mSystems最新文献

{"title":"DNA reference reagents isolate biases in microbiome profiling: a global multi-lab study.","authors":"Saba Anwar, Matthew Lamaudiere, Jack Hassall, Jacob Dehinsilu, Ravneet K Bhuller, Georgina L Hold, Xabier Vázquez-Campos, Alexander Mahnert, Christine Moissl-Eichinger, Birgit Gallé, Gudrun Kainz, Petra Pjevac, Bela Hausmann, Jasmin Schwarz, Gudrun Kohl, David Berry, Sarah J Vancuren, Emma Allen-Vercoe, Nynne Nielsen, Nikolaj Sørensen, Aron Eklund, Henrik Bjørn Nielsen, René Riedel, Jannike Lea Krause, Hyun-Dong Chang, Suenie Park, Ho-Yeon Song, Hoonhee Seo, Asad Ul-Haq, Sukyung Kim, Yongbin Kwon, Sunwha Park, Xavier Soberon, Eugenia Silva-Herzog, Joost A M Verlouw, Pascal Arp, Mila Jhamai, Robert Kraaij, Anoecim R Geelen, Quinten R Ducarmon, Wiep Klaas Smits, Ed J Kuijper, Romy D Zwittink, Niels van Best, John Penders, Giang Le, Christel Driessen, Jolanda Kool, Sudarshan A Shetty, Susana Fuentes, Mehmet Demirci, Akin Yigin, Celina Whalley, Andrew D Beggs, Christopher Quince, Rob James, Sebastien Raguideau, Martin Gordon, Ryan Mate, Martin Fritzsche, Nathan P Danckert, Jesus Miguens Blanco, Julian R Marchesi, Marcus Rauch, R Anthony Williamson, Angélique B Van't Wout, Angelika Kritz, Stephan Rosecker, Richard Stevens, Lynette Laws, Lizbeth Sayavedra, Stefano Romano, Andrea Telatin, David Baker, Arjan Narbad, Stephanie L Servetas, Jason G Kralj, Samuel P Forry, Monique E Hunter, Jennifer N Dootz, Scott A Jackson, Christopher E Mason, Daniel J Butler, Christopher Mozsary, Jonathan Foox, Namita Damle, Aidan Resh, Amanda Busswitz, Peter Lenz, Shane Sontag, Andrew Cross, Christian Sanchez, Mingsheng Guo, Kayla Olson, Eric A Smith, Alex J La Reau, Tonya Ward, Scott Kuersten, Fred Hyde, Irina Khrebtukova, Gary Schroth, Sjoerd Rijpkema, Gregory C A Amos, Chrysi Sergaki","doi":"10.1128/msystems.00466-25","DOIUrl":"https://doi.org/10.1128/msystems.00466-25","url":null,"abstract":"<p><p>When profiling the human gut microbiome, technical biases introduced by analytical approaches impede translational research, reducing data reliability and study comparability. Here, through a global study involving 23 labs, we analyzed a wide range of sequencing and bioinformatic approaches for the taxonomic profiling of two well-defined DNA reference reagents (RRs) comprised of 20 common gut bacteria. Through both shotgun and 16S rRNA gene amplicon sequencing, we aimed to isolate sources of bias and understand their impact on microbiome profiling accuracy. Importantly, minimum quality criteria (MQC) were established and are used to evaluate profiling performance. We found that the variability of shotgun sequencing data sets was greater than that of 16S rRNA gene amplicon sequencing and isolated sources of bias in wet and dry lab steps, such as sequencing depth, primer and database choices, rarefaction, and 16S copy number adjustment. This study presents well-defined RRs and MQC to combat technical bias, paving the way for reliable and comparable microbiome research.IMPORTANCEThis benchmark paper highlights the true level of variability in microbiome data across the world and across sectors, underscoring the critical need for the use of WHO International DNA Gut Reference Reagents (RRs) to elevate the quality of data in microbiome research. This global study is the first of its kind, revealing the reality of the bias in the field, comprehensively testing methodologies used by leading laboratories across the world, but also providing avenues for workflow optimization, to accelerate innovation and translational research and move the field forward.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0046625"},"PeriodicalIF":4.6,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145308667","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":"Bladder health and the urogenital microbiome in community-dwelling adult females.","authors":"L Brubaker, D McDonald, S Putnam, C Brennan, C S Fok, C E Lewis, J L Lowder, M G Mueller, L M Rickey, E R Mueller, S J Song, K Rudser, R Knight, E S Lukacz","doi":"10.1128/msystems.00558-25","DOIUrl":"https://doi.org/10.1128/msystems.00558-25","url":null,"abstract":"<p><p>Despite the established association with lower urinary tract symptoms, the relationship between a healthy bladder and the urogenital microbiome is unknown. This observational cohort study of 435 community-dwelling women examined bladder health and function using a validated instrument. Voided urine samples were self-collected, shipped to a repository, and underwent 16S rRNA amplicon sequencing. Two hundred seventy-four (56%) samples were retained following a limit-of-detection analysis for low biomass samples. A differential abundance analysis showed that <i>Lactobacillus,</i> the dominant genus, was associated with higher bladder function scores, but not global perception of bladder health, while <i>Prevotella</i> and <i>Anerococcus</i> were associated with lower scores. Associations between the female urogenital microbiome exist across the bladder health spectrum.