mSystems最新文献

{"title":"Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts","authors":"Elizaveta VinogradovaNurislam MukhanbetzhanovMadiyar NurgaziyevZharkyn JarmukhanovRakhilya AipovaAliya SailybayevaMakhabbat BekbossynovaSamat KozhakhmetovAlmagul Kushugulova1Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan2Kazakh Research Institute of Soil Science and Agricultural Chemistry named after U.Uspanov, Almaty, Kazakhstan3JSC “National Research Cardiac Surgery Center”, Astana, KazakhstanVanni Bucci","doi":"10.1128/msystems.00585-24","DOIUrl":"https://doi.org/10.1128/msystems.00585-24","url":null,"abstract":"mSystems, Ahead of Print. <br/>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254206","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":"The developing pig respiratory microbiome harbors strains antagonistic to common respiratory pathogens","authors":"Abel A. VlasblomBirgitta DuimShriram PatelRoosmarijn E. C. LuikenDaniel Crespo-PiazueloJulia EckenbergerChloe E. HuseyinPeadar G. LawlorChristian ElendJaap A. WagenaarMarcus J. ClaessonAldert L. Zomer1Faculty of Veterinary Medicine, Division of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands2WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands3School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland4SeqBiome Ltd., Cork, Ireland5Pig Development Department,Teagasc Animal & Grassland Research & Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland6EW Nutrition Innovation GmbH & Co.KG, Cologne, Germany7Wageningen Bioveterinary Research, Lelystad, The NetherlandsTricia A. Van Laar","doi":"10.1128/msystems.00626-24","DOIUrl":"https://doi.org/10.1128/msystems.00626-24","url":null,"abstract":"mSystems, Ahead of Print. <br/>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254207","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 phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes.","authors":"Suet-Ying Kwan, Caroline M Sabotta, Lorenzo R Cruz, Matthew C Wong, Nadim J Ajami, Joseph B McCormick, Susan P Fisher-Hoch, Laura Beretta","doi":"10.1128/msystems.00434-24","DOIUrl":"10.1128/msystems.00434-24","url":null,"abstract":"<p><p>Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of <i>Inoviridae</i> was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate <i>Escherichia</i> phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of <i>Lactococcus</i> phages r1t and BK5-T, and enrichment of the globally prevalent <i>Crassvirales</i> phages, including members of genus cluster IX (<i>Burzaovirus coli</i>, <i>Burzaovirus faecalis</i>) and VI (<i>Kahnovirus oralis</i>). The <i>Lactococcus</i> phages showed strong correlations and co-occurrence with <i>Lactococcus lactis</i>, while the <i>Crassvirales</i> phages, <i>B. coli</i>, <i>B. faecalis</i>, and UAG-readthrough crAss clade correlated and co-occurred with <i>Prevotella copri</i>. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of <i>Inoviridae</i>, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of <i>Escherichia coli</i>-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of <i>Lactococcus lactis</i>-infecting phages, and enrichment of <i>Crassvirales</i> phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406975/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142018072","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":"Species-level verification of Phascolarctobacterium association with colorectal cancer","authors":"Cecilie Bucher-JohannessenThulasika SenthakumaranEkaterina AvershinaEinar BirkelandGeir HoffVahid BemanianHege TunsjøTrine B. Rounge1Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway2Department of Tumor Biology, Oslo University Hospital, Oslo, Norway3Center for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway4Department of Life Sciences and Health, Oslo Metropolitan University, Oslo, Norway5Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway6Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway7Telemark Hospital, Skien, Norway8Department of Pathology, Akershus University Hospital, Lørenskog, NorwayJotham Suez","doi":"10.1128/msystems.00734-24","DOIUrl":"https://doi.org/10.1128/msystems.00734-24","url":null,"abstract":"mSystems, Ahead of Print. <br/>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254209","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":"Differential immunological responses in lamb rumen and colon to alfalfa hay and wheat straw in a concentrate-rich diet: insights into microbe-host interactions","authors":"Kefyalew GebeyewHui MiYong LiuYongbin LiuBiao WangTeka FeyeraTan ZhiliangZhixiong He1CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China2University of Chinese Academy of Sciences, Beijing, China3School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia, China4Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia, China5Department of Animal Science, School of Environmental and Rural Science, University of New England, Armidale, New South Wales, AustraliaTricia A. Van Laar","doi":"10.1128/msystems.00483-24","DOIUrl":"https://doi.org/10.1128/msystems.00483-24","url":null,"abstract":"mSystems, Ahead of Print. <br/>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254211","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":"Exploring the vitamin biosynthesis landscape of the human gut microbiota","authors":"Chiara TarracchiniGabriele Andrea