Applied and Environmental Microbiology最新文献

{"title":"CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment.","authors":"Dirk Hackenberger, Hamna Imtiaz, Amogelang R Raphenya, Brian P Alcock, Hendrik N Poinar, Gerard D Wright, Andrew G McArthur","doi":"10.1128/aem.01876-24","DOIUrl":"10.1128/aem.01876-24","url":null,"abstract":"<p><p>Better interrogation of antimicrobial resistance requires new approaches to detect the associated genes in metagenomic samples. Targeted enrichment is an ideal method for their sequencing and characterization. However, no open-source, up-to-date hybridization probe set targeting antimicrobial resistance genes exists. Here, we describe the Comprehensive Antibiotic Resistance Probe Design Machine (CARPDM), a probe design software package made to run alongside all future Comprehensive Antibiotic Resistance Database releases. To test its efficacy, we have created and tested two separate probe sets: allCARD, which enriches all genes encoded in the Comprehensive Antibiotic Resistance Database's protein homolog models (<i>n</i> = 4,661), and clinicalCARD, which focuses on a clinically relevant subset of resistance genes (<i>n</i> = 323). We demonstrate that allCARD increases the number of reads mapping to resistance genes by up to 594-fold. clinicalCARD performs similarly when clinically relevant genes are present, increasing the number of resistance-gene mapping reads by up to 598-fold. In parallel with this development, we have established a protocol to synthesize any probe set in-house, saving up to 350 dollars per reaction. Together, these probe sets, their associated design program CARPDM, and the protocol for in-house synthesis will democratize metagenomic resistome analyses, allowing researchers access to a cost-effective and efficient means to explore the antibiotic resistome.IMPORTANCEAntimicrobial resistance threatens to undermine all modern medicine and is driven by the spread of antimicrobial resistance genes among pathogens, environments, patients, and animals. DNA sequencing of complex samples, such as wastewater, shows considerable promise for tracking these genes and making risk assessments. However, these methods suffer from high costs and low detection limits, plus a requirement for frequent redesign due to the constantly evolving diversity of resistance genes. Building upon our Comprehensive Antibiotic Resistance Database, our research provides software for on-demand renewal, based on the latest knowledge of resistance gene diversity, of our novel bait-capture hybridization platform that simultaneously reduces cost and increases detection levels for DNA sequencing of complex samples. The significance of our research is in the development of new software tools, reagent synthesis protocols, and hybridization enrichment protocols to provide affordable, high-resolution metagenomics DNA sequencing, which we test using environmental and wastewater samples.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0187624"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522518","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":"Effects of Sup35 overexpression on the formation, morphology, and physiological functions of intracellular Sup35 assemblies.","authors":"Jianhui Feng, Ekaterina Osmekhina, Jaakko V I Timonen, Markus B Linder","doi":"10.1128/aem.01703-24","DOIUrl":"10.1128/aem.01703-24","url":null,"abstract":"<p><p>The yeast prion protein Sup35 is aggregation-prone at high concentrations. <i>De novo</i> Sup35 prion formation occurs at a significantly increased rate after transient overexpression of Sup35 in the presence of another prion, [<i>PIN</i>⁺], but it is still a rare event. Recent studies uncovered an additional and seemingly more prevalent role of Sup35: at its physiological level, it undergoes phase separation to form reversible condensates in response to transient stress. Stress-induced reversible Sup35 condensation in the [<i>psi</i>^-] strain enhances cellular fitness after stress ceases, whereas irreversible Sup35 aggregates in the [<i>PSI</i>⁺] strain do not confer this advantage. However, how Sup35 overexpression, which could potentially lead to irreversible aggregation, affects its condensation under stress conditions remains unclear. In this study, we used a combinatorial method to examine how different levels of Sup35 overproduction and cellular conditions affect the nature, formation, and physical properties of Sup35 assemblies in yeast cells, as well as their impacts on cellular growth. We observed notable morphological distinctions between irreversible Sup35 aggregates and reversible Sup35 condensates, possibly indicating different formation mechanisms. In addition, Sup35 aggregation caused by a very high overexpression level can strongly inhibit cell growth, diminish the formation of stress-induced condensates when Sup35 is completely aggregated, and impair cellular recovery from stress. Together, this study advances our fundamental understanding of the physical properties and formation mechanism of different Sup35 assemblies and their impacts on cellular growth. We conclude that <i>in vivo</i> studies are sensitive to overexpression and can lead to assembly routes that strongly affect functions.