</p><p><strong>Importance: </strong>There is increasing awareness that human microbiomes impact health and modulate certain health conditions. Recently, investigators developed a validated assessment of bladder health in adult women. This advance facilitated evaluation of the urogenital microbiome, across the adult lifespan and across the spectrum of bladder health in a population-based, observational study.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0055825"},"PeriodicalIF":4.6,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145301986","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":"High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral, <i>Madracis mirabilis,</i> in Curaçao's coral reefs.","authors":"Bailey A Wallace, Natascha S Varona, Alexandra K Stiffler, Mark J A Vermeij, Cynthia Silveira","doi":"10.1128/msystems.01208-25","DOIUrl":"https://doi.org/10.1128/msystems.01208-25","url":null,"abstract":"<p><p>Coral reefs have undergone extensive coral loss and shifts in community composition worldwide. Despite this, some coral species appear naturally more resistant, such as <i>Madracis mirabilis</i> (herein <i>Madracis</i>). <i>Madracis</i> has emerged as the dominant hard coral in Curaçao, comprising 26% of coral cover in reefs that declined by 78% between 1973 and 2015. Although life history traits and competitive mechanisms contribute to <i>Madracis</i>'s success, these factors alone may not fully explain it, as other species with similar traits have not shown comparable success. Here, we investigated the potential role of microbial communities in the success of <i>Madracis</i> on Curaçao reefs by leveraging a low-bias bacterial and viral enrichment method for metagenomic sequencing of coral samples, resulting in 77 unique bacterial metagenome-assembled genomes and 2,820 viral genomic sequences. Our analyses showed that <i>Madracis</i>-associated bacterial and viral communities are 12% and 20% richer than the communities of five sympatric coral species combined. The <i>Madracis</i>-associated bacterial community was dominated by <i>Ruegeria</i> and <i>Sphingomonas</i>, genera that have previously been associated with coral health, defense against pathogens, and bioremediation. These communities also displayed higher functional redundancy, which is often associated with ecological resilience. The viral community exhibited a 50% enrichment of proviruses relative to other corals. These proviruses had the genomic capacity to laterally transfer genes involved in antibiotic resistance, central metabolism, and oxidative stress responses, potentially enhancing the adaptive capacity of the <i>Madracis</i> microbiome and contributing to <i>Madracis</i>'s success on Curaçao's reefs.</p><p><strong>Importance: </strong>Understanding why some coral species persist and thrive while most are in fast decline is critical. <i>Madracis mirabilis</i> is increasingly dominant on degraded reefs in Curaçao, yet the role of microbial communities in its success remains underexplored. This study highlights the potential role of <i>Madracis</i>-associated bacterial and viral communities in supporting coral resilience and competitive success. By identifying key microbial partners and viral genes that may enhance host stress tolerance and defense against pathogens, we broaden the understanding of how the coral holobiont contributes to species persistence under environmental stress. These insights are valuable for predicting key microbial community players in reef interactions and may inform microbiome-based strategies to support coral conservation and restoration.