mSystems最新文献

{"title":"A novel robust network construction and analysis workflow for mining infant microbiota relationships.","authors":"Wei Jiang, Yue Zhai, Dongbo Chen, Qinghua Yu","doi":"10.1128/msystems.01570-24","DOIUrl":"10.1128/msystems.01570-24","url":null,"abstract":"<p><p>The gut microbiota plays a crucial role in infant health, with its development during the first 1,000 days influencing health outcomes. Understanding the relationships within the microbiota is essential to linking its maturation process to these outcomes. Several network-based methods have been developed to analyze the developing patterns of infant microbiota, but evaluating the reliability and effectiveness of these approaches remains a challenge. In this study, we created a test data pool using public infant microbiome data sets to assess the performance of four different network-based methods, employing repeated sampling strategies. We found that our proposed Probability-Based Co-Detection Model (PBCDM) demonstrated the best stability and robustness, particularly in network attributes such as node counts, average links per node, and the positive-to-negative link (P/N) ratios. Using the PBCDM, we constructed microbial co-existence networks for infants at various ages, identifying core genera networks through a novel network shearing method. Analysis revealed that core genera were more similar between adjacent age ranges, with increasing competitive relationships among microbiota as the infant microbiome matured. In conclusion, the PBCDM-based networks reflect known features of infant microbiota and offer a promising approach for investigating microbial relationships. This methodology could also be applied to future studies of genomic, metabolic, and proteomic data.</p><p><strong>Importance: </strong>As a research method and strategy, network analysis holds great potential for mining the relationships of bacteria. However, consistency and solid workflows to construct and evaluate the process of network analysis are lacking. Here, we provide a solid workflow to evaluate the performance of different microbial networks, and a novel probability-based co-existence network construction method used to decipher infant microbiota relationships. Besides, a network shearing strategy based on percolation theory is applied to find the core genera and connections in microbial networks at different age ranges. And the PBCDM method and the network shearing workflow hold potential for mining microbiota relationships, even possibly for the future deciphering of genome, metabolite, and protein data.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0157024"},"PeriodicalIF":5.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914975","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":"System-based insights into parasitological and clinical treatment failure in Chagas disease.","authors":"Luis Ernst, Giovana C Macedo, Laura-Isobel McCall","doi":"10.1128/msystems.00038-24","DOIUrl":"10.1128/msystems.00038-24","url":null,"abstract":"<p><p>Infectious disease treatment success requires symptom resolution (clinical treatment success), which often but not always involves pathogen clearance. Both of these treatment goals face disease-specific and general challenges. In this review, we summarize the current state of knowledge in mechanisms of clinical and parasitological treatment failure in the context of Chagas disease, a neglected tropical disease causing cardiac and gastrointestinal symptoms. Parasite drug resistance and persistence, drug pharmacokinetics and dynamics, as well as persistently altered host immune responses and tissue damage are the most common reasons for Chagas disease treatment failure. We discuss the therapeutics that failed before regulatory approval, limitations of current therapeutic options and new treatment strategies to overcome persistent parasites, inflammatory responses, and metabolic alterations. Large-scale omics analyses were critical in generating these insights and will continue to play a prominent role in addressing the challenges still facing Chagas disease drug treatment.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0003824"},"PeriodicalIF":5.