Applied and Environmental Microbiology最新文献

{"title":"Erratum for Huang et al., \"Insights into the regulatory mechanisms and application prospects of the transcription factor Cra\".","authors":"Ying Huang, Kai-Zhi Jia, Wei Zhao, Li-Wen Zhu","doi":"10.1128/aem.00047-25","DOIUrl":"https://doi.org/10.1128/aem.00047-25","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0004725"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063271","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":"Precision engineering of the probiotic <i>Escherichia coli</i> Nissle 1917 with prime editing.","authors":"Pei-Ru Chen, Ying Wei, Xin Li, Hai-Yan Yu, Shu-Guang Wang, Xian-Zheng Yuan, Peng-Fei Xia","doi":"10.1128/aem.00031-25","DOIUrl":"https://doi.org/10.1128/aem.00031-25","url":null,"abstract":"<p><p>CRISPR-Cas systems are transforming precision medicine with engineered probiotics as next-generation diagnostics and therapeutics. To promote human health and treat disease, engineering probiotic bacteria demands maximal versatility to enable non-natural functionalities while minimizing undesired genomic interferences. Here, we present a streamlined prime editing approach tailored for probiotic <i>Escherichia coli</i> Nissle 1917 utilizing only essential genetic modules, including Cas9 nickase from <i>Streptococcus pyogenes</i>, a codon-optimized reverse transcriptase, and a prime editing guide RNA, and an optimized workflow with longer induction. As a result, we achieved all types of prime editing in every individual round of experiments with efficiencies of 25.0%, 52.0%, and 66.7% for DNA deletion, insertion, and substitution, respectively. A comprehensive evaluation of off-target effects revealed a significant reduction in unintended mutations, particularly in comparison to two different base editing methods. Leveraging the prime editing system, we inserted a unique DNA sequence to barcode the edited strain and established an antibiotic-resistance-gene-free platform to enable non-natural functionalities. Our prime editing strategy presents a CRISPR-Cas system that can be readily implemented in any laboratories with the basic CRISPR setups, paving the way for future innovations in engineered probiotics.IMPORTANCEOne ultimate goal of gene editing is to introduce designed DNA variations at specific loci in living organisms with minimal unintended interferences in the genome. Achieving this goal is especially critical for creating engineered probiotics as living diagnostics and therapeutics to promote human health and treat diseases. In this endeavor, we report a customized prime editing system for precision engineering of probiotic <i>Escherichia coli</i> Nissle 1917. With such a system, we developed a barcoding system for tracking engineered strains, and we built an antibiotic-resistance-gene-free platform to enable non-natural functionalities. We provide not only a powerful gene editing approach for probiotic bacteria but also new insights into the advancement of innovative CRISPR-Cas systems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0003125"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063292","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":"Genetic identification of acetyl-CoA synthetases involved in acetate activation in <i>Haloferax mediterranei</i>.","authors":"Ruchira Mitra, Yang Xu, Lin Lin, Jing Guo, Tong Xu, Mengkai Zhou, Feng Guo, Hao Li, Hua Xiang, Jing Han","doi":"10.1128/aem.01843-24","DOIUrl":"10.1128/aem.01843-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Acetate/acetyl-CoA interconversion is an interesting metabolic node, primarily catalyzed by a set of various enzymes in prokaryotes. &lt;i&gt;Haloferax mediterranei&lt;/i&gt; is a promising haloarchaeaon, capable of utilizing acetate as a sole carbon source for biosynthesis of high value-added products. Here, we have reported the key enzymes that catalyzed acetate activation in &lt;i&gt;H. mediterranei&lt;/i&gt;. Based on bioinformatic and transcript analysis, thirteen possible candidate genes were screened. Simultaneous deletion of eleven genes led to a mutant strain (named as Δ11) that failed to grow on acetate. Gene complementation in Δ11 