Applied and Environmental Microbiology最新文献

{"title":"Deciphering the ammonia transformation mechanism of a novel marine multi-stress-tolerant yeast, <i>Pichia kudriavzevii</i> HJ2, as revealed by integrated omics analysis.","authors":"Kunmei Huang, Huashan Bai, Can Meng, Muhammad Kashif, Zhiling Wei, Zaihang Tang, Shu He, Shanguang Wu, Sheng He, Chengjian Jiang","doi":"10.1128/aem.02211-24","DOIUrl":"10.1128/aem.02211-24","url":null,"abstract":"<p><p>Ammonia nitrogen posed a significant threat to aquatic animals in aquaculture environments, and the substantial potential of microorganisms in removing ammonia nitrogen had garnered considerable attention. This study identified a marine yeast, <i>Pichia kudriavzevii</i> HJ2, which effectively removed ammonia nitrogen. By combining transcriptomics and metabolomics, the ammonia nitrogen transformation mechanism of HJ2 was elucidated. HJ2 achieved 100% ammonia nitrogen removal efficiency within 1 day of fermentation at 35°C with 300 mg/L ammonia nitrogen and 73.56% removal efficiency within 36 h with 600 mg/L ammonia nitrogen. Transcriptomics revealed that exposure to 600 mg/L ammonia nitrogen resulted in 541 up-regulated genes and 567 down-regulated genes in the HJ2 strain. Differentially expressed genes (DEGs) were primarily involved in the tricarboxylic acid (TCA) cycle and amino acid metabolism. Metabolomics revealed that HJ2 facilitated the production of 383 up-regulated metabolites and suppressed 137 down-regulated metabolites when exposed to 600 mg/L ammonia nitrogen. Integrating transcriptomics and metabolomics analyses showed that HJ2 removed ammonia nitrogen by sensing its presence in the extracellular environment, activating the TCA cycle, enhancing amino acid metabolism and nucleotide metabolism, and promoting its robust growth and reproduction. Amino acid metabolism played an important role in the ammonia transformation mechanism of HJ2. The result was confirmed by the increased activity of glutamate dehydrogenase (GDH) and aspartate aminotransferase (GOT). Up-regulated nitrogen metabolites such as L-glutamate, L-aspartic acid, spermidine, and trigonelline were produced. The results of enzyme activity tests, construction of overexpressing strains, and adding exogenous amino acid experiments demonstrated that HJ2 could utilize GDH and GOT ammonia assimilation pathways.<b>IMPORTANCE</b>Ammonia nitrogen removal ability was a universal characteristic among the ammonia-oxidizing bacteria or archaea. Recently, yeast strains from the genus <i>Pichia</i> were found to have ammonia nitrogen removal ability. However, the mechanism of ammonia nitrogen removal in <i>Pichia</i> had not been reported. In the study, the ammonia nitrogen removal efficiency of <i>Pichia kudriavzevii</i> HJ2 was identified, and the mechanisms by which HJ2 transformed ammonia nitrogen into non-toxic organic nitrogen were elucidated, offering potential solutions to pollution challenges in aquaculture and helping minimize resource waste. The study offered new insights into the transformation mechanism of microbial ammonia nitrogen removal and its environmentally friendly application.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0221124"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143960619","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":"Determinism and stochasticity drive microbial community assembly and microbial interactions in calcareous glacier forefields.","authors":"Edoardo Mandolini, Maraike Probst, Anusha Telagathoti, Beat Frey, Luis M Rodriguez-R, Flavio Fornasier, Nadine Praeg, Paul Illmer, Ursula Peintner","doi":"10.1128/aem.00302-25","DOIUrl":"10.1128/aem.00302-25","url":null,"abstract":"<p><p>Calcareous glacier forefields challenge prevailing ecological frameworks on microbial biodiversity and community assembly due to their unique bedrock. Early stages of soil development in these environments are notorious for their high turnover rates, demanding a high degree of replication for obtaining conclusive data. However, studies across different calcareous glaciers are still missing. Here, we robustly investigated both bacterial and fungal diversity, association networks, and assembly processes in four calcareous glacier forefields of the Alps, focusing on the earliest soil developmental stages (<25 years) early in the snow-free season. We found a diverse community of bacteria and fungi, potentially involved in P and N nutrient cycling. A core microbiome existing across all four locations suggests that certain microbes might be more successful colonizers of these ecosystems than others. Nearest taxon index revealed phylogenetically clustered microbial communities. These findings suggest that the distribution and colonization of some microbes were influenced by selective forces such as geography and climate during the early stages of soil development in calcareous glaciers. Interestingly, there were no common bacterial-fungal associations across the four locations, indicating that this habitat does not select for specific bacterial-fungal associations and that associations were driven by neutral processes. We discuss microbial communities and their interactions in these special calcareous