Applied and Environmental Microbiology最新文献

{"title":"Microbiomes of soils and leafy vegetables in urban agriculture systems reflect crop management and local environmental conditions.","authors":"Mairui Gao, Qingyue Zeng, Kevin Lam, Magaly Toro, Shirley A Micallef, Ryan A Blaustein","doi":"10.1128/aem.01551-26","DOIUrl":"https://doi.org/10.1128/aem.01551-26","url":null,"abstract":"<p><p>Soil and plant microbiomes influence crop quality and preharvest food safety, yet these processes have been largely unexplored in urban agriculture environments. Here, we investigated how the microbiota of soil and leafy greens (e.g., kale, lettuce, chard, and cabbage) interact with site-specific management practices and environmental conditions across seven urban agriculture sites in the greater Washington, DC, area. Samples of leaf tissue (<i>n</i> = 92), rhizosphere soil (<i>n</i> = 92), and \"native\" or bulk soil (<i>n</i> = 39) were collected and analyzed with 16S rRNA gene and ITS2 genomic region amplicon sequencing. Microbial community composition varied significantly across sites for all sample types, as influenced by irrigation water source (i.e., municipal vs natural water), crop type, soil pH, soil moisture content, and climatic conditions (i.e., rainfall, temperature). Rhizosphere soils harbored the most bacterial taxa known to respond to organic inputs (e.g., <i>Massilia</i> and various members of <i>Firmicutes</i> and <i>Verrucomicrobiota</i>), whereas fungal networks dominated by saprotrophic members of <i>Ascomycota</i> were more stable in the bulk soils. Source-tracking analysis indicated that the phyllosphere microbiota, although variable and transient in composition, were largely derived from the rhizosphere soil. Notably, leafy greens at some sites were enriched with taxa associated with biocontrol potential (e.g., <i>Lactobacillaceae</i>). Moreover, machine learning models yielded strong performance in predicting specific production sites based on the bacterial communities in the rhizosphere and phyllosphere, suggesting possible microbiome-based applications for food traceability. Collectively, these findings demonstrate how local environments and crop management practices shape preharvest leafy green microbiomes in urban production.IMPORTANCEUrban farming and gardening are rapidly expanding to support local communities and enhance food security, yet these small-scale food systems are often established in uniquely developed landscapes and with resource-dependent operations. This study shows that complex site-specific factors influence the soil and leafy green microbiomes in urban agriculture systems. Our findings have important implications for future efforts in targeted farm management to enhance sustainable production and preharvest food safety.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0155126"},"PeriodicalIF":4.2,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149126296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Pseudomonas</i> enhances soil phosphorus bioavailability and maize seedling growth and affects soil microbial community.","authors":"Jingxue Zhang, Sisi Li, Wenwen Ma, Shuai Zhao, Mei Zhai, Jia Zhou, Feng Huang, Leizhen Zhao, Jianhang Qu","doi":"10.1128/aem.00423-26","DOIUrl":"https://doi.org/10.1128/aem.00423-26","url":null,"abstract":"<p><p>The low bioavailability of phosphorus in soil is a significant limiting factor for crop production, and inoculation with phosphate-solubilizing bacteria (PSB) has been recognized as an effective method. In this study, two strains with high phosphate-solubilizing ability, namely, <i>Pseudomonas veronii</i> 1416X3 and <i>Pseudomonas</i> sp. 1616X1, were obtained and used in pot experiments to investigate the effects of strains on phosphorus content in soil, maize plant growth, and soil microbial community. Results showed that after 4-day post-inoculation with PSB, the content of available phosphorus in the 1416X3 group (8.11 mg/L) and the 1616X1 group (6.77 mg/L) was significantly higher than that in the control group (4.97 mg/L), increasing by 1.63- and 1.36-fold, respectively. After inoculation with PSB, the microbial community of the soil rhizosphere was varied. In the 1416X3 group, shifts in the microbial community were characterized by increased relative abundances of <i>Arthrobacter</i> and <i>Nocardioides</i>, while in the 1616X1 group, the bacterial strain alters the microbial community through effective colonization and phosphate solubilization. To further elucidate the mechanisms underlying phosphorus solubilization of <i>Pseudomonas</i>, whole-genome sequencing of <i>P. veronii</i> 1416X3 and <i>Pseudomonas</i> sp. 1616X1 was investigated. The results revealed several genes associated with phosphate solubilization metabolism and phosphorus transport systems (<i>pst</i>SCAB<i>-pho</i>U), as well as organic acid production (<i>gcd</i>, <i>pqq</i>B-F, <i>mqo</i>, and <i>ttu</i>C). Therefore, this study establishes a basis for utilizing <i>Pseudomonas</i> strains as microbial phosphorus fertilizers, offering an effective and eco-friendly alternative in the pursuit of sustainable agriculture.