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951968","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":"An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the <i>Saccharomyces</i> genus.","authors":"Artai R Moimenta, Diego Troitiño-Jordedo, David Henriques, Alba Contreras-Ruíz, Romain Minebois, Miguel Morard, Eladio Barrio, Amparo Querol, Eva Balsa-Canto","doi":"10.1128/msystems.01615-24","DOIUrl":"10.1128/msystems.01615-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;During batch fermentation, a variety of compounds are synthesized, as microorganisms undergo distinct growth phases: lag, exponential, growth-no-growth transition, stationary, and decay. A detailed understanding of the metabolic pathways involved in these phases is crucial for optimizing the production of target compounds. Dynamic flux balance analysis (dFBA) offers insight into the dynamics of metabolic pathways. However, explaining secondary metabolism remains a challenge. A multiphase and multi-objective dFBA scheme (MPMO model) has been proposed for this purpose. However, its formulation is discontinuous, changing from phase to phase; its accuracy in predicting intracellular fluxes is hampered by the lack of a mechanistic link between phases; and its simulation requires considerable computational effort. To address these limitations, we combine a novel model with a genome-scale model to predict the distribution of intracellular fluxes throughout batch fermentation. This integrated multiphase continuous model (IMC) has a unique formulation over time, and it incorporates empirical regulatory descriptions to automatically identify phase transitions and incorporates the hypotheses that yeasts might vary their cellular objective over time to adapt to the changing environment. We validated the predictive capacity of the IMC model by comparing its predictions with intracellular metabolomics data for &lt;i&gt;Saccharomyces uvarum&lt;/i&gt; during batch fermentation. The model aligns well with the data, confirming its predictive capabilities. Notably, the IMC model accurately predicts trehalose accumulation, which was enforced in the MPMO model. We further demonstrate the generalizability of the IMC model, explaining the dynamics of primary and secondary metabolism of three &lt;i&gt;Saccharomyces&lt;/i&gt; species. The model provides biological insights consistent with the literature and metabolomics data, establishing it as a valuable tool for exploring the dynamics of novel fermentation processes.IMPORTANCEThis work presents an integrated multiphase continuous dynamic genome-scale model (IMC model) for batch fermentation, a crucial process widely used in industry to produce biofuels, enzymes, pharmaceuticals, and food products or ingredients. The IMC model integrates a continuous kinetic model with a genome-scale model to address the critical limitations of existing dynamic flux balance analysis schemes, such as the difficulty of explaining secondary metabolism, the lack of mechanistic links between growth phases, or the high computational demands. The model also introduces the hypothesis that cells adapt the FBA objective over time. The IMC improves the accuracy of intracellular flux predictions and simplifies the implementation process with a unique dFBA formulation over time. Its ability to predict both primary and secondary metabolism dynamics in different &lt;i&gt;Saccharomyces&lt;/i&gt; species underscores its versatility and robustness. Furthermore, its alignment with emp","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0161524"},"PeriodicalIF":5.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11838008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008525","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":"Tracking clonal and plasmid transmission in colistin- and carbapenem-resistant <i>Klebsiella pneumoniae</i>.","authors":"Ifeoluwa Akintayo, Marko Siroglavic, Daria Frolova, Mabel Budia Silva, Hajo Grundmann, Zamin Iqbal, Ana Budimir, Sandra Reuter","doi":"10.1128/msystems.01128-24","DOIUrl":"10.1128/msystems.01128-24","url":null,"abstract":"<p><p>The surveillance of mobile genetic elements facilitating the spread of antimicrobial resistance genes has been challenging. Here, we tracked both clonal and plasmid transmission in colistin- and carbapenem-resistant <i>Klebsiella pneumoniae</i> using short- and long-read sequencing technologies. We observed three clonal transmissions, all containing Incompatibility group (Inc) L plasmids and New Delhi metallo-beta-lactamase <i>bla</i>_NDM-1, although not co-located on the same plasmid. One IncL-<i>bla</i>_NDM-1 plasmid had been transferred between sequence type (ST) 392 and ST15, and the promiscuous IncL-<i>bla</i>_OXA-48 plasmid was likely shared between a singleton and a clonal transmission of ST392. Plasmids within clonal outbreaks and between clusters and STs had 0-2 single nucleotide polymorphism (SNP) differences, showing high stability upon transfer to same or different STs. The simplest explanation, without a comprehensive analysis with long-read sequencing, would be the spread of a single common IncL-<i>bla</i>_NDM-1 plasmid. However, here, we report <i>bla</i>_NDM-1 in five different plasmids, emphasizing the need to investigate plasmid-mediated