glacier forefield habitats. Moreover, we present innovative approaches for studying microbial assembly that address both deterministic, intrinsic drivers, like specific microbial traits, and stochastic, extrinsic drivers, such as the opportunistic behavior of microbes.IMPORTANCEOur study is based on three fundamental and unique approaches: (i) we utilize the early stages of soil development in four glacier forefields across the Alpine range. This design implies high replicability in a natural setting, which is crucial for drawing general conclusions. (ii) Our study investigates glacier forefields with calcareous bedrock directly after snowmelt. These habitats and periods remain surprisingly underexplored. (iii) Our results underline the relevance of bacterial-fungal associations in microbial community assembly alongside dispersal, drift, and natural selection. Taken together, our study provides new insights into the development of complex microbial communities, their stabilization and predictability, including ecological implications.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0030225"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075443","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":"Synergistic treatment of linoleic acid and cefazolin on <i>Staphylococcus aureus</i> biofilm-related catheter infections.","authors":"Soyoung Ham, Han-Shin Kim, Min Jee Jo, Eunji Cha, Hwa-Soo Ryoo, Hyojin Kim, Heeho Lee, Gang-Jee Ko, Hee-Deung Park","doi":"10.1128/aem.00770-25","DOIUrl":"10.1128/aem.00770-25","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> is a human pathogen that causes severe infections through biofilm formation. <i>S. aureus</i> biofilm is particularly susceptible to catheters in patients undergoing peritoneal dialysis. Although antibiotics are used to treat catheter infections, high-concentration treatments adversely affect human host immune systems and change the physicochemical properties of the catheters. To improve therapeutic outcomes without side effects, we combined antibiotics and natural products. In this study, we propose a combination of linoleic acid (LA) and cefazolin (CFZ) to treat <i>S. aureus</i> infections synergistically and apply it to catheter environments and <i>in vivo</i> systems. LA is a polyunsaturated fatty acid derived from natural products, and CFZ is a major antibiotic used to treat <i>S. aureus</i> catheter-related infections. The optimum synergistic condition was determined using silicon pad-forming biofilm similar to catheter materials. <i>S. aureus</i> biofilms were considerably inhibited <i>in vitro</i> and <i>in vivo</i> owing to the improved antibacterial effects. Furthermore, the combination negatively regulated the chemokine levels in the peritoneum, kidney, and liver extracted from mouse models. Moreover, it did not affect the cytotoxicity of human omentum mesothelial cells and the functions of the kidney and liver. Therefore, the combination of LA and CFZ could be a potential synergistic therapy for <i>S. aureus</i> catheter infections.IMPORTANCECatheter contamination is commonly caused by <i>Staphylococcus aureus</i> biofilm formation, primarily in peritoneal dialysis patients. Although antibiotics are used to treat catheter infections, high concentrations of antibiotics impair the immune system of the human host and alter the physicochemical properties of catheters. Therefore, it is crucial to improve therapeutic outcomes while minimizing the side effects of antibiotics. Combined treatments with natural products can be solutions to alleviate these problems. Our study offers a new synergistic combination (linoleic acid and cefazolin) for the control of catheter infections caused by <i>S. aureus</i> biofilms, especially in peritoneal dialysis.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0077025"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109518","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":"A foodborne outbreak caused by atypical enteropathogenic <i>Escherichia coli</i> O45:H15 in the Kinki region of Japan.","authors":"Etsuko Saito, Kenichi Ogita, Tetsuya Harada, Yuki Wakabayashi, Takako Yagi, Takahiro Yamaguchi, Tomohiro Oshibe, Tetsuhiko Oooka, Takao Kawai","doi":"10.1128/aem.00123-25","DOIUrl":"10.1128/aem.00123-25","url":null,"abstract":"<p><p>Atypical enteropathogenic <i>Escherichia coli</i> (aEPEC) mainly causes sporadic diarrhea and occasional outbreaks. However, the genetic determinant of aEPEC causing large outbreaks is still unknown. In June 2022, 171 of 934 people presented with diarrhea and abdominal pain after eating a lunch box in the Kinki region of Japan. We investigated 44 fecal samples from persons who ate the cuisine and isolated enteropathogenic <i>Escherichia coli</i> (EPEC) serotype O45:H15 from 38 of them. The same pathogen was also isolated from the feces of two employees and a leftover sample (mashed tofu salad with spinach). Pulsed-field gel electrophoresis and whole genome sequencing supported the clonality of the isolates. The isolates were negative for <i>bfpA</i>, encoding the bundle-forming pilus, and were accordingly identified as aEPEC. Whole genome sequencing revealed the presence of a plasmid-encoded type 