mSystems最新文献

{"title":"Interactions between native soil microbiome and a synthetic microbial community reveals bacteria with persistent traits.","authors":"Jessica M Velte, Sameerika Mudiyanselage, Olivia F Hofmann, Sonny T M Lee, Jose Huguet-Tapia, Mariza Miranda, Samuel J Martins","doi":"10.1128/msystems.00921-25","DOIUrl":"10.1128/msystems.00921-25","url":null,"abstract":"<p><p>Synthetic microbial communities (SynComs) are curated microbial groups that can be designed to optimize microbial functions, such as enhancing plant growth or disease resistance. Attaining SynCom stability in the presence of native soil communities remains a key challenge. This study investigated the survival, persistence, and chemical interactions of a SynCom with a native soil microbial community using a transwell system that spatially constrains bacteria while permitting chemical interactions. The SynCom, composed of six compatible <i>Pseudomonas</i> species identified through whole-genome sequencing, was analyzed for antagonistic interactions with native microbes over time and assessed using biomass and viability measurements. Over time, the SynCom exhibited reduced growth in the presence of native soil microbes compared to the SynCom not exposed to the native microbes. Flow cytometry analysis showed an 81% reduction of live cells for the persistent strain in the presence of native microbes and a 78% and 99% increase in dead and unstained cells, respectively. Compared to a non-persistent strain, one persistent SynCom strain showed lower metabolic utilization across five key compound classes: polymers, carboxylic acids, amino acids, amines, and phenols when exposed to the native soil microbes. These findings underscore the importance of understanding complex SynCom-environment interactions to enhance SynCom stability and optimize <i>in situ</i> applications.IMPORTANCESynComs are an emerging technology that can augment plant health. Still, their application <i>in situ</i> depends on deciphering the complex interactions between SynCom microbes and native microbial communities. This study provides insight into several <i>Pseudomonas</i> strains displaying persistent characteristics. Understanding the persistent traits of these bacteria is a vital advancement in SynCom technology and an important next step toward implementing SynComs in agricultural systems.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0092125"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961780","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":"Cross-cohort microbiome-wide study reveals consistent alterations in the gut bacteriome, but not the gut mycobiome, in patients with hypertension.","authors":"Yidan Gao, Dangrang Wang, Tong Lu, Kan Liu, Shenghui Li, Jian Kang, Shanshan Sha, Guorui Xing, Lin Cheng, Shao Fan, Wei Yang, Qiulong Yan, Yanchun Ding, Dafeng Xu","doi":"10.1128/msystems.00657-25","DOIUrl":"10.1128/msystems.00657-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Hypertension, one of the most prevalent cardiovascular diseases, has been linked to the gut microbiota. However, there is a lack of well-defined, cross-population validated gut microbial signatures associated with hypertension, particularly at both the bacterial and fungal levels. To address this gap, we conducted a metagenome-wide analysis of fecal samples from 159 hypertensive patients and 101 healthy controls, using two publicly available data sets from the Beijing and Dalian regions. Our results showed that hypertensive patients exhibit a significant reduction in gut bacterial diversity, accompanied by substantial alterations in bacterial composition. A total of 61 bacterial species were identified with significantly different relative abundance between patients and controls across both regions (combined &lt;i&gt;P&lt;/i&gt; &lt; 0.05, &lt;i&gt;q&lt;/i&gt; = 0.25). Hypertension-enriched species included &lt;i&gt;Lachnospiraceae&lt;/i&gt; (&lt;i&gt;Clostridium symbiosum&lt;/i&gt;, &lt;i&gt;Enterocloster bolteae&lt;/i&gt;) and &lt;i&gt;Clostridium&lt;/i&gt; sp. AT4, while &lt;i&gt;Lachnospiraceae bacterium&lt;/i&gt;, &lt;i&gt;Firmicutes bacterium&lt;/i&gt;, and &lt;i&gt;Clostridium&lt;/i&gt; sp. AM49 4BH were significantly decreased in hypertensive patients. In contrast, no significant differences were observed in gut fungal diversity between hypertensive patients and healthy controls, and only minor differences in fungal composition were noted. Specifically, six fungal species were identified as potentially significant in the combined data set (&lt;i&gt;P&lt;/i&gt; &lt; 0.05, &lt;i&gt;q&lt;/i&gt; = 0.73), but they only &lt;i&gt;Blastomyces emzantsi&lt;/i&gt; c231 meet the same consistency across the two cohorts as the bacterial signatures. Furthermore, we developed classification models using gut bacterial and fungal signatures to distinguish hypertension patients from healthy controls. The bacterium-based models achieved area under the curves (AUCs) greater than 0.70 in cross-cohort classification and validation, while the fungus-based models only achieved AUCs between 0.55 and 0.57. In summary, our study identifies cross-cohort gut bacterial and fungal signatures associated with hypertension, suggesting that the gut bacteriome may serve as a more reliable target for hypertension intervention compared to the gut mycobiome.