</p><p><strong>Importance: </strong>This study identified two <i>Pseudomonas</i> strains capable of efficiently activating soil phosphorus and significantly promoting maize growth. It revealed their synergistic biological mechanisms involving colonization competition, organic acid secretion, and phosphorus transport systems. The research not only provides high-quality microbial resources for developing bio-phosphate fertilizers based on indigenous functional strains but also offers a theoretical foundation and technical pathway for addressing the challenge of \"high total phosphorus reserve but low available phosphorus supply\" in soil, reducing the dependence on chemical phosphate fertilizers, and advancing green agricultural development.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0042326"},"PeriodicalIF":4.2,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102943","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":"Autoinducer-2 functions as both a quorum-sensing and metabolic signal in <i>Escherichia coli</i>.","authors":"Noémie Godrie, Xuanlin Chen, Nicolas Näpflin, Lukas Malfertheiner, Assa Yeroslaviz, Christopher Schubert, Rinho Kim, Christian von Mering, Leanid Laganenka","doi":"10.1128/aem.01160-26","DOIUrl":"https://doi.org/10.1128/aem.01160-26","url":null,"abstract":"<p><p>Bacteria integrate diverse environmental signals to coordinate behavior, yet the relationship between nutrient sensing and quorum sensing (QS) remains incompletely understood. Autoinducer-2 (AI-2) is unique among QS signals in that its production is tightly linked to central metabolism, raising fundamental questions about the boundary between metabolic and signaling functions. In <i>Escherichia coli</i>, AI-2 coordinates collective behaviors through the <i>lsr</i> operon, whose expression is controlled not only by the AI-2-responsive repressor LsrR but also by the cAMP receptor protein (CRP), placing it at the intersection of carbon sensing and population-level signaling. While inhibition of <i>lsr</i> expression by PTS sugars was previously established, we show that non-PTS sugars similarly suppress <i>lsr</i> expression through CRP, further decoupling QS activation from cell density and coupling it to carbon source availability. Genomic analysis across <i>Enterobacteriaceae</i> reveals that CRP binding sites in the <i>lsr</i> promoter are broadly conserved, indicating that metabolic modulation of AI-2 signaling is an ancestral regulatory feature. Using a FRET-based biosensor, we further show that AI-2 uptake modulates intracellular cAMP levels similarly to non-PTS carbon transport, suggesting AI-2 may have originally functioned as a nutrient substrate. Additionally, we isolated soil- and phyllosphere-associated bacteria capable of utilizing AI-2 as a sole carbon source. Interestingly, this capacity seems to have evolved independently from the ability to produce and metabolize AI-2 through the LuxS/Lsr pathway. Overall, our findings reveal an underappreciated metabolic basis of AI-2 QS and suggest that, in some species, nutrient utilization and intercellular signaling may have diverged from a common ancestral pathway.IMPORTANCEQuorum sensing allows bacteria to coordinate collective behaviors by detecting secreted signaling molecules, yet the evolutionary origins of these systems remain poorly understood. AI-2, one of the most broadly conserved bacterial signals, is derived from central metabolism and processed by machinery in <i>Escherichia coli</i> that strikingly resembles a sugar utilization system. Here, we show that nutrient availability overrides cell density as the primary determinant of AI-2 responsiveness, that this regulatory logic is conserved among <i>Enterobacteriaceae</i> genomes, and that environmental bacteria can grow on AI-2 as a sole carbon source. These findings reframe AI-2 as a signal embedded within, and potentially evolved from, nutrient-sensing pathways, with direct implications for understanding how byproducts of cellular metabolism can acquire signaling functions.