revealed six AMP-ACS (encoded by HFX_0870, HFX_1242, HFX_1451, HFX_6342, HFX_5131, and HFX_1643) and one ADP-ACS (encoded by HFX_0998) to be functional in acetate activation. Furthermore, heterologous expression of ADP-ACS genes from &lt;i&gt;Haloarcula hispanica&lt;/i&gt; and &lt;i&gt;Haloferax volcanii&lt;/i&gt; catalyzed acetate activation in Δ11. Subsequently, it was observed that, deletion of the six AMP-ACS genes in &lt;i&gt;H. mediterranei&lt;/i&gt; ceased the cell growth of the resulting mutant (Δ6AMP-ACS) on acetate. An &lt;i&gt;in vivo&lt;/i&gt; function of ADP-ACS in acetate activation could be excluded since ADP-ACS was downregulated on acetate. However, plasmid-based overexpression of ADP-ACS enabled Δ6AMP-ACS to grow on acetate, even better than the parent strain. Thus, it can be inferred that native ADP-ACS with low expression level was unable to mediate cell growth of Δ6AMP-ACS on acetate. This is the first genetic evidence exhibiting that overexpression of haloarchaeal ADP-ACS catalyzed acetate activation &lt;i&gt;in vivo&lt;/i&gt;. Collectively, this is a comprehensive study of acetate activation in &lt;i&gt;H. mediterranei,&lt;/i&gt; and the current findings would surely enrich the understanding of acetate metabolism in archaea.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Owing to the high demand and supply challenge of glucose, acetate might be considered a potential alternative carbon source for microbial growth and fermentation. &lt;i&gt;Haloferax mediterranei&lt;/i&gt; is capable of utilizing acetate as a carbon source for growth and subsequent value-added product synthesis. Thus, it is essential to identify the genes responsible for acetate utilization in &lt;i&gt;H. mediterranei&lt;/i&gt;. As per available literature, haloarchaeal ADP-forming acetyl-CoA synthetase (APD-ACS) catalyzes the reversible conversion of acetate to acetyl-CoA &lt;i&gt;in vitro&lt;/i&gt;. However, &lt;i&gt;in vivo&lt;/i&gt;, acetate activation and acetate formation are catalyzed by AMP-forming acetyl-CoA synthetase (AMP-ACS) and ADP-ACS, respectively. In this study, we have identified six AMP-ACS enzymes that catalyzed acetate activation in &lt;i&gt;H. mediterrane&lt;/i&gt;i. Deletion of these six genes abolished the growth of the resulting mutant (Δ6AMP-ACS) in acetate medium. The natively expressed ADP-ACS was unable to mediate its acetate activation &lt;i&gt;in vivo&lt;/i&gt;. Interestingly, an artificial system based on plasmid overexpression of ADP-ACS in Δ6AMP-ACS restored","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0184324"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142913755","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":"Inactivation of deposited bioaerosols on food contact surfaces with UV-C light emitting diode devices.","authors":"Aakash Sharma, Amritpal Singh, Brahmaiah Pendyala, Sampathkumar Balamurugan, Ankit Patras","doi":"10.1128/aem.01093-24","DOIUrl":"10.1128/aem.01093-24","url":null,"abstract":"<p><p>The airborne transmission of infectious diseases and bioaerosol-induced cross-contamination pose significant challenges in the food, dairy, and pharma industries. This study evaluated the effectiveness of 279 nm UV-C LED irradiation for decontaminating bioaerosols, specifically containing microorganisms such as <i>Escherichia coli</i> (C3040- Kanamycin resistant), <i>Salmonella</i> Enteritidis (ATCC 4931), and <i>Pseudomonas fragi</i> (ATCC 4973), on food contact surfaces. Borosilicate glass, silicon rubber, and stainless steel (316L) surfaces were selected for experimentation for their usage in the food industry. A 50 µL cell suspension was aerosolized at 25 psi pressure using a 4-jet BLAM Nebulizer within a customized glass chamber and then deposited onto the surface of the coupons. The serial dilution approach was used for the microbial enumeration, followed by duplicate plating. With a low Root Mean Square Error (RMSE) and high <i>R</i>² values, the biphasic kinetic model for UV-C inactivation curves of all three pathogens demonstrated the excellent goodness of fit parameters. At a UV-C dose of 6 mJ cm^-2, glass surfaces showed the maximum microbial inactivation (i.e., 