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Hypertension (HTN) represents a global health burden affecting billions of individuals worldwide; however, the relationship between HTN and gut microbial ecosystems remains inadequately characterized. This study presents the first cross-cohort microbiome analysis revealing significant alterations in the gut bacteriome of HTN patients, with limited changes observed in the mycobiome. These findings highlight the critical role of the gut bacteriome in the pathogenesis of HTN and provide new microbial biomarkers for early diagnosis. Furthermore, the identification of bacterial species establishes a foundation for future intervention approaches, enhancing the applicability of microbiome research in cardiovascular health and opening new","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0065725"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455987/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855711","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":"Genetic exchange shapes ultra-small Patescibacteria metabolic capacities in the terrestrial subsurface.","authors":"Emilie Gios, Olivia E Mosley, Nobuto Takeuchi, Kim M Handley","doi":"10.1128/msystems.00046-25","DOIUrl":"10.1128/msystems.00046-25","url":null,"abstract":"<p><p>Bacterial genomes are highly dynamic entities, mostly due to horizontal gene transfer (HGT). HGT is thought to be the main driver of genetic variation and adaptation to the local environment in bacteria. However, little is known about the modalities of HGT within natural microbial communities, especially the implications of genetic exchange for streamlined microorganisms such as Patescibacteria (Candidate Phyla Radiation). We searched for evidence of genetic exchange in 125 Patescibacteria genomes recovered from aquifer environments and detected the presence of hundreds of genomic islands, individually transferred genes, and prophages combined, with up to 13% of genome length attributed to HGT. Results show that most individual gene transfer events occurred between Patescibacteria, although putative donors included phylogenetically diverse groundwater microorganisms. For example, results indicate exchange of a <i>lysR</i> transcriptional regulator gene between Omnitrophota and Patescibacteria taxa with highly similar relative abundance patterns across 16 groundwater samples. Overall, results indicate a wide variety of metabolic functions were introduced into Patescibacteria genomes by HGT, including transcription, translation, and DNA replication, recombination and repair. This study illustrates the evolutionarily dynamic nature of Patescibacteria genomes despite the constraints of streamlining and that HGT in these organisms is also mediated via viral infection.</p><p><strong>Importance: </strong>Genomic fluidity and diversity in bacteria are mainly governed by horizontal gene transfer (HGT), leading to a variety of genome structures and physiological diversity. The predominantly uncultivated Patescibacteria comprise highly diverse bacteria that consistently exhibit small cell and genome sizes. Despite strong pressures to reduce genetic content, we predict that these ultra-small bacteria use HGT to the same extent as other bacteria and that HGT may help facilitate recovery and maintenance of critical metabolic functions, niche exploitation, and putative symbiont-host interactions. Here, we determine the contribution of gene exchange to the evolution and diversification of Patescibacteria, despite the constraints of streamlining. We provide evidence of gene gains in Patescibacteria genomes recovered from aquifer environments and describe the large extent to which ultra-small bacterial genomes are subjected to HGT. Results suggest distinct metabolic functions acquired by Patescibacteria compared to general groundwater communities, suggesting specific evolutionary pressures on gene transfer dynamics occurring in ultra-small prokaryotes.