transmission for effective containment of outbreaks.IMPORTANCEAntimicrobial resistance occupies a central stage in global public health emergencies. Recently, efforts to track the genetic elements that facilitate the spread of resistance genes in plasmids outbreaks, utilizing short-read sequencing technologies, have been described. However, incomplete plasmid reconstruction from short-read sequencing data hinders full knowledge about plasmid structure, which makes the exploration very challenging. In this study, we used both short- and long-read sequencing in clinical <i>Klebsiella pneumoniae</i> from University Hospital Centre Zagreb, Croatia, which was resistant to both last-resort antibiotics colistin and carbapenem. Our results show complex transmission networks and sharing of plasmids, emphasizing multiple transmissions of plasmids harboring carbapenem and/or colistin resistance genes between and within <i>K. pneumoniae</i> clones. Only full-length sequencing plus a novel way of determining plasmid clusters resulted in the complete picture, showing how future active monitoring of plasmids as a vital tool for infection prevention and control could be implemented.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0112824"},"PeriodicalIF":5.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834398/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142951981","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":"Induction of conidial traps in the nematode-trapping fungus <i>Drechslerella dactyloides</i> by soil microbes.","authors":"Ling Zhang, Tao Zhang, Yan-Rui Xu, Jia-Mei Sun, Xue-Rong Pan, Kun-Ze Gu, Ke-Qin Zhang, Zhi-Gang Zhang, Lian-Ming Liang","doi":"10.1128/msystems.01291-24","DOIUrl":"https://doi.org/10.1128/msystems.01291-24","url":null,"abstract":"<p><p>Nematode-trapping fungi, renowned for their specialized predatory structures that ensnare nematodes, offer a promising biological approach to managing plant-parasitic nematodes. However, the efficacy of these fungi is frequently hampered by biotic and abiotic factors within the soil, which can significantly impede fungal germination (fungistasis). To counteract these environmental challenges, certain nematode-trapping fungi have evolved to produce traps from their conidia, referred to as conidial traps. This adaptation allows them to bypass the inhibitory effects of their surroundings, enhancing their predatory capabilities. In this study, we explored how soil affects conidial trap formation in <i>Drechslerella dactyloides</i>. Our findings revealed that <i>Acinetobacter</i> spp. and <i>Pantoea</i> spp. present in soil extracts play pivotal roles in triggering the development of these traps. Using metagenomic sequencing, we mapped the shifts in bacterial communities and their relative abundances before and after incubation for up to 24 hours to optimize soil induction effects. This analysis highlighted the enrichment of specific functional genes in soil microbes and provided insights into the mechanisms driving conidial trap formation, based on changes in soil characteristics. Furthermore, through bacterial isolation procedures, we successfully cultured and characterized the bacteria responsible for this phenomenon, confirming their potent ability to stimulate the production of conidial traps in nematode-trapping fungi. This study not only underscores the critical role of bacterial diversity in modulating the life cycle transitions of nematode-trapping fungi but also sets the stage for the development of more effective and sustainable strategies to harness these fungi in the battle against pathogenic nematodes.</p><p><strong>Importance: </strong>Predatory nematode-trapping fungi are important microbial antagonists of nematodes and can be developed into biocontrol agents. However, microbial biocontrol agents often suffer from inconsistent efficacy, primarily due to biotic and abiotic stresses in the rhizosphere soil. <i>Drechslerella dactyloides</i>, a nematode-trapping fungus, produces conidial traps in soil, serving as a survival strategy to overcome these stresses. In this study, we optimized soil suspensions to efficiently induce the formation of conidial traps. We found that bacteria in the soil directly trigger this formation. Metagenomic sequencing revealed bacterial enrichment during optimization, and we isolated and purified these bacteria with inducible activity. Our research deepens the understanding of this survival strategy of nematode-trapping fungi in nature, laying the foundation for enhancing the effectiveness of nematode biocontrol using this mechanism.