3 secretion system effector gene, <i>espT</i>, involving the invasive phenotype of EPEC. Finally, we concluded that this was a foodborne outbreak caused by aEPEC O45:H15. Since the food poisoning case caused by aEPEC O45:H15 harboring <i>espT</i> has not been reported previously, the current study broadens our understanding of aEPEC food poisoning and its genetic background.IMPORTANCEaEPEC causes diarrhea in humans, despite the reported asymptomatic carriers of aEPEC worldwide. Several outbreaks caused by aEPEC also support that this pathogen is a diarrheagenic agent; however, the genetic determinant of aEPEC causing large outbreaks is still unclear. In 2022, a large foodborne outbreak by aEPEC O45:H15 affected more than 170 people in the Kinki region of Japan. We sequenced the whole genomes of the etiological agents and identified a potential virulent plasmid carrying <i>espT</i>, which is a virulence factor of aEPEC O111 that caused diarrhea in more than 600 people in Finland. Our data strengthen the importance of <i>espT</i> as a virulence factor of aEPEC outbreaks.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0012325"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144149002","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":"AcMNPV, a viral insecticide of Lepidoptera pests, stimulates the immune response of the natural enemy <i>Arma chinensis</i> Fallou.","authors":"Ximei Yuan, Qingyao Meng, Zhengjie Lu, Chen Wang, Yiqing He, Ke Li, Juan Du, Yuejun Fu","doi":"10.1128/aem.00613-25","DOIUrl":"10.1128/aem.00613-25","url":null,"abstract":"<p><p><i>Autographa Californica</i> multiple nucleopolyhedrovirus (AcMNPV) is the most widely studied baculovirus currently used as a biopesticide application for crop pest control. AcMNPV has a good control effect on Lepidoptera pests, but the impact of AcMNPV on other insects in the environment, especially natural enemies, is worth further discussion. <i>Arma chinensis</i> Fallou, an essential natural enemy insect widely distributed in China, can prey on multiple pests that cause severe damage to the production economy and can play an effective role in preventing agroforestry pests. In this study, the natural enemy <i>Arma chinensis</i> Fallou was used as the research material to analyze the effect of AcMNPV on the immune system of <i>Arma chinensis</i> Fallou. The immune mechanism of AcMNPV-EGFP in infecting <i>A. chinensis</i> was revealed for the first time, and the critical factor miR-8 was found. The relationship between AcMNPV, miR-8, and <i>A. chinensis</i> was described. RNAi pathway and JAK/STAT signaling pathway are the main antiviral pathways in insects, and we have newly discovered the molecular regulation mechanism of the Toll signaling pathway in antiviral immunity. In a word, AcMNPV, a Lepidopteran insecticide, affects the immune response of <i>Arma chinensis</i> Fallou and has side effects on natural enemies in the process of pest control.IMPORTANCEAcMNPV is a viral pesticide that is widely used to control Lepidoptera pests. However, the impact on other insects has yet to be thoroughly studied. Therefore, the toxicity and side effects of AcMNPV on non-target organisms need to be effectively evaluated. As a biological control agent in agricultural ecosystems, natural enemy insects can effectively control the number of pests and reduce crop damage. Compared with chemical pesticides, natural enemy insects can avoid or reduce pesticide residues in agricultural products and have no environmental pollution, and pests do not quickly develop resistance to them. It will help ensure crops' safe production and balance the ecosystem. In this study, AcMNPV-EGFP was used to infect the natural enemy-<i>Arma chinensis</i> Fallou, which proved the effect of the virus pesticide on <i>Arma chinensis</i> Fallou. This work helps optimize the joint use of the natural enemy-<i>Arma chinensis</i> Fallou and other insecticides in applying biological control and also provides a reference for understanding the mechanism of insect antiviral infection.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0061325"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144149006","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":"Harnessing flagellin of <i>Ligilactobacillus agilis</i> as a surface display scaffold for an HIV-1 epitope.","authors":"Shunya Suzuki, Gregg A Dean, Akinobu Kajikawa","doi":"10.1128/aem.00674-25","DOIUrl":"10.1128/aem.00674-25","url":null,"abstract":"<p><p>Lactic acid bacteria (LAB) are promising mucosal vaccine vectors due to their safety, immunostimulatory properties, and the availability of genetic tools for certain strains. Bacterial flagellin has attracted attention as both a versatile scaffold for antigen surface display and a potent adjuvant via Toll-like receptor 5 (TLR5) activation. Despite these advantages, LAB-derived flagellin remains largely unexplored as an antigen display platform. In this study, we demonstrate the potential of flagellin (FliC2) from <i>Ligilactobacillus agilis</i>, one of the few flagellated LAB species, as a scaffold for the surface display of the HIV-1 membrane-proximal external region (MPER) epitope. Recombinant <i>L. agilis</i> strains