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0004625"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855714","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":"Metabolic remodeling of microorganisms by mobile genetic elements alters mutualistic community composition.","authors":"Ave T Bisesi, Ross P Carlson, Lachlan Cotner, William R Harcombe","doi":"10.1128/msystems.00144-25","DOIUrl":"10.1128/msystems.00144-25","url":null,"abstract":"<p><p>Mobile genetic elements (MGEs) are ubiquitous in prokaryotes and exert significant influence on microbial communities, in part through their effects on host metabolism. While some MGEs directly alter host metabolism by introducing novel enzymes, all MGEs can indirectly change bacterial metabolism by redirecting intracellular host resources away from native bacterial processes toward MGE production. As a result, even when MGEs do not provide new metabolic functions, their carriage can influence host traits such as growth rate, nutrient uptake, and waste excretion, with consequences for how bacteria contribute to community and ecosystem functions. However, there are few empirical tests of how the indirect metabolic consequences of MGE carriage shape interactions between host and non-host bacterial species. We integrated genome-scale metabolic modeling with an <i>in vitro</i> obligate cross-feeding system to investigate the metabolic consequences of two MGEs in <i>Escherichia coli</i>: the conjugative plasmid F128 and the filamentous phage M13. We examined the impact of these MGEs on interactions between bacteria in a multispecies cross-feeding community composed of <i>E. coli</i>, <i>Salmonella enterica,</i> and <i>Methylobacterium extorquens</i>. Both modeling and <i>in vitro</i> experiments suggested that MGE carriage can change the growth rate and excretion profile of <i>E. coli</i>. We also found that indirect changes to host metabolism induced by our MGEs increased the density of cross-feeding species. Our work emphasizes that microbes carrying MGEs can have different metabolisms than MGE-free cells, even when MGEs do not encode metabolic enzymes, and demonstrates that these metabolic shifts can have significant consequences for microbial community structure and function.IMPORTANCEMobile genetic elements (MGEs) often shape the structure and function of microbial communities by influencing the metabolism of bacterial cells. Though some MGEs change metabolism directly by transferring genetic material that provides access to novel niche space, all MGEs should alter host metabolism indirectly to some degree by shifting intracellular metabolic processes toward MGE replication. This study uses a combination of flux balance analysis and an <i>in vitro</i> system consisting of <i>Escherichia coli</i>, <i>Salmonella enterica</i>, <i>Methylobacterium extorquens</i>, and two MGEs in <i>E. coli</i> to investigate how MGEs change the community contributions of their hosts via metabolic conflict alone. Flux balance analysis suggests that MGEs can change intracellular demand for different metabolic processes, leading to shifts in the identities and concentrations of compounds that hosts externalize into the environment. This finding is supported by experimental results and extends our understanding of how MGEs shape the structure and function of microbial communities.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0014425"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455974/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855802","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":"Gut-kidney axis modulation by viable and inactivated <i>Akkermansia muciniphila</i> mitigates avian hyperuricemia through microbial-metabolic crosstalk.","authors":"Yang Fu, Jiaqing Chen, Qingyun Cao, Shanshan Zhu, Wenjing Chen, Haotong Luo, Yue Zhao, Lukuyu A Bernard, Xue Wang, Qiang Tu, Youming Zhang, Xianzhi Jiang, Ling Yang, Wence Wang","doi":"10.1128/msystems.00773-25","DOIUrl":"10.1128/msystems.00773-25","url":null,"abstract":"<p><p>Hyperuricemia (HUA) has become the fourth most important health-threatening risk factor after hypertension, hyperglycemia, and hyperlipidemia, but the efficacy of existing uric acid-lowering treatments (ULT) is poor, and there is an urgent need to explore novel ULT strategies. <i>Akkermansia muciniphila</i> (<i>A. muciniphila</i>), a next-generation probiotic, shows promise in promoting intestinal homeostasis and metabolic regulation. Previous studies have demonstrated the potential application of <i>A. muciniphila</i> in ULT, but its specific mechanism has not been elucidated. In this study, we isolated a strain of <i>A. muciniphila</i>, named K101, from the cecum of goslings. <i>In vitro</i> experiments showed that K101 directly degrades uric acid, suggesting a potential microbial-metabolic crosstalk mechanism for anti-HUA. <i>In vivo</i> experiments showed that K101 increased the abundance of uric acid metabolism-related microbiota, such as <i>A. muciniphila</i> and <i>Lactobacillus</i>. Functionally, K101 