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0120825"},"PeriodicalIF":4.6,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145302027","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":"Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level.","authors":"Anastasiia Rusanova, Viktor Mamontov, Maxim Ri, Dmitry Meleshko, Anna Trofimova, Victor Fedorchuk, Margarita Ezhova, Alexander Finoshin, Yulia Lyupina, Artem Isaev, Dmitry Sutormin","doi":"10.1128/msystems.01147-25","DOIUrl":"https://doi.org/10.1128/msystems.01147-25","url":null,"abstract":"<p><p>Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge-associated microbiomes contribute to the health of host organisms by defending them against invading bacteria and providing them with essential metabolites. Here, we describe the microbiomes of three sympatric species of cold-water marine sponges<i>-Halichondria panicea</i>, <i>Halichondria sitiens</i>, and <i>Isodictya palmata</i>-sampled at three time points over a period of 6 years in the White Sea. We identified the sponges as low microbial abundance species and detected stably associated bacteria that represent new taxa of sponge symbionts within Alpha- and Gammaproteobacteria. The sponges carried unique sets of unrelated species of symbiotic bacteria, illustrating the varying complexity of their microbiomes. At the community level, sponge-associated microbiomes shared common symbiotic features: they encoded multiple eukaryotic-like proteins, biosynthetic pathways and transporters of amino acids and vitamins essential for sponges. At the species level, however, different classes of eukaryotic-like proteins and pathways were distributed between dominant and minor symbionts, indicating specialization within microbiomes. Particularly, the taurine and sulfoacetate import and degradation pathways were associated exclusively with dominant symbionts in all three sponge species, suggesting that these pathways may represent symbiotic features. Our study indicates convergent evolution in the microbiomes of sympatric cold-water sponge species, as reflected by strong functional similarity despite the presence of distinct, taxonomically unrelated symbiotic communities.</p><p><strong>Importance: </strong>Sponges are regarded among the earliest multicellular organisms and the most ancient examples of animal-bacterial symbiosis. The study of host-microbe interactions in sponges has advanced rapidly due to the application of next-generation sequencing (NGS) technologies that help overcome the challenges of investigating their communities. However, many sponge species, particularly those from polar ecosystems, remain poorly characterized. Here, we demonstrate that three sympatric cold-water sponge species, including two analyzed for the first time, harbor distinct sets of bacterial symbionts, stably associated over 6 years. Using CORe contigs ITerative Expansion and Scaffolding, an algorithm developed in this study, we reconstructed high-quality symbiont genomes and revealed shared features indicative of convergent evolution toward symbiosis. Notably, we identified a potentially novel symbiotic feature-a gene cluster likely involved in sulfoacetate uptake and dissimilation. We also observed shifts in microbiome composition, associated with increasing water temperatures, raising concerns about the impact of global warming on cold-water ecosystems.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0114725"},"PeriodicalIF":4.6,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145301989","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":"Exogenous glutamate potentiates gentamicin to kill multidrug- and carbapenem-resistant <i>Pseudomonas aeruginosa</i> by activating the biosynthesis of unsaturated fatty acids.","authors":"Hao-Feng Lai, Li Pan, Kang-Yu Song, Zhen-Yuan Dai, Ying Liang, Wu Yuan, Zhuang-Gui Chen, Li-Fen Yang","doi":"10.1128/msystems.01234-25","DOIUrl":"https://doi.org/10.1128/msystems.01234-25","url":null,"abstract":"<p><p>Multidrug- and carbapenem-resistant <i>Pseudomonas aeruginosa</i> (MDR-PA and CR-PA) are difficult to control due to the predicament caused by their limited membrane permeability. The metabolic reprogramming approach is an effective strategy to promote membrane permeability. In this study, a gas chromatography-mass spectrometer-based metabolomics identified decreased abundance of glutamate as the most characteristic feature in gentamicin-resistant <i>P. aeruginosa</i> (PA-R_GEN). Exogenous glutamate enhanced gentamicin killing to lab-evolved PA-R_GEN as well as clinical MDR-PA and CR-PA isolates. By applying a multi-faceted approach, including glutamate-reprogramming metabolomics, isotope-tracing