2.80, 3.81, and 3.56 log CFU/mL for <i>E. coli</i>, <i>Salmonella</i>, and <i>P. fragi</i>, respectively). Stainless steel and silicon rubber surfaces showed significant microbial inactivation, but log₁₀ reductions observed were consistently lower than glass surface. Our research indicates that UV-C LEDs (279 nm) can effectively disinfect bioaerosols on food contact surfaces.IMPORTANCEFood safety is a major public health concern, with contaminated food causing serious illnesses. UV-C light, used for germicidal action, is effective in disinfecting surfaces and is not subject to the same strict legal restrictions as chemical disinfectants, simplifying compliance with food safety regulations. In this study, we evaluated the efficacy of UV-C (279 nm) LED systems for inactivation of surface-deposited bioaerosols of kanamycin-resistant <i>Escherichia coli</i> (C3040), <i>Salmonella</i> Enteritidis (ATCC 4931), and <i>Pseudomonas fragi</i> (ATCC 4973). The research outcomes can be used to develop UV-based surface disinfection systems to minimize the risk of foodborne illnesses and enhance safety in high-traffic food preparation areas.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0109324"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784281/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680689","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":"Tracing <i>Staphylococcus capitis</i> and <i>Staphylococcus epidermidis</i> strains causing septicemia in extremely preterm infants to the skin, mouth, and gut microbiota.","authors":"Forough L Nowrouzian, Kirth Lumingkit, Monica Gio-Batta, Daniel Jaén-Luchoro, Thordur Thordarson, Anders Elfvin, Agnes E Wold, Ingegerd Adlerberth","doi":"10.1128/aem.00980-24","DOIUrl":"10.1128/aem.00980-24","url":null,"abstract":"<p><p>Coagulase-negative staphylococci (CoNS) comprise about 50 species, some of which cause septicemia in preterm neonates. CoNS establish early on the skin and in the oral and gut microbiota, from where they may spread to the bloodstream. The colonization pattern preceding septicemia is not well-defined. Forty-two extremely preterm neonates (≤28 + 0 gestational weeks) were followed from birth to 2 months with regular sampling and culturing of the skin and oral and gut microbiota. Blood samples were drawn upon clinical suspicion of septicemia and cultured. CoNS species were identified using matrix-assisted laser-desorption ionization time of flight mass spectrometry (MALDI-TOF). Random amplified polymorphic DNA was used for strain typing, and strains were characterized regarding biofilm production and virulence gene carriage. CoNS blood isolates underwent whole genome sequencing. <i>Staphylococcus epidermidis</i> represented 72% of the CoNS isolates on skin or mucous membranes, followed by <i>Staphylococcus capitis</i> (13%) and <i>Staphylococcus haemolyticus</i> (7%). CoNS septicemia was diagnosed in nine infants, yielding 11 septicemia isolates: seven <i>S</i>. <i>capitis</i> and four <i>S</i>. <i>epidermidis,</i> of which nine were further analyzed. The <i>S. capitis</i> septicemia isolates belonged to the NRCS-A clone. Two-thirds of the septicemia strains were traced back to the commensal microbiota. Colonization of the oral cavity by <i>S. capitis</i> was significantly associated with CoNS septicemia development, although the blood-borne <i>S. capitis</i> strains were more commonly found on the skin than in the mouth prior to invasion. Biofilm production was not associated with septicemia. Our results implicate CoNS colonization as a step that precedes septicemia in preterm neonates. Early colonization of the oral cavity by <i>S. capitis</i> may represent a particular risk.