synergistically promoted uric acid excretion by activating the intestinal excretory protein ABCG2 and inhibiting the renal uric acid reabsorption protein GLUT9. In addition, K101 provides a stable environment for uric acid metabolism by inhibiting renal inflammatory responses. Overall, <i>A. muciniphila</i> K101 exerts anti-HUA effects by remodeling the intestinal microbiota and excretion of uric acid through the gut-renal axis. This study offers new insights into microbial-metabolic crosstalk in uric acid metabolism in <i>A. muciniphila</i> and identifies potential targets for gout prevention and ULT strategy development.IMPORTANCEThe rising prevalence of hyperuricemia (HUA) underscores the need for new therapies and treatment approaches. Our study highlights the developmental and therapeutic potential of natural uric acid-degrading bacteria discovered in the avian gut, expanding the range of bacteria with possible medical applications. Another key finding is the notable efficacy of microbiota metabolites in alleviating HUA. While the underlying mechanisms warrant further investigation, these findings offer promising insights into microbiota-based therapeutics.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0077325"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455951/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961711","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":"GplR1, an unusual TetR-like transcription factor in <i>Mycobacterium abscessus,</i> controls the production of cell wall glycopeptidolipids, colony morphology, and virulence.","authors":"Scarlet S Shell, Michal Bar-Oz, Junpei Xiao, Manitosh Pandey, Juan Bellardinelli, Opeyemi I Ibitoye, Mary Jackson, Stefan H Oehlers, Daniel Barkan, Michal Meir","doi":"10.1128/msystems.00872-25","DOIUrl":"10.1128/msystems.00872-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Mycobacterium abscessus&lt;/i&gt; is a major human pathogen, mostly infecting people with pre-existing lung conditions, such as cystic fibrosis. The production of glycopeptidolipids (GPL) is a major determinant of virulence of this bacterium, with clinical isolates that lack GPL generally exhibiting more aggressive clinical behavior. The current paradigm is that GPL production is abolished &lt;i&gt;in vivo&lt;/i&gt; via irreversible, spontaneous mutations taking place as part of in-host evolution. Little is known about the mechanisms or extent to which GPL production may be regulated. Here, we describe an unusual TetR-like transcription factor of &lt;i&gt;M. abscessus&lt;/i&gt;, &lt;i&gt;mab_1638&lt;/i&gt;, that appears to be a strong positive regulator of the entire GPL biosynthesis and export gene cluster through a combination of direct and indirect mechanisms. The inactivation of &lt;i&gt;mab_1638&lt;/i&gt; abolished GPL production, leading to stable rough colony morphology and increased virulence in infection models, characteristics of rough, non-GPL producers. Transcriptome analysis found that the &lt;i&gt;mab_1638&lt;/i&gt; mutant had 118 differentially expressed genes, including the GPL locus and a second, recently described GPL-like locus that produces a related glycosylated lipopeptide called GP8L. Chromatin immunoprecipitation and sequencing revealed a consensus inverted-repeat DNA sequence motif, characteristic of genes regulated by &lt;i&gt;mab_1638&lt;/i&gt;. Together, these findings found that &lt;i&gt;mab_1638&lt;/i&gt; encodes a transcription factor required for GPL production and, therefore, has a profound effect on virulence traits. We propose naming this gene GPL regulator 1 (&lt;i&gt;gplR1&lt;/i&gt;). This finding raises the important possibility that &lt;i&gt;M. abscessus&lt;/i&gt; strains appearing smooth in laboratory growth conditions may nonetheless downregulate GPL-cluster genes in other conditions, including in-patient conditions, and thus acquire the phenotypic characteristics of rough strains.IMPORTANCE&lt;i&gt;Mycobacterium abscessus&lt;/i&gt; is an important human pathogen, causing disease that is difficult to treat. &lt;i&gt;M. abscessus&lt;/i&gt; strains have been observed to have two distinct colony morphologies, smooth and rough, which substantially impact clinical presentation. Rough strains are associated with later-stage, more severe disease and are more virulent in animal models. Smooth morphology is conferred by a molecule called glycopeptidolipid in the outer cell envelope, and rough morphology is known to occur when mutations inactivate genes required for glycopeptidolipid biosynthesis. Little is known about the possibility that glycopeptidolipid production could be regulated. Here, we have identified a transcription factor that is required for glycopeptidolipid biosynthesis, indicating that glycopeptidolipid production is indeed a