analysis, glutamate-reprogramming lipidomics, membrane permeability measurement, and oleic acid replacement test, we demonstrated that the glutamate metabolic flux increases the biosynthesis of unsaturated fatty acids and decreases the biosynthesis of saturated fatty acids. This change in lipid composition promotes membrane permeability and enhances gentamicin uptake in the presence of glutamate. However, the opposite phenotypes were exhibited in MDR- and CR-PA in the absence of glutamate. These results identify an effective reprogramming metabolite to combat MDR- and CR-PA with gentamicin and reveal a resistance mechanism of membrane permeability that limits drug uptake and its reversal approach in MDR- and CR-PA.</p><p><strong>Importance: </strong>Antibiotic-resistant <i>Pseudomonas aeruginosa</i> is a major clinical challenge due to limited drug uptake. This study shows that exogenous glutamate restores gentamicin efficacy by reprogramming bacterial metabolism to enhance membrane permeability. The effect is mediated through increased biosynthesis of unsaturated fatty acids, which is further confirmed by oleic acid supplementation. These findings reveal a novel metabolic approach to overcome multidrug and carbapenem resistance, offering a promising adjunct strategy to improve antibiotic treatment outcomes.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0123425"},"PeriodicalIF":4.6,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280717","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":"Floodplain nitrifiers harbor the genetic potential for utilizing a wide range of organic nitrogen compounds.","authors":"Anna N Rasmussen, Katie Langenfeld, Bradley B Tolar, Zach Perzan, Kate Maher, Emily L Cardarelli, John R Bargar, Kristin Boye, Christopher A Francis","doi":"10.1128/msystems.00829-25","DOIUrl":"https://doi.org/10.1128/msystems.00829-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Organic compounds such as urea and cyanate can serve as nitrogen (N) sources for nitrifying microorganisms, including ammonia-oxidizing archaea (AOA) and bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Here we investigated metagenome-assembled genomes (MAGs) for all four nitrifier guilds generated from hydrologically variable floodplain sediments of the Wind River Basin (WRB; Riverton, WY, USA) for their genetic potential to utilize organic N compounds. A vast majority of WRB nitrifier MAGs harbored urease (&lt;i&gt;ure&lt;/i&gt;) and at least one urea transporter (&lt;i&gt;utp&lt;/i&gt;, &lt;i&gt;urt&lt;/i&gt;, &lt;i&gt;dur3&lt;/i&gt;). AOA were the most abundant and phylogenetically diverse nitrifiers in WRB floodplain sediments. Several AOA MAGs encoded cyanase (&lt;i&gt;cynS&lt;/i&gt;), nitrilase (&lt;i&gt;nit1&lt;/i&gt;), omega-amidase (&lt;i&gt;nit2&lt;/i&gt;), nitrile hydratase (&lt;i&gt;nthA&lt;/i&gt;), and genes related to purine degradation, including biuret hydrolase (&lt;i&gt;biuH&lt;/i&gt;), oxamic transcarbamylase (&lt;i&gt;allFGH&lt;/i&gt;), and catabolic carbamate kinase (&lt;i&gt;allK&lt;/i&gt;). AOA often encoded an uncharacterized amidohydrolase collocated with &lt;i&gt;biuH&lt;/i&gt;, rather than allophanate hydrolase (&lt;i&gt;atzF&lt;/i&gt;). A small number of AOA encoded &lt;i&gt;atzF&lt;/i&gt;, functioning in an unknown pathway. AOB and comammox were of relatively low abundance and taxonomic diversity and were present only at certain depths in WRB; however, they encoded triuret/biuret degradation genes (&lt;i&gt;trtA&lt;/i&gt;, &lt;i&gt;biuH&lt;/i&gt;, and &lt;i&gt;atzH&lt;/i&gt;), and in comammox, these genes were also collocated with &lt;i&gt;allFGHK&lt;/i&gt;. The genetic potential of ammonia oxidizers in the WRB floodplain suggests that organic N may support nitrification in this system. The proposed pathways for utilizing purine degradation products other than urea potentially expand the known metabolic capabilities of AOA, AOB, and comammox bacteria and reveal the possibility for cryptic N cycling between microbial community members.