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0116026"},"PeriodicalIF":4.2,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102933","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":"The gut within: reframing the coral gastrovascular cavity as a discrete anaerobic microbial ecosystem.","authors":"Claudia Pogoreutz","doi":"10.1128/aem.01430-26","DOIUrl":"https://doi.org/10.1128/aem.01430-26","url":null,"abstract":"<p><p>Coral holobionts are typically studied at colony or fragment scale, erasing the spatial context of the microenvironments which microbial life occupies. Recent microsensor work (Q. Zhang, E. Bollati, and M. Kühl, Appl Environ Microbiol 92:e02441-25, 2026, https://doi.org/10.1128/aem.02441-25) shows the coral gastrovascular cavity (GVC) sustains active anaerobic metabolism, reflecting patterns of symbiotic state and heterotrophic feeding. These findings recast the GVC as a discrete, gut-like ecosystem with its own redox regime, substrate supply, and bacterial community, calling for spatially explicit approaches in coral research to resolve metabolism at microscopic scales.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0143026"},"PeriodicalIF":4.2,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102982","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":"Pyridoxine can inhibit salvage of other B₆ vitamers in <i>Salmonella enterica</i>.","authors":"Brandi A Buckner, Diana M Downs","doi":"10.1128/aem.01499-26","DOIUrl":"https://doi.org/10.1128/aem.01499-26","url":null,"abstract":"<p><p>Pyridoxal 5'-phosphate (PLP) is a nutrient required by all life. As an essential cofactor, PLP powers enzymatic reactions in primary and secondary metabolism. Microbes can obtain PLP through either <i>de novo</i> PLP biosynthesis or the salvage of exogenous vitamin B₆. Vitamin B₆ exists in multiple forms (vitamers) in the natural environment, but the effect of mixed B₆ vitamer supplementation on microbial physiology has not been explored. In this study, the ability of <i>Salmonella enterica</i> to obtain PLP during growth in media containing various ratios of B₆ vitamers is examined. The data show that the B₆ vitamer, pyridoxine (PN), can inhibit the salvage of B₆ vitamers, pyridoxamine and pyridoxal, by <i>S. enterica pdxH</i> mutants. Genetic analyses were performed to determine the mechanism by which PN disrupts pyridoxamine and pyridoxal salvage. Mutants resistant to PN inhibition during the salvage of pyridoxamine were isolated and found to encode variants of B₆ kinase (PdxK) with altered activity toward the B₆ vitamer substrates. Suppressor analysis suggests that PN inhibition is, at least, partially due to competitive inhibition of the pyridoxamine kinase activity of PdxK by PN. Additionally, the data indicate that pyridoxine 5'-phosphate (PNP)-mediated toxicity also contributes to growth inhibition by PN.</p><p><strong>Importance: </strong>Without successful acquisition and utilization of vitamin B₆, microbes cannot survive or perform their essential roles in human health and the natural environment. Vitamin B₆ exists in multiple forms (vitamers) in the natural world, but the effect of B₆ vitamer mixtures on microbial growth has not been analyzed. This work shows that the B₆ vitamers are not necessarily interchangeable sources of PLP, and they may have distinct effects on microbial physiology.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0149926"},"PeriodicalIF":4.2,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149103005","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":"Impacts of temperature on hydrogenotrophic denitrifying aquifer microbiota.","authors":"Felix Pfaff, Dimitri Meier, Adrian Seeholzer, Anja Wunderlich, Florian Einsiedl, Tillmann Lueders","doi":"10.1128/aem.01206-26","DOIUrl":"https://doi.org/10.1128/aem.01206-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Groundwater is a globally relevant drinking water resource, yet nitrate pollution from agriculture increasingly threatens its quality, especially in shallow, oxygen-rich aquifers where natural attenuation is limited. This study examined whether gaseous hydrogen can stimulate autochthonous chemolithoautotrophic denitrification in nitrate-polluted, gravel aquifer sediments, and whether this process remains effective across temperatures relevant for laboratory and field conditions. We hypothesized that both microbial community composition and the kinetics of nitrate reduction will change under distinct temperature regimes. Microcosm incubations of sediments from a nitrate-polluted aquifer successfully enriched native hydrogenotrophic denitrifiers. Denitrification activity was quantified at 12°C, 15°C, 20°C, and 25°C, with maximum rates ranging from ~1 to ~1.8 µmol g⁻¹ sediment day⁻¹, and average rates generally following the expected kinetic temperature responses. Higher temperatures supported greater microbial biomass and community diversity, including a broader range of denitrifiers. Nevertheless, a single population, a novel strain of &lt;i&gt;Acidovorax defluvii&lt;/i&gt;, dominated the community across all temperatures. Unlike the heterotrophic type strain, it possessed a conserved, likely transferable gene cluster for hydrogen oxidation, hydrogen sensing, and CO₂ fixation, as revealed by metagenomics. Although complete denitrifiers with hydrogen-oxidation capacity dominated at all temperatures, nitrite accumulated transiently below 15°C. The presence of aerobic respiration genes in all enriched denitrifiers indicates their ability to switch to oxygen as an electron acceptor if available. Our study demonstrates a notable presence of an autochthonous hydrogenotrophic denitrification potential in the studied aquifer and its effective stimulation by hydrogen injection alone. Furthermore, it identifies mass transfer constraints and redox control as targets for future process optimization.IMPORTANCENitrate contamination of groundwater remains a widespread challenge in agricultural regions, and effective &lt;i&gt;in situ&lt;/i&gt; remediation strategies are urgently needed. Hydrogen-stimulated chemolithoautotrophic denitrification represents a promising, low-carbon approach, yet its robustness under environmentally relevant temperature conditions has remained unclear. Our findings show that indigenous aquifer microorganisms can rapidly and consistently perform hydrogenotrophic denitrification across a broad temperature range (12-25°C), driven by a dominant &lt;i&gt;Acidovorax&lt;/i&gt; species with a specialized hydrogen-oxidizing gene cluster. Identification of a conserved, potentially transferable gene cluster conferring chemolithoautotrophic lifestyle is not only biotechnologically interesting but also contributes to debate about genomic and ecological definitions of microbial species. This demonstrates that hydrogen injection can reliably activate existing microbial potential","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0120626"},"PeriodicalIF":4.2,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Pichia occidentalis</i> volatiles elicit divergent behavioral responses in <i>Drosophila suzukii</i> and <i>Drosophila melanogaster</i>.","authors":"Beth Ferguson, James J Polashock, Tia Hart, Cesar Rodriguez-Saona, Jennifer S Sun","doi":"10.1128/aem.01135-26","DOIUrl":"https://doi.org/10.1128/aem.01135-26","url":null,"abstract":"<p><p><i>Drosophila suzukii</i> (spotted-wing drosophila) is an invasive pest that infests ripe, market-ready fruit, posing a significant threat to fruit production. To develop alternatives to conventional chemical control, environmentally derived fungi (EF) were evaluated for their potential to modulate <i>D. suzukii</i> behavior and viability. <i>Pichia occidentalis</i>, isolated from <i>Drosophila melanogaster</i> oral and fecal secretions, exhibited species-specific repellency in <i>D. suzukii</i>. In <i>D. suzukii</i>, exposure to <i>P. occidentalis</i> reduced survival, most pronounced in males, and significantly inhibited female oviposition. In contrast, <i>D. melanogaster</i> showed no reduction in survival and increased oviposition in the presence of the fungus. Solid-phase microextraction coupled with gas chromatography-mass spectrometry (SPME GC-MS) identified volatile metabolites produced by <i>P. occidentalis</i>. Subsequent cafeteria-style assays of individual volatiles revealed that several of these compounds elicited aversive responses in <i>D. suzukii</i> while remaining attractive to <i>D. melanogaster</i>, highlighting species-specific olfactory effects. Isoamyl butanoate, 2-phenyl-1-propanal, and benzyl alcohol demonstrated consistent repellent activity with superior efficacy compared to established <i>D. suzukii</i> repellents (2-pentylfuran, 1-octen-3-ol, and geosmin). Collectively, these findings demonstrate that EF metabolites can differentially influence closely related species and may be leveraged as targeted, behavior-based tools for managing <i>D. suzukii</i>.IMPORTANCE<i>Drosophila suzukii</i> is a major invasive pest that damages fresh fruit by laying eggs in ripening crops, leading to significant agricultural losses. Current control strategies rely heavily on chemical insecticides, which provide incomplete control and can harm non-target organisms. Here, we show that volatile metabolites produced by the environmental yeast <i>Pichia occidentalis</i> differentially influence closely related <i>Drosophila</i> species, decreasing oviposition and longevity in <i>D. suzukii</i> while stimulating oviposition in <i>D. melanogaster</i>. This species-specific divergence highlights the potential of microbial volatiles as precision tools for pest management, further supporting a behavior-based approach that selectively disrupts pest reproduction while minimizing ecological impact.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0113526"},"PeriodicalIF":4.