regulated process and raising the important possibility that strains exhibiting smooth morphology in the lab may downregulate GPL production in the human host, thereby acquiring the virulence properties ","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0087225"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961797","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":"Phylogenetic intermixing reveals stable fly-mediated circulation of mastitis-associated bacteria in dairy settings.","authors":"Andrew J Sommer, Travis K Worley, Panagiotis Sapountzis, Kerri L Coon","doi":"10.1128/msystems.00215-25","DOIUrl":"10.1128/msystems.00215-25","url":null,"abstract":"<p><p><i>Stomoxys</i> flies are common blood-feeding pests on dairy farms and are suspected carriers of pathogenic bacteria due to their close association with manure and cattle hosts. While prior studies have used amplicon sequencing and culture-dependent methodologies to characterize the composition of the <i>Stomoxys</i> microbiota, little is known about strain-level acquisition of mastitis-causing bacteria from manure by <i>Stomoxys</i> or the functional diversity of <i>Stomoxys</i>-associated taxa. In this study, we address these key knowledge gaps by using whole genome sequencing to provide the first comparative genomic analysis of <i>Stomoxys-</i>derived <i>Escherichia coli</i>, <i>Klebsiella pneumoniae</i>, and <i>Staphylococcaceae</i> isolates. Our results show that fly and manure isolates collected from the same farm system are phylogenetically interspersed, with subsequent pairwise genome alignments revealing near-identical strains and plasmids shared between the two sources. We further identify a phylogenetic clade of <i>Mammaliicoccus sciuri</i> containing known mastitis agents associated with both flies and manure. Functional analysis reveals that this clade is highly enriched in xylose metabolism genes that are rare across other <i>M. sciuri</i> lineages, suggesting potential niche differentiation within the genus. Collectively, our results provide strong evidence for the acquisition of fecal-associated bacteria by adult <i>Stomoxys</i> flies, confirming the link between biting muscid flies and manure habitats. The intermixing of fly and manure isolates in clinically relevant taxonomic groups strongly suggests that flies serve as carriers of opportunistic mastitis-causing or other fecal-borne pathogens and may serve as important vehicles of pathogen dissemination across the dairy farm environment.IMPORTANCEBovine mastitis causes up to $32 billion dollars in losses annually in the global dairy industry. Opportunistic intramammary pathogens can be transmitted through incidental contact with bacteria in environmental reservoirs like manure. However, factors affecting the abundance, persistence, and spread of these bacteria are not well understood. Our research shows that mastitis pathogens are present in the guts of blood-feeding <i>Stomoxys</i> (stable) flies, which develop in cow feces and bite cows. Genomic analysis of isolates from flies, manure, and mastitis cases reveals that strains and antimicrobial resistance genes are shared between these sources. Further analysis of fly gut isolates shows virulence factors and possible niche specialization, identifying fly-associated clades with known mastitis agents from mastitic cows. This strongly suggests that <i>Stomoxys</i> flies play a role in the carriage and circulation of bovine mastitis pathogens from manure in dairy settings.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0021525"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455971/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760499","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":"Phenotypic and omics analyses of the Sordariomycetes <i>Marquandomyces marquandii</i> and <i>Albophoma yamanashiensis</i> isolated from estuarine sediments.","authors":"Z Agirrezabala, A Otamendi, R Liébana, M Azkargorta, C Perez-Cruz, M T Dueñas, M Ostra, R López, I V Grigoriev, L Alonso-Sáez, F Elortza, A Lanzén, S Haridas, Oier Etxebeste","doi":"10.1128/msystems.00625-25","DOIUrl":"10.1128/msystems.00625-25","url":null,"abstract":"<p><p>Marine environments harbor a vast diversity of microorganisms, which have developed multiple strategies to adapt to challenging conditions and represent a valuable source for new products such as pigments, enzymes, and bioactive compounds. From all microorganisms inhabiting marine environments, fungi have been the least studied, despite their ubiquitous presence and great biotechnological potential. Here, we focused on the isolation and characterization of filamentous fungi from marine sediment samples, which were collected along the Basque coast in Spain. Through phenotypic characterization, we identified