</p><p><strong>Importance: </strong>The role of condensates in living cells is often studied by overexpression. For understanding their physiological role, this can be problematic. Overexpression can shift cellular functions, thereby changing the system under study, and overexpression can also affect the phase behavior of condensates by shifting the position of the system in the underlying phase diagram. Our detailed study of overexpression of Sup35 in <i>S. cerevisiae</i> shows the interplay between these factors and highlights basic features of intracellular condensation such as the balance between condensation and aggregation as well as how cellular localization and responsiveness depend on protein levels. We also apply super-resolution microscopy to highlight details within the cells.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0170324"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254351","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":"Puerarin combined with <i>Hericium erinaceus</i> insoluble dietary fiber alleviates obesity induced by high-fat diet through regulating the glycerophospholipid metabolism pathway influenced by gut microbiota.","authors":"Guoze Wang, Binbin Wang, Qin Zhou, Zhimei Cheng, Li Liu, Shuai Zhang, Shi Zhou, Peng Luo","doi":"10.1128/aem.02376-24","DOIUrl":"10.1128/aem.02376-24","url":null,"abstract":"<p><p>The purpose of this study was to evaluate the combined effects of puerarin (Pue) and insoluble dietary fiber from <i>Hericium erinaceus</i> (HEIDF) on obesity induced by a high-fat diet (HFD) in mice, focusing on their effects on lipid and glucose metabolism, gut microbiota (GM), and serum metabolites. Glucose tolerance, tissue pathology, and serum biochemical levels were conducted to assess the effects of puerarin combined with <i>Hericium Erinaceus</i> insoluble dietary fiber (LH) on glucose and lipid metabolism. 16S rRNA sequencing and untargeted metabonomics were employed to explore the underlying mechanisms. The results showed that the LH group significantly reduced body weight and hepatic and adipose lipid accumulation, and improved glucose tolerance and dyslipidemia compared to the Pue or HEIDF groups alone. Moreover, the LH group exhibited enhanced regulation of GM, including increased microbial diversity, higher abundance of beneficial bacteria such as g__Lactobacillus and g__Bacillus, and a decreased Firmicutes-to-Bacteroidota ratio. In addition, the LH group ameliorated HFD-induced serum metabolite changes and promoted the activation of tryptophan and glycerophospholipid metabolism pathways. The combination of Pue and HEIDF exhibits a synergistic anti-obesity effect by modulating specific GM (g__Lactobacillus and g__Bacillus) and serum metabolites.IMPORTANCEThe combination of HEIDF and Pue holds significant importance in the context of obesity. This synergistic effect not only aids in weight management but may also enhance metabolic health through various mechanisms, including increased satiety and promotion of fat oxidation. Therefore, incorporating these two components into the daily diet could offer effective strategies for the prevention and intervention of obesity and its related diseases.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0237624"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921353/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456814","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":"Autoinducer-2 signaling promotes intestinal colonization of <i>Aeromonas veronii</i> and induces cell apoptosis in loach (<i>Misgurnus anguillicaudatus</i>).","authors":"Yi Li, Shuo Han, Wenfang Niu, Chao Gao, Yuqi Wang, Mengyuan Qin, Jingjing Han, Xiaohua Xia, Hailei Wang","doi":"10.1128/aem.00143-25","DOIUrl":"10.1128/aem.00143-25","url":null,"abstract":"<p><p>Quorum sensing systems, particularly autoinducer-2 (AI-2) signaling, have significant effects on bacterial colonization and virulence. However, how they affect intestinal colonization by pathogens and subsequent host immune responses remains unclear. Here, we investigated the influence of AI-2 signaling on the intestinal colonization ability of <i>Aeromonas veronii</i> Z12 and the host's immune response. We found that