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A <i>Salmonella</i> phage steers bacterial populations toward hypersensitivity to benzalkonium chloride, hydrogen peroxide, and triclosan.","authors":"Shelyn Wongso, Philip Lauman, Lin Chen, Siyun Wang","doi":"10.1128/aem.01437-26","DOIUrl":"https://doi.org/10.1128/aem.01437-26","url":null,"abstract":"<p><p>Phage steering is an emerging antimicrobial strategy that exploits the evolutionary consequences of phage predation to sensitize bacterial populations to existing antimicrobials. While phage steering toward hypersensitivity to antibiotics and immune effectors has been well documented, little is known about whether a similar mechanism can enhance bacterial sensitivity to commercial disinfectants. Here, we show that SF1, a lytic siphovirus infecting <i>Salmonella enterica</i>, requires an intact O-antigen layer for adsorption and lytic replication, and that in-frame deletion mutants with O-antigen or deeper LPS defects had increased susceptibility to several commercial disinfectants. Critically, SF1 enhanced the activity of all disinfectants tested in combination assays and, moreover, exhibited mathematical synergy with benzalkonium chloride, hydrogen peroxide, and triclosan, compounds to which SF1-selected LPS mutants were hypersensitive. These findings are consistent with the hypothesis that SF1 functions not only as a bactericidal agent, but as an evolutionary steering tool that potentiates sanitizer activity through selection for sanitizer-hypersensitive phenotypes. Broadly, these results support phage steering as a promising strategy for deploying bacteriophages as adjuvants to commercial disinfectants.IMPORTANCECommercial disinfectants are essential for controlling pathogens throughout the food production and processing chain, but their effectiveness is increasingly compromised by bacterial tolerance and persistence. Although bacteriophages are being investigated as direct bactericidal agents, their utility as adjuvants to commercial sanitizers remains underexplored. In this study, we demonstrate that <i>Salmonella</i> phage SF1 selects for LPS-deficient mutants that exhibit increased susceptibility to several commercial disinfectants. Importantly, we further show that SF1 synergizes with sanitizers to which phage-selected mutants are hypersensitive, supporting a steering-mediated mechanism whereby phage predation enhances sanitizer activity. To our knowledge, this is the first report demonstrating phage steering as a strategy for deploying bacteriophages as synergizing adjuvants to commercial disinfectants. These findings highlight the potential value of exploiting evolutionary trade-offs to improve pathogen control in food processing environments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0143726"},"PeriodicalIF":4.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102935","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":"Survival, growth, and potential of horizontal gene transfer of antibiotic resistance genes of bovine <i>Salmonella</i> on the cantaloupe surface.","authors":"Zaira L Castro-Delgado, Norma Heredia, Jose Angel Merino-Mascorro, Eduardo Franco-Frías, Jorge E Dávila-Aviña, Santos García","doi":"10.1128/aem.01076-26","DOIUrl":"https://doi.org/10.1128/aem.01076-26","url":null,"abstract":"<p><p><i>Salmonella</i> outbreaks are often linked to contaminated cantaloupes, and bacterial multiple antibiotic resistance is frequently observed. Research is needed to understand the growth and survival of <i>Salmonella</i> on cantaloupe surfaces, and the mechanisms of antibiotic resistance in that environment. This study investigated the growth, survival, and capacity for horizontal gene transfer of antibiotic resistance genes in <i>Salmonella</i> on the surface of cantaloupe. Bovine-derived <i>Salmonella</i> isolates were inoculated onto the surface of cantaloupe and incubated at 35°C under 65-75% humidity for 5 days. Each isolate was co-inoculated with donor <i>E. coli</i> CSH56 harboring helper plasmid RP4-8 and mobilizable plasmid pSC27, which carries kanamycin, neomycin, and ampicillin resistance genes. One hundred microliters of the <i>Salmonella</i> suspension (1 × 10⁸ CFU/mL) and 100 µL of the <i>E. coli</i> suspension (1 × 10⁷ CFU/mL) was applied to each cantaloupe (1:10 ratio). <i>Salmonella</i> survival and growth were monitored on Hektoen agar, transconjugants were enumerated on Hektoen agar with kanamycin, and donor <i>E. coli</i> were quantified on MacConkey agar. All <i>Salmonella</i> isolates survived and exhibited growth within the 5-day period, with increases ranging from 0.94 log₁₀ CFU/mL to 3.43 log₁₀ CFU/mL. Notably, all <i>Salmonella</i> isolates possess the capability to accept and integrate sequences derived from the pSC27 plasmid from <i>E. coli</i> into their chromosome, both <i>in vitro</i> and on cantaloupe. After conjugation, the count of <i>Salmonella</i> mutants carrying the plasmid was 2.79 log₁₀ CFU/mL <i>in vitro</i>. The survival, growth, and horizontal