</p><p><strong>Importance: </strong>Septicemia is a major cause of morbidity in preterm infants. Coagulase-negative staphylococci (CoNS) can colonize skin, oral cavity, and intestines and are a common cause of septicemia in this group. The relation between CoNS colonization pattern at the species and strain level and septicemia has scarcely been studied. We mapped colonization of the skin, oral cavity, and intestines by CoNS species in extremely preterm infants and speciated and strain-typed the skin, mucosal, and blood isolates. Two-thirds of the CoNS septicemia blood strains, including a majority of <i>S. capitis</i> strains belonging to the NRCS-A clone, were tracked to the commensal microbiota. We demonstrated that CoNS species differ in their colonization patterns, whereby <i>S. capitis</i> was primarily a skin colonizer. However, its colonization of the oral cavity was enhanced among infants developing septicemia. Our study provides a starting point for further explorations of the relationship between CoNS colonization and septicemia in preterm infants.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0098024"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784025/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845655","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":"Development and application of a quadruple RT-qPCR assay for the simultaneous detection of NoV GI, NoV GII, and HAV in bivalve shellfish.","authors":"Yan Wang, Jinfeng Wang, Maolin Wei, Libing Liu, Jianchang Wang, Xiangdong Xu","doi":"10.1128/aem.01839-24","DOIUrl":"10.1128/aem.01839-24","url":null,"abstract":"<p><p>To achieve rapid and simultaneous detection of NoV GI, NoV GII, and HAV, a quadruple real-time fluorescence quantitative PCR (RT-qPCR) assay was developed using MS2 bacteriophage as a process control virus. The quadruple RT-qPCR assay effectively detected NoV GI, NoV GII, HAV, and MS2 RNA with detection limits of 10² copies/μL, 10³ copies/μL, 10² copies/μL, and 10³ copies/μL, respectively, within 1 hour 50 minutes. The quadruple RT-qPCR assay could specifically detect NoV GI, NoV GII, HAV, and MS2 without cross-reactions with other common pathogens, demonstrating good reproducibility with intra-assay and inter-assay coefficients of variation all below 2.11%. In this study, 337 bivalve shellfish samples collected from various regions of Hebei Province were pretreated using the proteinase K-PEG 8000 precipitation-chloroform method, and viral nucleic acids were enriched and extracted from a volume of viral solution that was doubled. The developed quadruple RT-qPCR assay was used to detect NoV GI, NoV GII, and HAV in bivalve shellfish samples, and the positive rates were 19.88% (67/337), 20.47% (69/337), and 4.75% (16/337), respectively. In addition, mixed infections of NoV GI and NoV GII (10.68%, 36/337) and NoV GI and HAV (0.89%, 3/337) were observed. In all, 200 bivalve shellfish samples were randomly selected for the assay, and it was found that the total, positive, negative coincidence rates, and Kappa values of the quadruple RT-qPCR assay were 98.3%, 99.1%, 98.2%, and 0.945, respectively, compared with the single RT-qPCR assay. These results show that the developed quadruple RT-qPCR assay has comparable performance to the single RT-qPCR assay.IMPORTANCEFood-borne diseases caused by viral contamination have become a growing concern, and bivalve shellfish is a crucial source of infection, with many outbreaks of non-bacterial acute gastroenteritis associated with raw food or the use of undercooked shellfish such as oysters. As food contamination problems caused by NoV and HAV become more severe, it is important to study and establish a sensitive and efficient assay to simultaneously detect NoV and HAV by applying the MS2 process control virus for the protection of bivalve shellfish food safety and the monitoring of the above food-borne viral contamination. In addition, bivalve shellfish samples contain a large number of PCR inhibitors such as polysaccharides, lipids, and proteins, so optimization of the virus enrichment and extraction method is essential and is expected to provide a research basis for subsequent related experiments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0183924"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142851705","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":"The healthy human gut can take it all: vancomycin-variable, linezolid-resistant strains and specific bacteriocin-species interplay in <i>Enterococcus</i> spp.","authors":"Ana C Almeida-Santos, Bárbara Duarte, Ana P Tedim, Maria J Teixeira, Joana C Prata, Rui M S Azevedo, Carla Novais, Luísa Peixe, Ana R