AI-2 signaling promoted the colonization of <i>A. veronii</i> to the intestine of loach (<i>Misgurnus anguillicaudatus</i>) and caused severe intestinal damage, while D-ribose, an AI-2 signaling inhibitor, effectively inhibited the colonization of <i>A. veronii</i>. Transcriptomic sequencing elucidated the molecular mechanism of this damage, revealing upregulation of p53 pathway genes associated with apoptosis. Furthermore, intestinal microbiota dysbiosis induced by <i>A. veronii</i> colonization was associated with host cell apoptosis, leading to nitrite accumulation, which increased intracellular reactive oxygen species (ROS) levels, which activated the p53 pathway, and induction of cell apoptosis. These findings provide insights into the interaction among bacterial quorum sensing, intestinal microbiota, and the host immune response, which highlight potential therapeutic targets for mitigating bacterial-induced intestinal damage.IMPORTANCEThe intestinal colonization of pathogens regulated by autoinducer-2 (AI-2) signaling and its induced host response have not been fully characterized. Here, we revealed the effect of AI-2 on intestinal colonization of <i>Aeromonas veronii</i> and its induced cell apoptosis in loach. Our study demonstrated that the deficiency of AI-2 significantly reduced <i>A. veronii</i> colonization in the loach intestine and mitigated the tissue damage. Additionally, <i>A. veronii</i> colonization induced significant upregulation of p53 pathway genes and proteins, indicating a key role of AI-2 signaling in host responses. Understanding these mechanisms not only helps to elucidate the pathogenicity of <i>A. veronii</i> but also may provide broader insights into the pathogenic mechanisms of other pathogens, thus revealing general principles of pathogen-host interactions across different models. Furthermore, we found that <i>A. veronii</i> colonization led to intestinal microbiota dysbiosis, notably an increase in the abundance of <i>Hypomicrobium</i> sp., which was associated with nitrite accumulation, elevating reactive oxygen species levels, activating the p53 pathway, and inducing cell apoptosis. These findings provide important insights into the complex mechanisms of AI-2 signaling in bacterial-host interactions. Additionally, the regulatory role of AI-2 signaling may have potential clinical applications as an intervention strategy, offering new directions for developing treatments against intestinal infections.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0014325"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143405545","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":"Minimal changes in microbial abundances and diversity over 7 years of emplacement for modules of compacted bentonite exposed to natural groundwater.","authors":"Harmanpreet S Sidhu, Katja Engel, Sian E Ford, Peter Keech, Mehran Behazin, W Jeffrey Binns, Nivetha Srikanthan, Myrna J Simpson, Josh D Neufeld, Gregory F Slater","doi":"10.1128/aem.01950-24","DOIUrl":"10.1128/aem.01950-24","url":null,"abstract":"<p><p>The multi-national <i>in situ</i> Materials Corrosion Test (MaCoTe), being conducted at the Grimsel Test Site in Switzerland, assesses the stability of bentonite as it may be utilized within deep geological repositories (DGRs), which are proposed for the safe, long-term disposal of used nuclear fuel. This experiment provides an opportunity for long-term assessments of changes in microbial communities associated with compacted subsurface bentonite samples exposed to a natural groundwater. Leveraging samples from MaCoTe, herein, we report temporal data for the abundance and community composition of microorganisms associated with compacted bentonite samples emplaced over 7 years under <i>in situ</i> subsurface conditions. Phospholipid fatty acid analysis, 16S rRNA gene quantification and sequencing, cultivation, and natural organic matter analyses all indicated no significant changes for microbial community abundances associated with inner layers of bentonite samples over the 7 years. While microbial abundances did not change in the inner layers, the PLFA data suggest potential changes in microbial community composition and could also indicate prolonged microbial turnover rates. Overall, the results support microbial stability in compacted bentonite exposed to DGR-like conditions for at least 7 years.IMPORTANCELong-term assessments of changes in microbial activity in compacted low-biomass bentonite systems analogous to deep geological repositories (DGRs) are critical to test conditions for stable engineered bentonite barrier components. This study assesses long-term temporal changes in microbial communities of compacted bentonites exposed to natural