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Floodplains are critical ecosystems where terrestrial and riverine systems meet. Floodplain sediments experience many, sometimes dramatic, changes in moisture and oxygen concentrations because of changes in water table height, flooding, and drought, leading to active microbial cycling of contaminants and nutrients. Nitrogen is one such nutrient that is not only essential for the building blocks of life but can also be used as an energy source by some microorganisms. Microorganisms that oxidize ammonia and nitrite are a crucial part of the nitrogen cycle and can lead to eventual nitrogen loss from a system. Investigating the genes present in microorganisms responsible for nitrification in a dynamic floodplain suggests that organic nitrogen-from decaying plants or potentially other sources, such as fertilizers, grazing livestock feces, or contaminants (e.g., pesticides, pharmaceuticals)-is an important nitrogen source to these microorganisms. This study identifies genes not previously described in nitrifying","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0082925"},"PeriodicalIF":4.6,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280665","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":"AFM characterization of early <i>P. aeruginosa</i> aggregates highlights emergent mechanical properties.","authors":"Caroline D Miller, Meisam Asgari, Sophie E Darch","doi":"10.1128/msystems.01312-25","DOIUrl":"https://doi.org/10.1128/msystems.01312-25","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> (<i>Pa</i>) is a leading cause of chronic lung infections in people with cystic fibrosis (pwCF), where its ability to form resilient, multicellular communities contributes to antibiotic tolerance and long-term persistence. While much of our understanding of <i>Pa</i> biofilms comes from surface-attached models, recent studies have emphasized the clinical relevance of suspended bacterial aggregates-dense, three-dimensional clusters that form early during infection and exhibit key biofilm-like properties. However, the physical characteristics of these aggregates remain poorly defined. Here, we apply atomic force microscopy (AFM) to visualize and quantify the structural and mechanical properties of <i>Pa</i> aggregates formed in synthetic cystic fibrosis sputum medium (SCFM2). Compared to planktonic cultures grown without mucin, aggregates formed in SCFM2 exhibited complex architecture and increased resistance to deformation, as measured by force spectroscopy. These differences emerged despite the absence of mature extracellular matrix components, suggesting that environmental cues and spatial organization alone may be sufficient to enhance aggregate mechanical resilience. Our results demonstrate that AFM provides a powerful, high-resolution approach for studying early-stage bacterial aggregates under physiologically relevant conditions. By resolving structural features and quantifying localized mechanical strength, this method offers new insight into how aggregate architecture contributes to persistence during chronic infection. These findings lay the groundwork for future studies targeting the physical robustness of bacterial communities as an early vulnerability in the pathogenesis of <i>Pa</i> both in CF and in other infection settings.IMPORTANCEChronic infections in people with cystic fibrosis are notoriously difficult to treat, in part due to the ability of <i>Pseudomonas aeruginosa</i> (<i>Pa</i>) to form protective communities known as aggregates. These suspended, multicellular clusters are not well captured by traditional surface-attached biofilm models but are now recognized as an important feature of persistent infection. Understanding how these aggregates resist physical and antimicrobial disruption is essential for developing better therapies. This study uses atomic force microscopy (AFM) to examine <i>Pa</i> aggregates at nanometer resolution in a laboratory model that mimics cystic fibrosis lung secretions. AFM not only visualizes individual aggregates but also measures how strongly they resist being physically deformed. Our findings show that aggregates formed in this environment are structurally robust, compared to single cells. These results highlight the importance of early physical organization in bacterial persistence and suggest new directions for therapies aimed at disrupting bacterial communities before they become established.