Freitas","doi":"10.1128/aem.01699-24","DOIUrl":"10.1128/aem.01699-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Enterococcus&lt;/i&gt; spp. are opportunistic human pathogens colonizing the human gut and a significant reservoir for the continuous adaptation of hospital clones. However, studies on the features of enterococci species co-colonizing healthy individuals are scarce. We investigated the prevalence, antibiotic resistance, and bacteriocin profiles of &lt;i&gt;Enterococcus&lt;/i&gt; species in fecal samples from healthy adults in Portugal using culture-based methods, WGS, and bacteriocin inhibition assays. Results were compared with data from a 2001 study in the same region. &lt;i&gt;Enterococcus&lt;/i&gt; spp. (&lt;i&gt;n&lt;/i&gt; = 315; 24% MDR) were recovered from all volunteers. &lt;i&gt;Enterococcus lactis&lt;/i&gt; was the prevalent species (75%), followed by &lt;i&gt;Enterococcus faecalis&lt;/i&gt; (65%) and &lt;i&gt;Enterococcus faecium&lt;/i&gt; (47%). &lt;i&gt;E. lactis&lt;/i&gt; prevalence increased 2.5-fold since 2001. Linezolid resistance genes (&lt;i&gt;optrA/poxtA&lt;/i&gt;) were detected in &lt;i&gt;E. faecium&lt;/i&gt; and &lt;i&gt;Enterococcus thailandicus&lt;/i&gt; isolates, while a vancomycin-variable &lt;i&gt;E. faecium&lt;/i&gt; was also identified. Virulence and plasmid profiles were diverse across species, with evidence of exchange of virulence markers and plasmid replicons between &lt;i&gt;E. faecium&lt;/i&gt; and &lt;i&gt;E. lactis&lt;/i&gt;. Bacteriocin gene repertoires were extensive and species-specific. Higher numbers of bacteriocin genes were associated with stronger inhibition profiles, and 25% of &lt;i&gt;E. faecium&lt;/i&gt; and &lt;i&gt;E. lactis&lt;/i&gt; isolates were capable of inhibiting relevant VRE clones. This study unveils the co-occurrence and ecological dynamics of &lt;i&gt;Enterococcus&lt;/i&gt; species in the healthy human gut, reinforcing its role as a reservoir for key antibiotic resistance genes and potentially pathogenic strains. The shift toward &lt;i&gt;E. lactis&lt;/i&gt; prevalence and the detection of linezolid resistance genes in healthy individuals underscore the need for ongoing surveillance of the gut microbiome to guide public health strategies and antibiotic stewardship efforts.IMPORTANCEThis study highlights the role of &lt;i&gt;Enterococcus&lt;/i&gt; species in the healthy human gut, revealing important insights into their prevalence and antibiotic resistance. It emphasizes that the human gut serves as a significant reservoir for antibiotic-resistant strains and shows a notable increase and prevalence of &lt;i&gt;Enterococcus lactis,&lt;/i&gt; which has been underappreciated due to identification challenges. The research also underscores the bacteriocins' role in microbial competition, where commensal strains inhibit clinical VRE, potentially aiding the restoration of the gut microbiota, after antibiotic treatment. The findings accentuate the need for ongoing surveillance to track changes in gut bacteria, especially with the emergence of resistance genes to last resort antibiotics. Such monitoring is crucial for shaping public health strategies and managing the growing threat of antibiotic-resistant infections. Profiling bacteriocins at the species and strain level can identify ecological adaptation factors","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0169924"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784074/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142852081","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>Bacillus safensis</i> APC 4099 has broad-spectrum antimicrobial activity against both bacteria and fungi and produces several antimicrobial peptides, including the novel circular bacteriocin safencin E.","authors":"E Kamilari, P M O'Connor, F Miceli de Farias, C N Johnson, C Buttimer, A Deliephan, D Hill, O Fursenko, J Wiese, C Stanton, C Hill, R P Ross","doi":"10.1128/aem.01942-24","DOIUrl":"10.1128/aem.01942-24","url":null,"abstract":"<p><p><i>Bacillus safensis</i> APC 4099, isolated from bees' gut, has been identified as a promising candidate for food biopreservation. Antimicrobial activity screening revealed