groundwater. It offers 7-year data that indicate stability of bentonite-based materials intended for use in engineered barrier systems of a DGR for the safe, long-term disposal of used nuclear fuel, with wider implications for microbial persistence in a deep subsurface environment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0195024"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921334/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An astrobiological perspective on microbial biofilms: their importance for habitability and production of detectable and lasting biosignatures.","authors":"Sarah Gonzalez-Henao, Matthew O Schrenk","doi":"10.1128/aem.01778-24","DOIUrl":"10.1128/aem.01778-24","url":null,"abstract":"<p><p>The search for life elsewhere in the universe has remained one of the main goals of astrobiological exploration. In this quest, extreme environments on Earth have served as analogs to study the potential habitability of Mars and icy moons, which include but are not limited to hydrothermal vent systems, acid lakes, deserts, and polar ice, among others. Within the various forms that life manifests, biofilms constitute one of the most widespread phenotypes and are ubiquitous in extreme environments. Biofilms are structured communities of microorganisms enclosed in a matrix of extracellular polymeric substances (EPS) that protect against unfavorable and dynamic conditions. These concentrated structures and their associated chemistry may serve as unique and persistent signatures of life processes that may aid in their detection. Here we propose biofilms as a model system to understand the habitability of extraterrestrial systems and as sources of recognizable and persistent biosignatures for life detection. By testing these ideas in extreme analog environments on Earth, this approach could be used to guide and focus future exploration of samples encompassing the geologic record of early Earth as well as other planets and moons of our solar system.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0177824"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921390/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381586","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":"Microfluidic droplets with amended culture media cultivate a greater diversity of soil microorganisms.","authors":"Jing Dai, Yang Ouyang, Rohit Gupte, Xiao Jun A Liu, Yuwen Li, Fang Yang, Shaorong Chen, Tony Provin, Erin Van Schaik, James E Samuel, Arul Jayaraman, Aifen Zhou, Paul de Figueiredo, Jizhong Zhou, Arum Han","doi":"10.1128/aem.01794-24","DOIUrl":"10.1128/aem.01794-24","url":null,"abstract":"<p><p>Uncultivated but abundant soil microorganisms have untapped potential for producing broad ranges of natural products, as well as for bioremediation. However, cultivating soil microorganisms while maintaining a broad microorganism diversity to enable phenotyping and functional analysis of as diverse individual isolates as possible remains challenging. In this study, we developed and tested the ability of several culture media formulations that contain defined soil metabolites or soil extracts to maintain microorganism diversity during culture. We also assessed their performance in microfluidic droplet cultivation where single-soil microorganism isolates were encapsulated and cultivated in picoliter-volume water-in-oil emulsion droplets to enable clonal growth needed for downstream functional analyses. Our results show that droplet cultivation with media supplemented by soil extract or soil metabolites enables the recovery of soil microorganisms with higher diversity (up to 1.5-fold higher richness) compared to bulk cultivation methods. Importantly, 1.7-fold more of less abundant (<1%) phyla and 11-fold more of unique genera were recovered, demonstrating the utility of this method for interrogating highly diverse soil microorganisms for broad ranges of applications.IMPORTANCEAlthough soil microorganisms hold a significant value in bioproduction and bioremediation, only a small fraction-less than 1%-can be cultured under specific media and cultivation conditions. This indicates that there are ample opportunities in harvesting the diverse environmental microorganisms if isolating and recovering these uncultured microorganisms are possible. This paper presents a new cultivation technique composed of isolating single-soil microorganism cell from an <i>in situ</i> soil microorganism community in microfluidic droplets and conducting in-droplet cultivation in media supplemented by soil extract or soil metabolites. This method enables the recovery of a broader diversity of the original microorganism community, laying the groundwork for a high-throughput phenotyping of these diverse microorganisms from their natural habitats.