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0131225"},"PeriodicalIF":4.6,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145275299","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":"Neutral plasma-activated solution reverses polymyxin to inhibit polymyxin-resistant <i>Acinetobacter baumannii</i> by promoting the release of ROS and destroying the outer membrane <i>in vitro</i>.","authors":"Wenjie Yuan, Ting Yu, Xinxing Yang, Tao Lin, Tingting Guo, Xiaobin Wang, Guocai Li, Kaizheng Gong, Weili Liu","doi":"10.1128/msystems.00784-25","DOIUrl":"https://doi.org/10.1128/msystems.00784-25","url":null,"abstract":"<p><p><i>Acinetobacter baumannii</i> is a prominent pathogen linked to ventilator-associated pneumonia (VAP) and has demonstrated widespread multidrug resistance globally. While the exploration of synergistic antibiotic combinations is increasingly viewed as an innovative treatment strategy, the antibacterial potential of plasma activated water (PAW) in neutralizing formulations remains underdeveloped. This study investigates the synergistic interactions between neutral plasma activated water (NPAW) and polymyxin B against multidrug-resistant strains of <i>A. baumannii</i>. We evaluated the antibacterial activity of the combination of NPAW and polymyxin B against polymyxin-resistant <i>A. baumannii</i> strains both <i>in vitro</i> and <i>in vivo</i>, further exploring the underlying mechanisms of synergy. Through checkerboard assay and time-kill studies, we demonstrated that the combination of NPAW and polymyxin B exhibited a synergistic effect against polymyxin-resistant <i>A. baumannii</i>. In the mouse pneumonia model, we confirmed that the combined treatment significantly reduced bacterial colonization in the lungs. Mechanistic studies indicated that NPAW enhances the bactericidal activity of Polymyxin B by promoting the release of reactive oxygen species (ROS). When used together, NPAW and polymyxin B decreased the production of intracellular ATP and membrane potential and compromised outer membrane integrity. In conclusion, the synergistic interactions between these agents may enable the use of lower concentrations of polymyxin B in treating <i>A. baumannii</i> infections, thereby minimizing dose-dependent side effects and providing a novel therapeutic option for managing these infections.IMPORTANCEPolymyxin-resistant <i>Acinetobacter baumannii</i> poses a global threat as last-line therapies fail. We demonstrate that neutral plasma activated water (NPAW), a reactive oxygen species-rich non-antibiotic agent, synergizes with polymyxin B to overcome resistance. Mechanistically, NPAW disrupts membrane integrity, depletes ATP, and amplifies oxidative stress, enhancing polymyxin B's bactericidal activity and reducing lung bacterial burdens in mice. This synergy enables lower polymyxin B doses, a critical advance for treating ventilator-associated pneumonia.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0078425"},"PeriodicalIF":4.6,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251899","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":"High-throughput cytological profiling uncovers genotype-phenotype associations in <i>Mycobacterium tuberculosis</i> clinical isolates.","authors":"Qingyun Liu, Yue J Liu, Ruiyuan Liu, Peter H Culviner, Xin Wang, Ian D Wolf, Ken Chen, Yiwang Chen, Yi Xiao, Guiming Zhang, Rongfeng Sun, Shoko Wakabayashi, Nicole C Howard, Mingyu Gan, Eric J Rubin, Sarah M Fortune, Junhao Zhu","doi":"10.1128/msystems.00972-25","DOIUrl":"10.1128/msystems.00972-25","url":null,"abstract":"<p><p>Understanding the functional impact of bacterial genetic diversity is crucial for linking pathogen variants to clinical outcomes. Here, we introduce a high-throughput cytological profiling pipeline optimized for <i>Mycobacterium tuberculosis</i> (Mtb) clinical strains, integrating OD-calibrated feature analysis and high-content microscopy. Our system quantifies single-bacterium morphological and physiological traits related to DNA replication, redox state, carbon metabolism, and cell envelope dynamics. Applied to 64 Mtb clinical isolates from lineages 1, 2, and 4, the approach revealed that cytological phenotypes recapitulate genetic relationships and exhibit both lineage- and density-dependent dynamics. Notably, we identified a link between a convergent \"small cell\" phenotype and a convergent <i>ino1</i> mutation that is associated with the presence of an antisense transcript, suggesting a potential non-canonical regulatory mechanism under selection. In summary, we present a resource-efficient approach for mapping Mtb's phenotypic landscape, uncovering cellular traits that underlie its evolution and providing new insights into the functional consequences of bacterial genetic diversity.