isolates potentially able to produce secondary metabolites or grow on minimal culture medium supplemented with recalcitrant algal polysaccharides. Based on this screening, two Sordariomycetes strains were selected for further analyses through genome sequencing and omics techniques: (i) a <i>Marquandomyces marquandii</i> strain (M60) able to stain the culture medium in yellow, indicative of secretion of pigments and secondary metabolites and (ii) an <i>Albophoma yamanashiensis</i> strain (M98) able to grow in minimal culture medium supplemented with the recalcitrant algal polysaccharide fucoidan. Fungal co-culture experiments suggested an inhibitory effect of the secretome of <i>M. marquandii</i> (strain M60) on fungal growth. Under culture conditions inducing pigment secretion, a set of secondary metabolite gene clusters was differentially expressed, as analyzed by RNA-seq. On the other hand, transcriptomic and proteomic experiments on <i>A. yamanashiensis</i> (strain M98) unveiled the enzymatic activities expressed in response to the presence of fucoidan. Overall, our results indicate that the isolated marine fungal strains could serve as a source of new enzymatic activities and secondary metabolites.IMPORTANCECharacterization of the mycobiota of marine and estuarine environments is important for the identification of new potential biotechnological products such as pigments, enzymes, and bioactive compounds. In this work, we describe the phenotypes and genomics, transcriptomics, and proteomics features of the Sordariomycetes <i>Marquandomyces marquandii</i> (strain M60) and <i>Albophoma yamanashiensis</i> (strain M98). The former was selected as a pigment/secondary metabolite producer, and the secondary metabolite gene clusters differentially expressed under conditions inducing pigment production were identified. <i>A. yamanashiensis</i> (strain M98) was characterized as a potential degrader of fucoidan, and the carbohydrate-active enzymes and sulfatases induced in response to the presence of this sulfated, recalcitrant algal polysaccharide were identified.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0062525"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799584","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":"Genotypic and phenotypic characterization of <i>Staphylococcus aureus</i> isolated from human milk of asymptomatic women or women with acute mastitis.","authors":"Rubén Jurado, Alberto Aragón, Natalia Hernando, Josué Jara, Juan Miguel Rodriguez, Belén Orgaz, Leonides Fernández","doi":"10.1128/msystems.00797-25","DOIUrl":"10.1128/msystems.00797-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Acute mastitis is a common infection during lactation, primarily caused by &lt;i&gt;Staphylococcus aureus&lt;/i&gt;, a bacterium known for its ability to form biofilms within mammary ducts and develop antibiotic resistance. This study aimed to genomically characterize &lt;i&gt;S. aureus&lt;/i&gt; strains isolated from women with acute mastitis and healthy asymptomatic women to better understand how &lt;i&gt;S. aureus&lt;/i&gt; strains transition from harmless components of the human milk microbiota to pathogenic agents responsible for mastitis. Whole-genome sequencing was performed on nine &lt;i&gt;S&lt;/i&gt;. &lt;i&gt;aureus&lt;/i&gt; strains-six from women with mastitis and three from healthy women-followed by &lt;i&gt;in silico&lt;/i&gt; analyses of core and accessory genes, resistome, virulome, mobilome, and secondary metabolite synthesis to identify genes related to virulence, antibiotic resistance, biofilm formation, and mobile genetic elements such as plasmids, bacteriophages, and pathogenicity islands. Antimicrobial resistance profiles were evaluated using Sensititre EUST2 plates, antimicrobial activity by an agar diffusion method, biofilm formation in 96-well plates, and siderophore production with the Chrome Azurol S assay. Results showed that complete bacteriophage genomes were only present in &lt;i&gt;S. aureus&lt;/i&gt; strains isolated from mastitis cases. Some virulence genes, including &lt;i&gt;fnbB&lt;/i&gt; and &lt;i&gt;cna&lt;/i&gt;, were absent in strains from healthy women. Both types of &lt;i&gt;S. aureus&lt;/i&gt; strains exhibited biofilm formation capacity, with mastitis-associated strains SA4 and SA5 being the highest biofilm producers. Similarly, although all strains secreted siderophores, SA4 and SA55 exhibited the strongest siderophore production, indicating a link between this trait and virulence in mastitis-associated strains. The analysis of key genomic features, including virulence factors, resistance genes, and biofilm-forming capabilities, revealed some mechanisms by which &lt;i&gt;S. aureus&lt;/i&gt; contributes to the pathogenesis of mastitis.IMPORTANCEAcute mastitis