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0129124"},"PeriodicalIF":5.0,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143408964","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":"Jellyfish blooms-an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments.","authors":"Alan X Elena, Neža Orel, Peiju Fang, Gerhard J Herndl, Thomas U Berendonk, Tinkara Tinta, Uli Klümper","doi":"10.1128/msystems.01012-24","DOIUrl":"https://doi.org/10.1128/msystems.01012-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Gelatinous zooplankton (GZ) represents an important component of marine food webs, capable of generating massive blooms with severe environmental impact. When these blooms collapse, considerable amounts of organic matter (GZ-OM) either sink to the seafloor or can be introduced into the ocean's interior, promoting bacterial growth and providing a colonizable surface for microbial interactions. We hypothesized that GZ-OM is an overlooked marine hotspot for transmitting antimicrobial resistance genes (ARGs). To test this, we first re-analyzed metagenomes from two previous studies that experimentally evolved marine microbial communities in the presence and absence of OM from &lt;i&gt;Aurelia aurita&lt;/i&gt; and &lt;i&gt;Mnemiopsis leidyi&lt;/i&gt; recovered from bloom events and thereafter performed additional time-resolved GZ-OM degradation experiments to improve sample size and statistical power of our analysis. We analyzed these communities for composition, ARG, and mobile genetic element (MGE) content. Communities exposed to GZ-OM displayed up to fourfold increased relative ARG and up to 10-fold increased MGE abundance per 16S rRNA gene copy compared to the controls. This pattern was consistent across ARG and MGE classes and independent of the GZ species, indicating that nutrient influx and colonizable surfaces drive these changes. Potential ARG carriers included genera containing potential pathogens raising concerns of ARG transfer to pathogenic strains. &lt;i&gt;Vibrio&lt;/i&gt; was pinpointed as a key player associated with elevated ARGs and MGEs. Whole-genome sequencing of a &lt;i&gt;Vibrio&lt;/i&gt; isolate revealed the genetic capability for ARG mobilization and transfer. This study establishes the first link between two emerging issues of marine coastal zones, jellyfish blooms and ARG spread, both likely increasing with future ocean change. Hence, jellyfish blooms are a quintessential \"One Health\" issue where decreasing environmental health directly impacts human health.IMPORTANCEJellyfish blooms are, in the context of human health, often seen as mainly problematic for oceanic bathing. Here we demonstrate that they may also play a critical role as marine environmental hotspots for the transmission of antimicrobial resistance (AMR). This study employed (re-)analyses of microcosm experiments to investigate how particulate organic matter introduced to the ocean from collapsed jellyfish blooms, specifically &lt;i&gt;Aurelia aurita&lt;/i&gt; and &lt;i&gt;Mnemiopsis leidyi&lt;/i&gt;, can significantly increase the presence of antimicrobial resistance genes and mobile genetic elements in marine microbial communities by up to one order of magnitude. By providing abundant nutrients and surfaces for bacterial colonization, organic matter from these blooms enhances ARG proliferation, including transfer to and mobility in potentially pathogenic bacteria like &lt;i&gt;Vibrio&lt;/i&gt;. Understanding this connection highlights the importance of monitoring jellyfish blooms as part of marine health assessments and developing strat","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0101224"},"PeriodicalIF":5.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143399060","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":"Identification and characterization of archaeal pseudomurein biosynthesis genes through pangenomics.","authors":"Valérian Lupo, Célyne Roomans, Edmée Royen, Loïc Ongena, Olivier Jacquemin, Coralie Mullender, Frédéric Kerff, Denis Baurain","doi":"10.1128/msystems.01401-24","DOIUrl":"https://doi.org/10.1128/msystems.01401-24","url":null,"abstract":"<p><p>The peptidoglycan (PG, or murein) is a mesh-like structure, which is made of glycan polymers connected by short peptides and surrounds the cell membrane of nearly all bacterial species. In contrast, there is no PG counterpart that would be universally found in Archaea but rather various polymers that are specific to some lineages. Methanopyrales and Methanobacteriales are two orders of Euryarchaeota that harbor pseudomurein (PM), a structural analog of the bacterial PG. Owing to the differences between PG and PM biosynthesis, some have argued that the origin of both polymers is not connected. However, recent studies have revealed that the genomes of PM-containing Archaea encode homologs of the bacterial genes involved in PG