</p><p><strong>Importance: </strong>Understanding how genetic variation in <i>Mycobacterium tuberculosis</i> (Mtb) shapes its physical traits is essential to unraveling the evolution of this global pathogen. Here, we introduce a systematically optimized, high-throughput imaging platform for the comprehensive characterization of Mtb clinical strains. We demonstrate that Mtb's phenotypic manifestation is shaped by both genetic background and culture density. By accounting for these factors, our analysis linked distinct cellular dynamics to specific lineages, sublineages, and even single nucleotide variations. Notably, we linked a recurring mutation to a unique cell-shortening phenotype, finding that it potentially acts by creating a cryptic antisense transcript. This platform provides a powerful framework for systematically dissecting the physiological dynamics underlying Mtb evolution and identifying new therapeutic vulnerabilities of this deadly pathogen.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0097225"},"PeriodicalIF":4.6,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251857","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":"A multi-omics analysis unveils functional and regulatory links between hydroxybenzene and aromatic amino acid metabolism in <i>Candida albicans</i>.","authors":"Enrico Garbe, Sascha Schäuble, Bettina Böttcher, Robert Jesse, Dominik Driesch, Lasse van Wilijck, Osama Elshafee, Tim Bastian Schille, Bernhard Hube, Gianni Panagiotou, Slavena Vylkova","doi":"10.1128/msystems.00226-25","DOIUrl":"https://doi.org/10.1128/msystems.00226-25","url":null,"abstract":"<p><p>The fungus <i>Candida albicans</i> is a frequent colonizer of humans but also an opportunistic pathogen causing superficial to severe infections, especially in vulnerable individuals. Its broad metabolic flexibility is key for the fungal adaptation to host environments, evasion from immune attack, and virulence. Amino acid metabolism and homeostasis, in particular, are critical for fungal fitness-illustrated by a rapid metabolic shift in response to amino acid starvation to restore intracellular metabolic balance. To investigate the cellular mechanisms underlying such compensatory metabolic processes, we performed data-driven genome-scale metabolic modeling based on transcriptional metabolic profiles of amino acid-starved cells to identify condition-specific fungal metabolic fluxes and pathway activities specific to cellular response to amino acid starvation. Most prominently, we predicted altered activity of the shikimate pathway upon amino acid limitation and identified a simultaneous induction of aromatic amino acid (AAA) biosynthesis and a metabolic gene cluster required for the catabolism of hydroxybenzenes. Further phenotypic and transcriptional analyses not only verified the transcription factor Zcf25 as the central regulator of the catechol-branch of this pathway, but also condition-specific co-regulation of AAA and hydroxybenzene metabolism mediated by Zcf25 and the transcriptional regulator of amino acid metabolism Stp2. These findings propose a so far unknown metabolic link between amino acid and hydroxybenzene metabolism in <i>C. albicans</i>, therewith adding another layer to its metabolic plasticity.</p><p><strong>Importance: </strong>The opportunistic human fungal pathogen <i>Candida albicans</i> possesses a remarkable metabolic plasticity, which is essential for both fungal commensalism and virulence and influences its physiology and behavior in multiple ways. The investigation of such processes particularly benefits from the emergence of multi-omics and <i>in silico</i> approaches. In this study, we combined a multi-omics approach with genome-scale metabolic modeling to investigate the fungal metabolic adaptation to amino acid utilization and starvation. Most strikingly, we found an altered activity of the shikimate pathway upon amino acid starvation, accompanied by a simultaneous induction of two metabolic gene clusters required for the metabolism of hydroxybenzenes. Further analyses revealed so far unknown potential functional and regulatory links between both metabolic pathways, which provide starting points for future research leading to a better understanding of the fungal adaptation to dynamic host conditions.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0022625"},"PeriodicalIF":4.6,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251880","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}