mSystems最新文献

{"title":"Long-term culture of germ-free zebrafish using gamma-irradiated feeds.","authors":"Lydia Okyere, Angela Di Fulvio, Christopher A Gaulke","doi":"10.1128/msystems.00353-26","DOIUrl":"10.1128/msystems.00353-26","url":null,"abstract":"<p><p>Host-associated microbiota play important roles in modulating key host functions, including digestion, nutrient acquisition, immunity, and xenobiotic metabolism. Disruption of these communities is linked to numerous diseases and health defects, though causal mechanisms underpinning these associations remain unclear in most cases. Gnotobiotic zebrafish provide a scalable low-cost <i>in vivo</i> model that is increasingly used to resolve causality in host-microbiota interactions. However, reliance on live diets and autoclaved diets limits the use of gnotobiotic zebrafish to early life stages where body systems and microbial communities are incompletely developed. As a result, many important host-microbiota interactions may be unable to be studied in this model system. Here, we tested a simple method for long-term husbandry of gnotobiotic zebrafish using gamma-irradiated chow diets and evaluated effects on growth, gene expression, and microbial community composition. In conventionally reared animals, gamma-irradiated diets did not affect growth or survival and only modestly impacted microbial community composition and diversity. In contrast, germ-free zebrafish maintained on sterile irradiated diets for 55 days post-fertilization were smaller, weighed less, and exhibited aberrant gene expression profiles relative to controls. These genes were enriched for pathways related to immune response, xenobiotic metabolism, organ development, liver function, and lipid metabolism, with many expression patterns linked to the abundance of specific microbial taxa. Together, these findings establish a practical protocol for long-term maintenance of gnotobiotic zebrafish and extend the utility of this model to study microbiome-dependent effects on host physiology and development beyond early larval stages of life.IMPORTANCEWhile the gnotobiotic zebrafish have been a powerful model for interrogation of host-microbiota interactions, their use has been limited to early life stages due to complications of long-term husbandry. To address this limitation, we developed a simple protocol that enables rearing germ-free zebrafish well beyond larval stages. Germ-free fish exhibit physiological and developmental defects that mirror those described in mammalian counterparts supporting a conserved role for microbiota in vertebrate development and physiology. Our protocol provides a method to investigate microbial influences on adaptive immunity, metabolism, and chronic disease processes in zebrafish not possible with current methodologies. Given the rapid and simple methods for gnotobiotic derivation and the large number of transgenic animal lines available for zebrafish, we anticipate this model will accelerate mechanistic discovery of microbial impacts on host health.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0035326"},"PeriodicalIF":4.6,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775960","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":"Insects shape the cadaver decomposition microbiome and postmortem interval estimation accuracy.","authors":"Victoria Nieciecki, Valerie A Seitz, Zachary M Burcham, Kristen Otto, Kalen Cantrell, Jonathan Kirkland, Gail Ackermann, Rob Knight, Aaron Lynne, Jessica L Metcalf, Sibyl Bucheli","doi":"10.1128/msystems.00681-25","DOIUrl":"https://doi.org/10.1128/msystems.00681-25","url":null,"abstract":"<p><p>The breakdown and recycling of carrion is a crucial ecological process that largely relies on a community of necrophagous insects and microbes. Recent work has shown that a specialized microbial network, likely dispersed throughout the environment by insects, assembles during cadaver decomposition to break down flesh regardless of climate and geography. Because of their broad distribution and successional nature, decomposer microbes have been used in machine learning models to predict the postmortem interval (PMI) of human remains, an important contribution to the field of forensics. How factors such as an indoor environment, which alters insect activity, impact the composition of microbial communities decomposing human remains is unclear. Here, we investigate the effects of enclosed shelter on microbial community assembly and successional patterns during human decomposition and provide important considerations for PMI modeling. Compared to outdoor cadavers, we show that indoor cadavers experienced delayed colonization of key decomposer microbes over the course of decomposition due to restricted insect access. Consequently, machine learning models trained on outdoor cadavers frequently underestimated the PMI of cadavers decomposing indoors. Delayed colonization by blow fly maggots (Diptera: Calliphoridae) was correlated with higher PMI prediction errors, suggesting that insects are an important source of microbial decomposers that drive PMI model predictions. Incorporating microbial data from indoor cadavers and insect activity into PMI models significantly improved prediction capabilities for both indoor and outdoor decomposition environments. Ultimately, we