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0179424"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397781","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":"Shifts in surface microbiota after cleaning and disinfection in broiler processing plants: incomplete biofilm eradication revealed by robotic high-throughput screening.","authors":"Thorben Reiche, Gunhild Hageskal, Mihai Mares, Sunniva Hoel, Anne Tøndervik, Tonje Marita Bjerkan Heggeset, Tone Haugen, Sigri Bakken Sperstad, Hanne Hein Trøen, Solfrid Bjørkøy, Anita Nordeng Jakobsen","doi":"10.1128/aem.02401-24","DOIUrl":"10.1128/aem.02401-24","url":null,"abstract":"<p><p>Broiler processing environments are a source of spoilage bacteria and potential pathogens. The aim of this study was to investigate the impact of cleaning and disinfection (C&D) on bacterial load and diversity in two broiler processing plants and to determine the efficacy of industry-standard disinfectants (DIs). C&D significantly reduced average bacterial loads on surfaces from 3.7 to 1.8 log CFU/cm² in Plant A and from 7.0 to 3.8 log CFU/cm² in Plant B (<i>P</i> < 0.001). Metataxonomics revealed that <i>Acinetobacter</i> and an unknown Enterobacteriaceae genus dominated before C&D in Plants A and B, respectively, while <i>Pseudomonas</i> was predominant after C&D in both plants. Bacterial diversity only declined significantly after C&D in Plant B. Bacterial loads also declined across hygienic zones along the broiler processing line in Plant A. During slaughter, <i>Staphylococcus</i>, <i>Lactobacillus</i>, and <i>Anoxybacillus</i> dominated, and bacterial loads were significantly higher compared with post-slaughter zones, which were dominated by <i>Pseudomonas</i>. Culture-dependent analyses confirmed the presence of <i>Pseudomonas</i> spp. and also bacteria affecting food safety, including <i>Listeria monocytogenes</i>, <i>Escherichia coli</i>, <i>Yersinia enterocolitica</i>, <i>Acinetobacter baumannii</i>, and <i>Pseudomonas aeruginosa</i>. A selection of these was tested against DIs using robotic high-throughput screening. At the recommended user concentrations, DIs effectively inhibited planktonic bacteria and significantly reduced mono-species biofilms. However, none of the DIs completely eradicated all biofilms at these concentrations, with survival rates ranging from 7% to 53%, depending on the DI. In conclusion, C&D effectively reduces the bacterial burden and reshapes the bacterial microbiota with incomplete biofilm eradication by commercial DIs.IMPORTANCEBroiler meat continues to be involved in bacterial disease outbreaks. The surface microbiota in broiler processing environments can be a source of contaminating bacteria. Our study highlights the importance of effective C&D routines since potential pathogens and spoilage bacteria are found in these environments. Furthermore, the study provides evidence of biofilms surviving high concentrations of industry-standard DIs. This emphasizes the importance of additional measures to facilitate biofilm removal, such as mechanical cleaning, but also suggests that there is a need for DIs with stronger biofilm eradication capabilities. Ultimately, it is important to understand and continuously improve the state of hygiene in broiler processing plants to mitigate the risk of foodborne disease outbreaks.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0240124"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143498024","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>Salmonella</i> serotypes in the genomic era: simplified <i>Salmonella</i> serotype interpretation from DNA sequence data.","authors":"Xiangyu Deng, Shaoting Li, Tongzhou Xu, Zhemin Zhou, Michelle M Moore, Ruth Timme, Shaohua Zhao, Charlotte Lane, Blake A Dinsmore, François-Xavier Weill, Patricia I Fields","doi":"10.1128/aem.02600-24","DOIUrl":"10.1128/aem.02600-24","url":null,"abstract":"<p><p>In the era of genomic characterization of strains for public health microbiology, whole genome sequencing (WGS)-enabled subtyping of <i>Salmonella</i> provides superior discrimination of strains compared to traditional methods such as serotyping. Nonetheless, serotypes are still very useful; they maintain historical continuity and facilitate clear communication. Genetic determination of serotypes from WGS data is now routine. Genetic determination of rarer serotypes can be problematic due to a lack of sequences for rare antigen types and alleles, a lack of understanding of the genetic basis for some antigens, or some inconsistencies in the White-Kauffmann-Le Minor (WKL) Scheme for <i>Salmonella</i> serotype designation. Here, we present a simplified interpretation