biosynthesis, even though neither their specific functions nor the relationships within the corresponding inter-domain phylogenies have been investigated so far. In this work, we devised a pangenomic bioinformatic pipeline to identify proteins for PM biosynthesis in Archaea without prior genetic knowledge. The taxonomic distribution and evolutionary relationships of the candidate proteins were studied in detail in Archaea and Bacteria through HMM sequence mining and phylogenetic inference of the Mur domain-containing family, the ATP-grasp superfamily, and the MraY-like family. Our results show that archaeal muramyl ligases are of bacterial origin but diversified through a mixture of horizontal gene transfers and gene duplications. However, in the ATP-grasp and MraY-like families, the archaeal members were not found to originate from Bacteria. Our pangenomic approach further identified five new genes potentially involved in PM synthesis and that would deserve functional characterization.IMPORTANCE<i>Methanobrevibacter smithii</i> is an archaea commonly found in the human gut, but its presence alongside pathogenic bacteria during infections has led some researchers to consider it as an opportunistic pathogen. Fortunately, endoisopeptidases isolated from phages, such as PeiW and PeiP, can cleave the cell walls of <i>M. smithii</i> and other pseudomurein-containing archaea. However, additional research is required to identify effective anti-archaeal agents to combat these opportunistic microorganisms. A better understanding of the pseudomurein cell wall and its biosynthesis is necessary to achieve this goal. Our study sheds light on the origin of cell wall structures in those microorganisms, showing that the archaeal muramyl ligases responsible for its formation have bacterial origins. This discovery challenges the conventional view of the cell-wall architecture in the last archaeal common ancestor and shows that the distinction between \"common origin\" and \"convergent evolution\" can be blurred in some cases.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0140124"},"PeriodicalIF":5.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143399040","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":"Erratum for Wintenberg et al., \"Global Transcriptional Response of <i>Escherichia coli</i> Exposed <i>In Situ</i> to Different Low-Dose Ionizing Radiation Sources\".","authors":"Molly Wintenberg, Lisa Manglass, Nicole E Martinez, Mark Blenner","doi":"10.1128/msystems.00159-25","DOIUrl":"https://doi.org/10.1128/msystems.00159-25","url":null,"abstract":"","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0015925"},"PeriodicalIF":5.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143399048","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":"Gut commensal <i>Alistipes shahii</i> improves experimental colitis in mice with reduced intestinal epithelial damage and cytokine secretion.","authors":"Xiaoying Lin, Mingchao Xu, Ruiting Lan, Dalong Hu, Suping Zhang, Shuwei Zhang, Yao Lu, Hui Sun, Jing Yang, Liyun Liu, Jianguo Xu","doi":"10.1128/msystems.01607-24","DOIUrl":"https://doi.org/10.1128/msystems.01607-24","url":null,"abstract":"<p><p>The commensal bacterium <i>Alistipes shahii</i> is a core microbe of the human gut microbiome and its abundance is negatively correlated with inflammatory bowel diseases (IBDs). However, its fundamental role in regulating inflammatory response remains unknown. Using a dextran sulfate sodium (DSS)-induced colitis mouse model, we examined the effect of <i>A. shahii</i> strain As360 intervention on host inflammatory response and found that <i>A. shahii</i> As360 alleviated disease activity index, colon shortening, and colonic histopathological lesion. The levels of tight junction proteins (mainly ZO1 and claudin-1) were decreased in DSS-induced colitis mice, whereas the levels of these proteins were elevated in colitis mice with <i>A. shahii</i> As360 treatment. In addition, <i>A. shahii</i> As360 treatment led to alterations in cytokine release, especially an increase of IL10. It also led to reduced expressions of <i>mtor</i> and <i>Nlrp3</i> and increased expression of mTOR inhibitor <i>Ddit4</i> at the transcriptional level. 