a broad-spectrum inhibition potential, ranging from gram-positive pathogenic bacteria to fungi responsible for food spoilage. Genomic analysis identified biosynthetic gene clusters coding for several antimicrobial peptides and secondary metabolites. Specifically, a novel, anionic, 6 kDa circular bacteriocin, named safencin E, was detected, showing 52.5% similarity to butyrivibriocin AR10. Additionally, gene clusters coding for the biosynthesis of bacteriocins such as pumilarin and plantazolicin and biosynthetic pathways for secondary metabolites, including pumilacidin A, bacilysin, and bacillibactin, were identified. Matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis detected molecular masses correlating to safencin E, plantazolicin, pumilarin, and pumilacidin A from the cell-free supernatant, cell extracts, or both. Overall, the broad-spectrum antimicrobial activity of <i>B. safensis</i> APC 4099 indicates that this strain is a promising candidate for the biological control of food ecosystems and thus has the potential to enhance food safety.</p><p><strong>Importance: </strong>The present article highlights the importance of the strain <i>Bacillus safensis</i> APC 4099 as a potential biocontrol agent. The strain possesses biosynthetic gene clusters coding for various antimicrobial peptides and secondary metabolites, including a novel circular bacteriocin, safencin E, and the bacteriocins pumilarin and plantazolicin. This diversity in the production of antimicrobial peptides renders the producer with broad-spectrum antimicrobial activity, ranging from gram-positive pathogenic and spoilage bacteria to spoilage molds. Considering that 1.3 billion tons of food appropriate for human consumption is lost or wasted annually, identifying strains or novel antimicrobial peptides capable of biopreservation is highly relevant. This strain and its bioactive compounds offer a solution to this global problem as biocontrol agents for food ecosystems against spoilage and pathogenic microbes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0194224"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7617318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142913752","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":"Hydration conditions as a critical factor in antibiotic-mediated bacterial competition outcomes.","authors":"Yana Beizman-Magen, Tomer Orevi, Nadav Kashtan","doi":"10.1128/aem.02004-24","DOIUrl":"10.1128/aem.02004-24","url":null,"abstract":"<p><p>Antibiotic secretion plays a pivotal role in bacterial interference competition; yet, the impact of environmental hydration conditions on such competition is not well understood. Here, we investigate how hydration conditions affect interference competition among bacteria, studying the interactions between the antibiotic-producing <i>Bacillus velezensis</i> FZB42 and two bacterial strains susceptible to its antibiotics: <i>Xanthomonas euvesicatoria</i> 85-10 and <i>Pseudomonas syringae</i> DC3000. Our results show that wet-dry cycles significantly modify the response of the susceptible bacteria to both the supernatant and cells of the antibiotic-producing bacteria, compared to constantly wet conditions. Notably<i>, X. euvesicatoria</i> shows increased protection against both the cells and supernatants of <i>B. velezensis</i> under wet-dry cycles, while <i>P. syringae</i> cells become more susceptible under wet-dry cycles. In addition, we observed a reciprocal interaction between <i>P. syringae</i> and <i>B. velezensis</i>, where <i>P. syringae</i> inhibits <i>B. velezensis</i> under wet conditions. Our findings highlight the important role of hydration conditions in shaping bacterial interference competition, providing valuable insights into the microbial ecology of water-unsaturated surfaces, with implications for applications such as biological control of plant pathogens and mitigating antibiotic resistance.IMPORTANCEOur study reveals that hydration conditions, particularly wet-dry cycles, significantly influence antibiotic-mediated competition between bacterial species. We revealed that the effectiveness of antibiotics produced by <i>Bacillus velezensis</i> against