demonstrate the important role insects play in the maintenance and distribution of microbes that help to recycle vertebrate remains.IMPORTANCEMicrobes are critical for the decomposition and recycling of organic matter. Recently, microbiome-based models have shown promising performance in estimating the postmortem interval (PMI). However, many deaths occur indoors, yet no studies have investigated the impact of enclosed shelter on the cadaver microbiome in a controlled setting. Here, cadavers were decomposed indoors, and we found that blow fly maggots serve as an important source of decomposer taxa that significantly alter the cadaver microbiome following infestation. Notably, PMI estimation models trained on outdoor data sets failed to accurately predict the PMI when insect colonization was delayed. We show that incorporating 16S rRNA amplicon data from cadavers decomposing indoors, along with environmental variables, significantly improves PMI estimates, suggesting a microbiome-based forensic tool may be feasible across decomposition environments. Importantly, this research demonstrates the critical ecological role insects play in the dispersal of specialized microbes that are involved in the breakdown and recycling of vertebrate remains.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0068125"},"PeriodicalIF":4.6,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776023","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":"Probing the genomic and proteomic basis of encystment in <i>Oxytricha granulifera</i>.","authors":"Miaomiao Wang, Juan Yang, Tao Hu, Zina Lin, Tian Wang, ZiJia Liu, Xiao Chen, Xinpeng Fan","doi":"10.1128/msystems.01757-25","DOIUrl":"https://doi.org/10.1128/msystems.01757-25","url":null,"abstract":"<p><p>Protozoan encystment constitutes a pivotal survival strategy against environmental stressors; however, the molecular architecture governing this transition remains enigmatic, owing to limited genomic resources and a scarcity of integrated multi-omics investigations. Here, we elucidate the mechanisms underlying encystment in <i>Oxytricha granulifera</i> by reporting the first macronuclear genome assembly and conducting a comprehensive integration of transcriptomic, proteomic, and morphological analyses across vegetative and cyst stages. Morphological restructuring, typified by ciliary dedifferentiation and cyst wall formation, is molecularly supported by the downregulation of microtubule dynamics-associated genes and the concurrent upregulation of vesicle transport machinery. Furthermore, expanded gene families linked to carbohydrate metabolism and cellular acidification coincide with observed autophagic clearance and mucocyst activity, highlighting a coordinated metabolic shift essential for cyst formation. Elevated expression of the ubiquitin-proteasome system and autophagy pathways, which mediate protein turnover, along with upregulation of antioxidant enzyme genes, contributes to alleviating oxidative damage. Notably, we identified rewired post-transcriptional regulation that increases spliceosome activity and alternative splicing frequency, with each trend validated at the protein level. Concurrently, we observed a distinct epigenetic signature characterized by the significant downregulation of DNA <i>N⁶</i>-adenine methylation (6mA) methyltransferases (homologs of AMT1 and AMT6/7), suggesting a potential repressive role of methylation during the cyst stage. Collectively, these findings provide a multidimensional atlas of the encystment process, revealing that <i>O. granulifera</i> accomplishes cellular structural remodeling through a multilayered regulatory network spanning morphological, genetic, transcriptomic, and proteomic levels.IMPORTANCE<i>Oxytricha</i> species are widely distributed in freshwater and terrestrial ecosystems, playing significant ecological roles in microbial communities. Their ability to undergo encystment provides a powerful model for studying cellular differentiation and stress adaptation in microbial eukaryotes. This study presents the first multi-omics analysis of encystment in <i>Oxytricha granulifera</i>, revealing microbial survival strategies through enhanced protein turnover, autophagy, alternative splicing, and DNA methylation reprogramming. These findings offer fundamental insights into dormancy mechanisms and environmental adaptation in protists, advancing our understanding of microbial resilience, evolutionary innovation, and ecological success in fluctuating environments.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0175725"},"PeriodicalIF":4.6,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776407","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":"Applying microbial ecology frameworks to microbial therapies for wildlife.","authors":"Sally L Bornbusch, Carly R Muletz-Wolz","doi":"10.1128/msystems.00598-25","DOIUrl":"https://doi.org/10.1128/msystems.00598-25","url":null,"abstract":"<p><p>Microbial ecology is increasingly incorporated into human and animal medicine via the study and purposeful manipulation of host-associated microbiomes. Microbial therapies-treatments with the aim of beneficially modulating microbiomes-are a burgeoning area of research and industry. These microbial therapies include prebiotic dietary items, live probiotics, and