LugliLeonardo MancabelliDouwe van SinderenFrancesca TurroniMarco VenturaChristian Milani1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy2Microbiome Research Hub, University of Parma, Parma, Italy3Department of Medicine and Surgery, University of Parma, Parma, Italy4APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, IrelandJack A. Gilbert","doi":"10.1128/msystems.00929-24","DOIUrl":"https://doi.org/10.1128/msystems.00929-24","url":null,"abstract":"mSystems, Ahead of Print. <br/>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254203","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":"Evolution of ceftazidime–avibactam resistance driven by mutations in double-copy blaKPC-2 to blaKPC-189 during treatment of ST11 carbapenem-resistant Klebsiella pneumoniae","authors":"Xiaofan ZhangYinrong XieYing ZhangTailong LeiLongjie ZhouJiayao YaoLin LiuHaiyang LiuJintao HeYunsong YuYuexing TuXi Li1Centre of Laboratory Medicine, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China2Department of Clinical Laboratory, Feicheng Hospital of Traditional Chinese Medicine, Feicheng, Shandong, China3Department of Clinical Laboratory, Xiamen Hospital of Traditional Chinese Medicine, Xiamen, Fujian, China4Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China5Center for General Practice Medicine, Department of Infectious Diseases, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China6Department of Critical Care Medicine, Tongde Hospital of Zhejiang Province, 234 Gucui Road, Hangzhou, Zhejiang, ChinaXiyang Dong","doi":"10.1128/msystems.00722-24","DOIUrl":"https://doi.org/10.1128/msystems.00722-24","url":null,"abstract":"mSystems, Ahead of Print. <br/>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254202","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":"Factors governing attachment of <i>Rhizobium leguminosarum</i> to legume roots at acid, neutral, and alkaline pHs.","authors":"Jack D Parsons, Clare R Cocker, Alison K East, Rachel M Wheatley, Vinoy K Ramachandran, Farnusch Kaschani, Markus Kaiser, Philip S Poole","doi":"10.1128/msystems.00422-24","DOIUrl":"10.1128/msystems.00422-24","url":null,"abstract":"<p><p>Rhizobial attachment to host legume roots is the first physical interaction of bacteria and plants in symbiotic nitrogen fixation. The pH-dependent primary attachment of <i>Rhizobium leguminosarum</i> biovar viciae 3841 to <i>Pisum sativum</i> (pea) roots was investigated by genome-wide insertion sequencing, luminescence-based attachment assays, and proteomic analysis. Under acid, neutral, or alkaline pH, a total of 115 genes are needed for primary attachment under one or more environmental pH, with 22 genes required for all. These include components of cell surfaces and membranes, together with enzymes that construct and modify them. Mechanisms of dealing with stress also play a part; however, exact requirements vary depending on environmental pH. RNASeq showed that knocking out the two transcriptional regulators required for attachment causes massive changes in the bacterial cell surface. Approximately half of the 54 proteins required for attachment at pH 7.0 have a role in the later stages of nodule formation. We found no evidence for a single rhicadhesin responsible for alkaline attachment, although sonicated cell surface fractions inhibited root attachment at alkaline pH. Our results demonstrate the complexity of primary root attachment and illustrate the diversity of mechanisms involved.</p><p><strong>Importance: </strong>The first step by which bacteria interact with plant roots is by attachment. In this study, we use a combination of insertion sequencing and biochemical analysis to determine how bacteria attach to pea roots and how this is influenced by pH. We identify several key adhesins, which are molecules that enable bacteria to stick to roots. This includes a novel filamentous hemagglutinin which is needed at all pHs for attachment. Overall, 115 proteins are required for attachment at one or more pHs.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142018070","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":"Pangenomic landscapes shape performances of a synthetic genetic circuit across <i>Stutzerimonas</i> species.","authors":"Dennis Tin Chat Chan, Hans C Bernstein","doi":"10.1128/msystems.00849-24","DOIUrl":"10.1128/msystems.00849-24","url":null,"abstract":"<p><p>Engineering identical genetic circuits into different species typically results in large differences in performance due to the unique cellular environmental context of each host, a phenomenon known as the \"chassis-effect\" or \"context-dependency\". A better understanding of how genomic and physiological contexts underpin the chassis-effect will improve biodesign strategies across diverse microorganisms. Here, we combined a pangenomic-based gene expression analysis with quantitative measurements of performance from an engineered genetic inverter device to uncover how genome structure and function relate to the observed chassis-effect across six closely related <i>Stutzerimonas</i> hosts. Our results reveal that genome architecture underpins divergent responses between our chosen non-model bacterial hosts to the engineered device. Specifically, differential expression of the core genome, gene clusters shared between all hosts, was found to be the main source of significant concordance to the observed