two susceptible bacterial species: <i>Xanthomonas</i> and <i>Pseudomonas</i> varies based on these hydration conditions. Unlike traditional laboratory environments, many real-world habitats, such as soil, plant surfaces, and even animal skin, undergo frequent wet-dry cycles. These conditions affect bacterial competition dynamics and outcomes, with wet-dry cycles providing increased protection for some bacteria while making others more susceptible. Our findings highlight the importance of considering environmental hydration when studying microbial interactions and developing biological control strategies. This research has important implications for improving agricultural practices and understanding natural microbial ecosystems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0200424"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875972","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":"Positive regulation of a LuxR family protein, MilO, in mildiomycin biosynthesis.","authors":"Zhiyu Li, Yuli Wang, Chen Lin, Yu Wen, Zixin Deng, Ming Jiang, Xinyi He","doi":"10.1128/aem.01654-24","DOIUrl":"10.1128/aem.01654-24","url":null,"abstract":"<p><p>Mildiomycin is a representative peptidyl nucleoside antibiotic and was first isolated from <i>Streptoverticillium rimofaciens</i>, which has been used as an important biological agent to control powdery mildew in plants. Despite its importance, the biosynthetic pathways and regulatory mechanisms remain to be fully elucidated. In this study, we identified MilO as a positive pathway-specific regulator of mildiomycin biosynthesis in the heterologous host <i>Streptomyces avermitilis</i>. Gene disruption of <i>milO</i> resulted in almost loss of mildiomycin production, and it was restored to the level comparable to that in the wild-type strain in complemented strain. Overexpression of <i>milO</i> using host native promoter <i>rpsJ</i>p, engineered promotor <i>SP44,</i> and <i>kasO</i>p* led to a 50%, 6.5-fold, and 9.2-fold increase in mildiomycin production compared with the wild-type strain, respectively. Quantitative real-time PCR and electrophoretic mobility shift assay (EMSA) experiments revealed that MilO directly enhances the transcription of the <i>milA</i> gene by 20 folds after 48 h fermentation and indirectly regulates the transcription levels of other genes from <i>milB</i> to <i>milM</i>. Using DNase I footprinting assays, <i>milO</i> was revealed to bind to a 44 bp DNA sequence of the <i>milA</i> promoter region. The binding region consists of three imperfect direct repeats of TGTC(N)₃CGGT separated by two-nucleotide spacers and each repeat is important to efficient binding to MilO. In addition, we identified two related compounds by overexpressing <i>milO</i> in a structural gene <i>milN</i>-deficient mutant. Taken together, this study indicates that pathway-specific regulator MilO is essential for mildiomycin biosynthesis and provides an effective strategy to improve the production of mildiomycin and its intermediates.IMPORTANCEAs an important biological agent to control powdery mildew on plants, mildiomycin has been commercialized and used in various plants. However, its regulatory mechanisms and biosynthetic pathways remain unknown. This study provides new insights into the regulation of mildiomycin biosynthesis through MilO, a LuxR family protein that modulates mildiomycin production by directly enhancing the transcription of <i>milA</i>. The yield of mildiomycin was significantly improved by overexpressing <i>milO</i> in a heterologous host. In addition, the positive regulatory effect of <i>milO</i> helped to discover two related compounds, which provide important clues for the timing of uploading of two amino acid side chains during mildiomycin biosynthesis for the first time. In brief, our findings on transcriptional regulation of mildiomycin biosynthesis by <i>milO</i> will be valuable to further increase the yield of mildiomycin and explore its biosynthetic pathways.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0165424"},"PeriodicalIF":3.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876000","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}