whole microbiota transplants (e.g., fecal microbiota transplants). Although microbial therapies for humans and domestic animals are now widely produced for commercial use and application, evidence supporting the efficacy of commercial microbial therapies is mixed. We suggest that microbial therapies are most effective when paired with concepts from ecology and rigorous empirical research. This is particularly relevant for the development and use of microbial therapies in wildlife animal species, in which we see large-scale variation in microbial communities across hosts of varying ecologies. Identifying and developing microbial therapies that can simultaneously be accessible and effective in a variety of hosts poses a novel challenge for microbial ecologists, animal scientists, and human and animal medical professionals. In addition to pre- and probiotics, we suggest that whole microbiota transplants provide a method of microbial supplementation that may better align with species-specific microbial ecology. Moving forward, emerging methods used in human medicine such as machine learning, network analysis, and microbiome engineering using high-throughput culturomics will likely be key to identifying and applying functionally relevant (e.g., disease suppressive) microbial taxa for wildlife therapies.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0059825"},"PeriodicalIF":4.6,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776565","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":"Ethnicity-specific microbiome in early childhood caries: a functional perspective of oral biofilm.","authors":"Kuei-Ling C Hsu, Tara N Furstenau, Isaac Shaffer, Mark D Macek, Robert K Ernst, Viacheslav Y Fofanov","doi":"10.1128/msystems.01787-25","DOIUrl":"https://doi.org/10.1128/msystems.01787-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;National surveillance data show persistent racial and ethnic disparities in early childhood caries (ECC), but the underlying causes of these differences have not been determined. This study examined both functional and taxonomic differences in ECC-related microbial activity between two high-risk groups of children: African American (AA) and Latin American Hispanic (LAH). Metatranscriptomic profiling of paired non-caries and caries plaque revealed consistent population-level shifts in gene expression and enabled species-level attribution of metabolically active microbes in caries lesions. A core set of well-established cariogenic organisms was consistently present and highly over-expressed in caries of both groups, including &lt;i&gt;Streptococcus mutans&lt;/i&gt;, &lt;i&gt;Veillonella parvula&lt;/i&gt;, &lt;i&gt;Propionibacterium acidifaciens&lt;/i&gt;, and &lt;i&gt;Lactobacillus rhamnosus&lt;/i&gt;. Beyond identifying the core organisms and functions active in lesions, we have also made two significant observations. First, the active communities in the two groups have substantially diverged: 4,900+ genes across 413 Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were consistently (25%+ of samples) over-expressed in AA children, and 6,500+ genes across 382 KOs were consistently (57% of samples) over-expressed in LAH children. This reproducibility across multiple samples indicates robust group-level differences rather than random variation or single-sample effects. Second, although AA and LAH children exhibited similar functional responses to caries (sharing 1,392 KOs), these shifts were expressed by different bacterial species, indicating that distinct taxa may occupy similar metabolic niches in different groups. Taken together, these findings suggest that there is no single universal caries-associated microbiome; instead, a shared cariogenic core is necessary, but differences among the non-core taxa and their functional activity may be key to understanding ECC disparities.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;The disparity in tooth decay among young children has long been demonstrated in national surveillance data. While various factors including family, culture, access to health insurance, and medical infrastructure have been studied, the global transcriptomic perspective remains underexplored. Employing RNA-Seq technology, we examine functional and taxonomic differences in caries-associated microbial activity between two high-risk populations. Besides a core set of well-established cariogenic organisms, we observed significant and consistent differences in the active microbial communities between these two high-risk populations, African American (AA) and Latin American Hispanic (LAH) children. In AA children, &lt;i&gt;Pseudopropionibacterium propionicum&lt;/i&gt; and &lt;i&gt;Cardiobacterium hominis&lt;/i&gt; consistently showed the highest caries-related gene expression. In contrast, among LAH children, &lt;i&gt;Propionibacterium acidifaciens&lt;/i&gt;, &lt;i&gt;Selenomonas&lt;/i&gt; sp., &lt;i&gt;Rothia dentocariosa&lt;/i&gt;, &lt;i","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0178725"},"PeriodicalIF":4.6,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776589","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":"Systematic evaluation of TCGA tumor microbiota reveals context-dependent reliability.","authors":"Chenchen Ma, Changxing Su, Jiaxuan Li, Jiaying