is a widespread infection in lactating women, and its main cause, &lt;i&gt;Staphylococcus aureus&lt;/i&gt;, has developed resistance to antibiotics, making treatment challenging. The ability of this bacterium to form biofilms complicates its eradication from the mammary glands. Understanding the genomic and phenotypic characteristics of &lt;i&gt;S. aureus&lt;/i&gt; strains associated with mastitis, compared to those isolated from asymtomatic women, is critical for developing better treatment strategies. This study provides new insights into the genetic features, such as virulence factors, antibiotic resistance profiles, and presence of bacteriophages, that make &lt;i&gt;S. aureus&lt;/i&gt; strains pathogenic in mastitis. It also highlights the potential of biofilm formation and siderophore production as key factors in mastitis progression. These findings could guide the development of novel therapeutic approaches, such as targeted therapies or probiotics, which can more effectively treat mastitis and redu","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0079725"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855715","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":"Morphological and molecular analyses of season-specific responses of freshwater ciliate communities to top-down and bottom-up experimental manipulations.","authors":"Usman Asghar, Indranil Mukherjee, Bettina Sonntag, Caio César Pires de Paula, Vojtěch Kasalický, Paul-Adrian Bulzu, Anusha Priya Singh, Tanja Shabarova, Kasia Piwosz, Karel Šimek","doi":"10.1128/msystems.00304-25","DOIUrl":"10.1128/msystems.00304-25","url":null,"abstract":"<p><p>In aquatic microbial food webs, ciliates represent an important trophic link in the energy transfer from prokaryotes, algae, and heterotrophic nanoflagellates (HNFs) to higher trophic levels. However, the trophic role of abundant small ciliates (<20 µm) is not clearly understood. To unveil their trophic linkages, we conducted two experiments manipulating both top-down and bottom-up controlling factors, thus modulating the trophic cascading and bacterial prey availability for protists during contrasting spring and summer seasons with samples collected from a freshwater meso-eutrophic reservoir. Water samples were size fractionated to modify food web complexity, i.e., 10 µm, 20 µm, and unfiltered control and amended with bacterial prey additions. The samples were analyzed by morphological and sequencing techniques. The bacterial amendments triggered strong ciliate growth following the peaks of HNFs in the 10 and 20 µm treatments, reflecting a trophic cascading from HNFs to raptorial prostome ciliates (<i>Balanion planctonicum</i> and <i>Urotricha</i> spp.) in spring. In summer, HNFs and ciliates peaked simultaneously, suggesting the important trophic cascade also from bacteria to bacterivorous scuticociliates (<i>Cyclidium glaucoma</i> and <i>Cinetochilum margaritaceum</i>) and HNFs. In spring, unfiltered treatments showed stronger ciliate top-down control by zooplankton than in summer. The sequence analysis revealed season-specific manipulation-induced shifts in ciliate communities and their large cryptic diversity. However, morphological and molecular analyses also revealed considerable discrepancies in the abundance of major ciliate taxa. The ciliate communities responded to our experimental manipulations in season-specific fashions, thereby highlighting the different roles of ciliates as an intermediate trophic link between prokaryotes and higher trophic levels.</p><p><strong>Importance: </strong>Ciliates represent an important trophic link in aquatic microbial food webs. In this study, we used the food web manipulation techniques to reveal their complex trophic interactions during seasonally different plankton scenarios occurring in spring and summer. Manipulating top-down controlling factors (grazing pressure of micro- and metazooplankton grazers) and bottom-up factors (an availability of bacterial prey) shaped distinctly the complexity and dynamics of natural plankton communities and thus yielded significant changes in ciliate community dynamics. The experimentally simplified plankton and ciliate communities responded to our manipulations in season-specific fashions, reflected in different roles of ciliates as an intermediate trophic link between prokaryotes and higher trophic levels. This study also demonstrates that the combination of molecular and morphological analyses is essential to gain more realistic insights into the structure of ciliate community and for providing robust, ecologically meaningful results.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0030425"},"PeriodicalIF":4.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855803","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}