differential genetic device performance, whereas specialty genes from respective accessory genomes were not significant. A data-driven investigation revealed that genes involved in denitrification and components of trans-membrane transporter proteins were among the most differentially expressed gene clusters between hosts in response to the genetic device. Our results show that the chassis-effect can be traced along differences among the most conserved genome-encoded functions and that these differences create a unique biodesign space among closely related species.IMPORTANCEContemporary synthetic biology endeavors often default to a handful of model organisms to host their engineered systems. Model organisms such as <i>Escherichia coli</i> serve as attractive hosts due to their tractability but do not necessarily provide the ideal environment to optimize performance. As more novel microbes are domesticated for use as biotechnology platforms, synthetic biologists are urged to explore the chassis-design space to optimize their systems and deliver on the promises of synthetic biology. The consequences of the chassis-effect will therefore only become more relevant as the field of biodesign grows. In our work, we demonstrate that the performance of a genetic device is highly dependent on the host environment it operates within, promoting the notion that the chassis can be considered a design variable to tune circuit function. Importantly, our results unveil that the chassis-effect can be traced along similarities in genome architecture, specifically the shared core genome. Our study advocates for the exploration of the chassis-design space and is a step forward to empowering synthetic biologists with knowledge for more efficient exploration of the chassis-design space to enable the next generation of broad-host-range synthetic biology.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142018074","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":"Fungal elemental profiling unleashed through rapid laser-induced breakdown spectroscopy (LIBS).","authors":"Tomás A Rush, Ann M Wymore, Miguel Rodríguez, Sara Jawdy, Rytas J Vilgalys, Madhavi Z Martin, Hunter B Andrews","doi":"10.1128/msystems.00919-24","DOIUrl":"10.1128/msystems.00919-24","url":null,"abstract":"<p><p>Elemental profiling of fungal species as a phenotyping tool is an understudied topic and is typically performed to examine plant tissue or non-biological materials. Traditional analytical techniques such as inductively coupled plasma-optical emission spectroscopy (ICP-OES) and inductively coupled plasma-mass spectrometry (ICP-MS) have been used to identify elemental profiles of fungi; however, these techniques can be cumbersome due to the difficulty of preparing samples. Additionally, the instruments used for these techniques can be expensive to procure and operate. Laser-induced breakdown spectroscopy (LIBS) is an alternative elemental analytical technique-one that is sensitive across the periodic table, easy to use on various sample types, and is cost-effective in both procurement and operation. LIBS has not been used on axenic filamentous fungal isolates grown in substrate media. In this work, as a proof of concept, we used LIBS on two genetically distinct fungal species grown on a nutrient-rich and nutrient-poor substrate media to determine whether robust elemental profiles can be detected and whether differences between the fungal isolates can be identified. Our results demonstrate a distinct correlation between fungal species and their elemental profile, regardless of the substrate media, as the same strains shared a similar uptake of carbon, zinc, phosphorus, manganese, and magnesium, which could play a vital role in their survival and propagation. Independently, each fungal species exhibited a unique elemental profile. This work demonstrates a unique and valuable approach to rapidly phenotype fungi through optical spectroscopy, and this approach can be critical in understanding these fungi's behavior and interactions with the environment.</p><p><strong>Importance: </strong>Historically, ionomics, the elemental profiling of an organism or materials, has been used to understand the elemental composition in waste materials to identify and recycle heavy metals or rare earth elements, identify the soil composition in space exploration on the moon or Mars, or understand human disorders or disease. To our knowledge, ionomic profiling of microbes, particularly fungi, has not been investigated to answer applied and fundamental biological questions. The reason is that current ionomic analytical techniques can be laborious in sample preparation, fail to measure all potential elements accurately, are cost-prohibitive, or provide inconsistent results across replications. In our previous efforts, we explored whether laser-induced breakdown spectroscopy (LIBS) could be used in determining the elemental profiles of poplar tissue, which was successful. In this proof-of-concept endeavor, we undertook a transdisciplinary effort between applied and fundamental mycology and elemental analytical techniques to address the biological question of how LIBS can used for fungi grown axenically in a nutrient-rich and nutrient-poor environment.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142073269","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}