphid <i>Sipha maydis</i> focusing on amino acid and vitamin metabolisms, as these compounds are known to be important in this strictly phloemophagous insect. We showed that the metabolic pathways of the insect host and its two obligate bacterial associates are interdependent and specialized in the exploitation of Poaceae phloem, particularly for the biosynthesis of sulfur-containing amino acids and most vitamins. This demonstrates that ArtSymbioCyc does not only reveal the individual metabolic capacities of each partner and their respective contributions to the holobiont they constitute but also allows to predict the essential inputs that must come from host nutrition.IMPORTANCEThe evolution has driven the emergence of complex arthropod-microbe symbiotic systems, whose metabolic integration is difficult to unravel. With its user-friendly interface, ArtSymbioCyc (https://artsymbiocyc.cycadsys.org) eases and speeds up the analysis of metabolic networks by enabling precise inference of compound exchanges between associated partners and helps unveil the adaptive potential of arthropods in contexts such as conservation or agricultural control.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0014025"},"PeriodicalIF":5.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673651","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}