Wang, Jianliang Liao, Lanlan Cheng, Jiuxin Qu, Guoquan Zhang, Jun Jiang, Shimin Shuai","doi":"10.1128/msystems.00180-26","DOIUrl":"https://doi.org/10.1128/msystems.00180-26","url":null,"abstract":"<p><p>Microbial profiles from The Cancer Genome Atlas (TCGA) are widely used to study the tumor microbiota, a key component of the cancer ecosystem, yet their reliability remains unclear. Here, we systematically benchmarked two leading TCGA microbial profiles (TMPs) to define their consistency, accuracy, and reliability in host-microbe association studies across 24 cancer types, with a primary focus on the bacterial component. We found that while the TMPs showed substantial agreement in microbial composition, their accuracy in detecting known oncomicrobes was variable, ranging from excellent for human papillomavirus (HPV) to poor for <i>Helicobacter pylori</i>. The concordance of downstream host-microbe associations was moderate for gene expression but nearly absent for methylation and protein data. Our permutation-based framework revealed that while most individual associations were statistically reliable, those involving cell type composition and patient survival were statistically spurious. To empower future research with these insights, we introduced Multi-Omics and Microbiome Associations in Cancer 2 (MOMAC2), an interactive web portal that stratifies all associations by confidence level. We demonstrated its utility by using high-confidence associations to confirm HPV-driven methylation-gene expression axes and guide a novel experimental investigation. Co-culture with <i>Streptococcus anginosus</i> not only validated its predicted gene expression changes in oral cancer cells but also revealed a significant promotion of cancer cell proliferation and migration. Our study provides a rigorous framework for interpreting TCGA's tumor microbiome and highlights that these data require careful, multi-layered validation to yield robust biological insights.</p><p><strong>Importance: </strong>Bacteria living inside tumors can influence how cancer grows and responds to treatment, but the field has been hampered by controversy over the reliability of the data. Our study provides a much-needed road map for researchers. We rigorously tested the massive Cancer Genome Atlas data set and developed a statistical framework to separate true biological signals from random noise. We discovered that many widely reported links are statistically unreliable and likely false leads. Importantly, our framework successfully pinpoints trustworthy signals. We used it to identify a specific bacterium, <i>Streptococcus anginosus</i>, and proved in the lab that it makes oral cancer cells grow faster and spread. Our publicly available Multi-Omics and Microbiome Associations in Cancer 2 (MOMAC2) web portal now allows scientists to use these reliability-graded findings to accelerate robust cancer microbiome research.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0018026"},"PeriodicalIF":4.6,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776531","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":"Enterohemorrhagic <i>Escherichia coli</i> O157:H7 responds to norepinephrine gradients by tRNA reprogramming and codon-biased translation of virulence genes.","authors":"Abigail E McShane, Chi-Kong Chan, Ruixi Chen, Michael S DeMott, Thomas J Begley, Peter C Dedon","doi":"10.1128/msystems.01418-25","DOIUrl":"https://doi.org/10.1128/msystems.01418-25","url":null,"abstract":"<p><p>Enterohemorrhagic <i>Escherichia coli</i> O157:H7 (EHEC) is a low-infectious-dose foodborne pathogen that uses norepinephrine gradients in the gut to locate sites for colonization and activate expression of virulence factors. Here, we identified features of transfer RNA (tRNA) reprogramming and codon-biased translation that play a role in this infectious process. Multivariate statistical analysis of genome-wide codon usage patterns revealed five gene clusters with unique codon biases, with one cluster containing all Locus of Enterocyte Effacement virulence genes that are all strongly biased for A/U-ending codons. EHEC cultures were then exposed to a norepinephrine gradient to induce type III secretion, as well as chemotaxis and flagellar motility, followed by a multi-omic interrogation of changes in tRNA modifications, tRNA abundance, and the proteome. We observed altered levels of multiple tRNA wobble modifications involved in G/C- versus A/U-ending codon recognition and a corresponding shift in the proteome toward genes enriched in A/U-ending codons. Our studies suggest EHEC can alter its tRNA pool in response to cues from the host, fine-tuning translational efficiency of its virulence program.IMPORTANCERegulation of microbial physiology and virulence during environmental changes has typically been ascribed to transcriptional mechanisms. Using convergent multi-omic technologies, we have discovered mechanisms of translational regulation of gene expression that regulate cell phenotype. Here, we applied these technologies to define mechanisms of translational regulation in the <i>Escherichia coli</i> O157:H7 response to norepinephrine exposure known to induce virulence.