of serotypes to address the shortcomings of genetic methods, which will allow the streamlined integration of serotype determination into the WGS workflow. The simplification represents a consensus perspective among major U.S. public health agencies and serves as a WGS-oriented interpretation of the WKL Scheme. We also present SeqSero2S, a bioinformatics tool for WGS-based serotype prediction using the simplified interpretation.IMPORTANCEThe utility of <i>Salmonella</i> serotyping has evolved from a primary subtyping method, where the need for strain discrimination justified its complexity, to a supplemental subtyping scheme and nomenclature convention, where clarity and simplicity in communication have become important for its continued use. Compared to phenotypic methods like serotyping, whole genome sequencing (WGS)-based subtyping methods excel in recognizing natural populations, which avoids grouping together strains from different genetic backgrounds or splitting genetically related strains into different groups. This simplified interpretation of serotypes addresses a shortcoming of the original scheme by combining some serotypes that are known to be genetically related. Our simplified interpretation of the White-Kauffmann-Le Minor (WKL) Scheme facilitates a complete and smooth transition of serotyping's role, especially from the public health perspective that has been shaped by the routine use of WGS.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0260024"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481998","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":"Identification and functional characterization of major gene <i>pcmfs</i>, controlling cap color formation in <i>Pleurotus cornucopiae</i>.","authors":"Yan Zhang, Siyu Xu, Yuting Li, QianQian Zhang, Wei Wang, Zhuang Li","doi":"10.1128/aem.01894-24","DOIUrl":"10.1128/aem.01894-24","url":null,"abstract":"<p><p>Oyster mushrooms are grown commercially worldwide, especially in many developing countries, for their easy cultivation and high biological efficiency. Cap color is an important commercial trait for oyster mushrooms. Little is known about the genetic mechanism of the cap color trait in oyster mushrooms, which limits molecular breeding for the improvement of cap color-type cultivars. In this study, an important candidate gene, <i>pcmfs</i>, for cap color in the oyster mushroom <i>Pleurotus cornucopiae</i> was identified based on the results of QTL (quantitative trait loci) mapping and comparative transcriptome analysis of our previous research. The <i>pcmfs</i> gene belonged to major facilitator superfamily (MFS) and was localized to the cell membrane. Expression pattern analysis and overexpression experiment demonstrated that <i>pcmfs</i> played an important positive role in cap color formation, with high expression levels leading to dark cap color. To our knowledge, this is the first reported gene that may be involved in the melanin transport in edible fungi. The results will enhance our understanding of the genetic basis for cap color formation in oyster mushrooms, ultimately facilitating the targeted molecular breeding of this phenotypic trait.IMPORTANCEOyster mushrooms are widely cultivated worldwide, particularly in developing countries, owing to their straightforward cultivation requirements and high biological efficiency. Cap color represents a significant commercial trait of oyster mushrooms. Despite its significance, the genetic basis of this trait remains poorly understood, limiting progress in molecular breeding to diversify cap color variants. Bridging this knowledge gap could improve the market appeal and consumer satisfaction of these cultivars by facilitating targeted breeding strategies. In our previous research, a major QTL of cap color in oyster mushroom <i>P. cornucopiae</i> was mapped and DEGs (differentially expressed genes) between the dark strains and white strains were identified. Based on this, the candidate gene for cap color <i>pcmfs</i> was further mined. The <i>pcmfs</i> gene, belonging to the major facilitator superfamily (MFS), is localized to the cell membrane. Expression pattern analysis and overexpression experiments have shown that <i>pcmfs</i> plays a significant role in cap color formation. To our knowledge, this is the first reported gene that may be involved in the melanin transport in edible fungi. The results contribute to elucidate the genetic mechanisms governing cap color formation in mushrooms, advancing targeted molecular breeding for this trait.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0189424"},"PeriodicalIF":3.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514448","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}