gene transfer of <i>Salmonella</i> on the surface of cantaloupe pose significant risks to public health.IMPORTANCE<i>Salmonella</i>, a leading cause of foodborne diseases, poses a global health threat, with multidrug resistance emerging as a severe problem. Cantaloupes have been implicated in salmonellosis outbreaks in multiple countries over the last three decades. We hypothesize that acquisition of antibiotic resistance genes from other bacteria may occur on the surface of the fruit. This study established that <i>Salmonella</i> can survive, proliferate, and acquire antibiotic resistance genes on cantaloupe surfaces. This observation underscores the potential risks on the growth and transfer of genes between pathogens such as <i>Salmonella</i> and <i>E. coli</i> in foods. This impact goes beyond disease production and contributes to the rapid escalation of antimicrobial resistance and transmission of virulence genes in foods and the environment, which is a significant threat to public health.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0107626"},"PeriodicalIF":4.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102979","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":"Formulations containing co-biotic compounds mediate microbiome function and composition without increased gas production in an <i>ex vivo</i> gastrointestinal model.","authors":"Brooke A Napier, Bryan D Merrill, Madeline Krieger, Dirk Gevers, Gregor Reid","doi":"10.1128/aem.01311-26","DOIUrl":"https://doi.org/10.1128/aem.01311-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Dietary supplement formulations that contain co-biotics or compounds that modulate biological processes in both the host and microbiome to confer a health benefit are an emerging strategy to fine-tune both host physiology and gut microbiome function. Here, we evaluated three novel formulations containing co-biotic compounds (DM-02, a multivitamin; AM-02, formulated for energy and focus; and PM-02, formulated to promote sleep) for their effects on human gut microbiome composition and function. The three formulations and untreated control (Unt-Ctrl) were subjected to upper gastrointestinal digestion, after which the digesta were exposed to 24-h simulated colonic fermentation in the validated &lt;i&gt;ex vivo&lt;/i&gt; systemic intestinal fermentation research (SIFR) technology (&lt;i&gt;n&lt;/i&gt; = 6 healthy adults). Outcomes included pH, short-chain fatty acid (SCFA) and gas production, ultra-deep metagenomic profiling, and untargeted metabolomics of post-colonic supernatants, each compared to Unt-Ctrl. All three formulations significantly reduced pH (3%-4%) and increased total SCFAs (9%-11%) and acetate (9%-12%), with AM-02 and PM-02 also increasing butyrate by 20% and propionate by 7%-8%, without increasing gas production. Each formulation significantly enriched specific SCFA- and B-vitamin-producing taxa. AM-02 significantly increased the abundance of two pyruvate fermentation to acetate/lactate pathways. PM-02 significantly increased the abundance of two tryptophan biosynthesis pathways, accompanied by an increase in available tryptophan and the abundance of tryptophan-producing microbes. All three formulations increased the availability of microbiome-derived metabolites, indicating microbiome functional modulation by the treatments. These findings support clinical evaluation of these novel formulations as a strategy to enhance microbiome composition and function.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;The gut microbiome produces metabolites, including short-chain fatty acids, B vitamins, and tryptophan derivatives, that are critical regulators of host physiology, from energy metabolism and gut barrier integrity to sleep and immune function. While probiotics introduce live microorganisms, and prebiotics selectively feed existing microbes, co-biotics represent a distinct category of compounds that simultaneously modulate host cell biology and microbiome activity. Despite growing interest in co-biotic supplementation, the impact of complete co-biotic-containing formulations on gut microbiome composition and functional output has not been evaluated. Using a validated &lt;i&gt;ex vivo&lt;/i&gt; gastrointestinal model inoculated with fecal microbiota from six healthy adults, we demonstrate that three supplement formulations containing co-biotic compounds consistently increased production of health-associated metabolites, selectively enriched beneficial microbial taxa, and modulated functional metabolic pathways, all without increasing gas production. These findings establish a me","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0131126"},"PeriodicalIF":4.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149102915","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}