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0141825"},"PeriodicalIF":4.6,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776647","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>Pseudomonas aeruginosa</i> dynamically prioritizes motility and resource recycling during prolonged starvation.","authors":"Findlay D Munro, Elize Ambulte, Claudia M Hemsley, Megan Bergkessel","doi":"10.1128/msystems.01439-25","DOIUrl":"10.1128/msystems.01439-25","url":null,"abstract":"<p><p>Heterotrophic bacteria rapidly deplete essential macronutrients during growth and must navigate subsequent periods of growth arrest imposed by starvation. Nutrient limitations can be dynamic in nature, requiring ongoing regulatory adjustments involving new protein synthesis despite total biosynthetic activities being dramatically lower than during growth. Here, we have characterized the responses of the opportunistic pathogen <i>Pseudomonas aeruginosa</i> to prolonged starvation for carbon or nitrogen sources and to transitions between these states. We find that most cells survive both types of starvation for more than a week and maintain low but robustly detectable levels of protein synthesis in the absence of growth. Nitrogen-starved cells are larger, make more proteins, and retain fewer ribosomes than carbon-starved cells, indicating that distinct physiological strategies are adopted during the two starvation types. We found that the newly synthesized proteomes of each starvation type are distinct although many of the most highly synthesized proteins are shared between both conditions. Interestingly, we observed a temporary burst of protein synthesis as cells were transitioned between the two starvation conditions, which may reflect active remodeling of the proteome during growth arrest. We also used transposon insertion sequencing to identify genes impacting fitness in both starvation conditions and during transitions between the two and found that a highly overlapping set of global regulators most strongly influenced survival. Combining these data sets, we highlight proteases and chaperones, flagellar motility, and the nitrogen-related phosphotransferase system as key fitness-impacting functions that are actively maintained by growth-arrested <i>Pseudomonas aeruginosa</i>.</p><p><strong>Importance: </strong>Molecular microbiology has traditionally focused on exponential growth in model organisms as the preferred context in which to study bacterial physiology, especially the regulation of new protein synthesis. However, in natural environments, including many infection contexts, bacteria frequently enter growth arrest due to nutrient limitation. The dynamics and regulation of protein synthesis in growth-arrested cells remain poorly understood, especially in pathogens. Furthermore, growth arrest increases tolerance to a variety of stresses, including many clinically used antimicrobials. We have conducted a comprehensive exploration of the proteins being made by growth arrested <i>Pseudomonas aeruginosa</i> during total nitrogen or carbon starvation and at the transition between these two starvation types, and the genes supporting fitness under these conditions. These datasets suggest dynamic redistribution of resources among important cellular functions and will serve as a resource for further investigations of starvation-induced growth arrest, a ubiquitous but understudied physiological state of heterotrophic bacteria.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0143925"},"PeriodicalIF":4.6,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13098243/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147486750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Pseudomonas aeruginosa</i> strains lack tissue specificity.","authors":"Alan R Hauser","doi":"10.1128/msystems.00076-26","DOIUrl":"10.1128/msystems.00076-26","url":null,"abstract":"<p><p>Bacterial pathogens vary markedly from species to species in their capacity to cause different types of infection. A recent study by Penaranda and colleagues in <i>mSystems</i> shows that the genetic backgrounds of <i>Pseudomonas aeruginosa</i> isolates do not dictate whether they infect the lungs, blood, urine, or other body sites (C. Penaranda, E. P. Brenner, A. E. Clatworthy, L. A. Cosimi, et al., mSystems 11:e01362-25, 2026, https://doi.org/10.1128/msystems.01362-25). These findings suggest that each <i>P. aeruginosa</i> strain is versatile and has the potential to infect a variety of tissues and organs.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0007626"},"PeriodicalIF":4.6,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13098220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147499423","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":"Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.","authors":"Sven P Tobias-Hünefeldt, Jason N Woodhouse, Hans-Joachim Ruscheweyh, Shinichi Sunagawa, Vanessa Russnak, Wolfgang R Streit, Hans-Peter Grossart","doi":"10.1128/msystems.01790-25","DOIUrl":"10.1128/msystems.01790-25","url":null,"abstract":"<p><p>Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage.</p><p><strong>Importance: </strong>Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0179025"},"PeriodicalIF":4.6,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13098242/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147574831","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}