16S rRNA amplicon sequencing found that <i>Bacteroides</i>, a producer of short-chain fatty acids (SCFAs), was enriched in the fecal samples of mice with <i>A. shahii</i> treatment. Metabolic analyses found that, following <i>A. shahii</i> As360 treatment, the SCFAs in the fecal content was increased whereas lactic acid was decreased in the cecal content. These findings suggest that supplementation with <i>A. shahii</i> As360 is a promising strategy to prevent colitis.IMPORTANCEAs one of the core microbes and keystone species in the human gut, <i>Alistipes shahii</i> has the potential to inhibit inflammation and improve inflammatory bowel diseases (IBDs) conditions. In this study, we experimentally demonstrated that oral administration of <i>A. shahii</i> As360 alleviated symptoms of colitis, altered the release of cellular inflammatory factors, reduced the intestinal epithelial barrier damage, and changed gut microbiota and fecal metabolites. These findings provide a deeper understanding of the beneficial effects of <i>A. shahii</i> and its perspective for better strategies to prevent IBD.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0160724"},"PeriodicalIF":5.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143399032","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":"Tracing the evolution: the rise of <i>Salmonella</i> Thompson co-resistant to clinically important antibiotics in China, 1997-2020.","authors":"Weishuai Zhai, Mi Lu, Lanxin Zhao, Pengcheng Du, Shenghui Cui, Yang Liu, Dongmei Tan, Xianying Zeng, Baowei Yang, Ruichao Li, Séamus Fanning, Dejun Liu, Lanqi Li, Xiaoman Zhang, Yang Wang, Li Bai","doi":"10.1128/msystems.01018-24","DOIUrl":"10.1128/msystems.01018-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;As clinical &lt;i&gt;Salmonella enterica&lt;/i&gt; serovar Thompson (&lt;i&gt;S&lt;/i&gt;. Thompson) emerged among the top ten prevalent serovars in China, understanding the distribution and origin of its multidrug-resistant (MDR) strains becomes imperative. This study employed antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatics analysis to investigate the prevalence and genomic profiles of clinically important &lt;i&gt;S&lt;/i&gt;. Thompson ST26 across China from 1997 to 2020. Upon analyzing 141 isolates from various sources, we identified 29 isolates, derived from 25 diarrhea patients and four animal-derived foods, displayed co-resistance to ciprofloxacin, cefotaxime, and azithromycin (CIP&lt;sup&gt;R&lt;/sup&gt;CTX&lt;sup&gt;R&lt;/sup&gt;AZI&lt;sup&gt;R&lt;/sup&gt;), all of which are considered the front-line and critically-important antimicrobial agents for treating &lt;i&gt;Salmonella&lt;/i&gt; infections in humans. The IncC plasmid was the predominant mobile vector identified among the CIP&lt;sup&gt;R&lt;/sup&gt;CTX&lt;sup&gt;R&lt;/sup&gt;AZI&lt;sup&gt;R&lt;/sup&gt; isolates, harboring four crucial resistance genes &lt;i&gt;qnrS1&lt;/i&gt;, &lt;i&gt;qepA4&lt;/i&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;CMY-2&lt;/sub&gt;, and &lt;i&gt;mph&lt;/i&gt;(A) that confer resistance to three critically important antimicrobials. However, the closely related and clustered IncC-harboring CIP&lt;sup&gt;R&lt;/sup&gt;CTX&lt;sup&gt;R&lt;/sup&gt;AZI&lt;sup&gt;R&lt;/sup&gt; isolates (0-23 single nucleotide polymorphisms [SNPs]) indicated the clonal spreading of these clinically important isolates in different provinces of China. Notably, the CIP&lt;sup&gt;R&lt;/sup&gt;CTX&lt;sup&gt;R&lt;/sup&gt;AZI&lt;sup&gt;R&lt;/sup&gt; isolates appeared in aquatic products of animal-derived food, highlighting the possibility of aquaculture practices in the emergence and transmission of important antimicrobial resistance. Our findings emphasize the critical public health implications of IncC-carrying clinically important &lt;i&gt;S&lt;/i&gt;. Thompson ST26. The study calls for enhanced surveillance of the clinically important &lt;i&gt;S&lt;/i&gt;. Thompson ST26 clone in clinical and aquaculture and implementation of targeted interventions to mitigate its spread, thereby protecting food safety and public health.IMPORTANCEWe highlighted the critical veterinary public health issue of clinically important &lt;i&gt;Salmonella enterica&lt;/i&gt; serovar Thompson (&lt;i&gt;S&lt;/i&gt;. Thompson) prevalence in animal-derived foods, particularly aquatic products, calling for urgent action. The ability of &lt;i&gt;S&lt;/i&gt;. Thompson to resist critically important antimicrobials across diverse environments highlights the transmission and survival of resistant strains within the livestock and poultry industry, aquaculture, and food production chains. This study underscores the importance of continuous surveillance of clinically important &lt;i&gt;S&lt;/i&gt;. Thompson, especially in aquaculture settings, and considers the global trade of aquatic products as a potential vector for international dissemination. Further investigation on the factors contributing to the clone spread of clinically important &lt;i&gt;Salmonella&lt;/i&gt; strain and the development of intervention strategi","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0101824"},"PeriodicalIF":5.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143399066","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}