were engineered to express FliC2 with the MPER epitope inserted at various positions within its hypervariable domain, identifying optimal sites for effective surface display. To enhance the adjuvant activity of FliC2, specific amino acid substitutions were introduced into the TLR5 recognition site, resulting in improved TLR5-stimulating activity <i>in vitro</i>. Immunization of mice with MPER-displaying <i>L. agilis</i> strains induced MPER-specific IgA and IgG responses, demonstrating the efficacy of the <i>L. agilis</i> flagellin-based display platform in eliciting both mucosal and systemic immune responses. This study is the first to demonstrate LAB-derived flagellin as an antigen display scaffold, highlighting <i>L. agilis</i> flagellin as a promising platform for mucosal vaccine development.IMPORTANCELactic acid bacteria (LAB) are promising delivery vehicles of active molecules, and surface display systems are gaining interest for efficiently displaying heterologous peptides and proteins. Flagellin, a TLR5 agonist, has been widely used as an adjuvant and an antigen scaffold, making it a potentially valuable platform for such systems. However, the potential of LAB-derived flagellin as a surface display scaffold remains largely unexplored. This study demonstrates that flagellin from <i>Ligilactobacillus agilis</i>, a flagellated LAB species, effectively functions as an antigen display platform, eliciting mucosal and systemic immune responses. Our findings highlight the feasibility of LAB-derived flagellin as a versatile tool for surface display of heterologous peptides, expanding its potential applications in vaccine development and mucosal immunotherapy.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0067425"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175526/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172151","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 two-component system CpxAR controls biofilm formation by directly regulating the T3SS needle tip protein EseB in <i>Edwardsiella piscicida</i>.","authors":"Shu Ya Zhang, Shan Shan Sun, Lu Yi Liu, Thusyakaanth Sivaranjan, Pin Nie, Hai Xia Xie","doi":"10.1128/aem.02264-24","DOIUrl":"10.1128/aem.02264-24","url":null,"abstract":"<p><p>The type III secretion system (T3SS) translocon protein EseB (needle tip protein) forms filamentous appendages on the surface of <i>Edwardsiella piscicida</i> to facilitate autoaggregation and biofilm formation. By contrast, another T3SS translocon protein EseC inhibits biofilm formation by sequestering EseC's chaperone EseE, which also functions as a positive regulator of the <i>escC-eseE</i> operon, in which EseB is encoded. The two-component system (TCS) EsrAB and the regulator EsrC tightly and positively regulate the T3SS in <i>E. piscicida</i>. The TCS CpxAR provides an adaptive response to external environmental changes. In this study, we have shown that disruption of the histidine kinase CpxA (sensor) instead of CpxR (response regulator) significantly reduces biofilm formation in <i>E. piscicida</i>. CpxR is negatively regulated by CpxA, and significant amounts of CpxR accumulate in <i>E. piscicida</i> in the absence of CpxA. CpxR, together with EsrB and EsrC, directly binds the promoter of the <i>cpxR-cpxA</i> operon to promote CpxR transcription and expression. The elevated phosphorylated CpxR (CpxR-<i>P</i>) binds to the promoter of the <i>escC-eseE</i> operon to repress <i>eseB</i> transcription and expression, while EseE, EsrB, and EsrC bind directly to the same promoter to promote EseB transcription and expression. <i>E. piscicida</i> is an enteric pathogen that senses microbiota-derived indole in the gut lumen. EseB filament-mediated biofilm formation in <i>E. piscicida</i> is inversely proportional to exogenous indole. Together, CpxR inhibits while EsrB, EsrC, and EseE stimulate transcription and expression of the <i>escC-eseE</i> operon, thereby coordinately controlling EseB filament-mediated biofilm formation in <i>E. piscicida</i> in response to environmental stimuli.IMPORTANCE<i>Edwardsiella piscicida</i> is primarily an enteric pathogen of fish and can form a biofilm to resist the lethal effects of host or antimicrobial agents. The assembly of filamentous appendages on the bacterial surface, mediated by the type III secretion system (T3SS) needle tip protein EseB, promotes bacterial-bacterial interactions and biofilm formation when <i>E. piscicida</i> is cultured in Dulbecco's modified Eagle's medium (DMEM). In this study, we have shown that the histidine kinase CpxA regulates biofilm formation in <i>E. piscicida</i> by negatively regulating its response regulator CpxR. Binding to the promoter of the <i>escC-eseE</i> operon, CpxR negatively regulates, whereas EsrB, EsrC, and EseE positively regulate the <i>escC-eseE</i> operon, of which EseB is encoded, coordinately regulating biofilm formation in <i>E. piscicida</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0226424"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172234","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":"Genome-wide investigation of outer membrane protein families under mosaic evolution in <i>Escherichia coli</i>.","authors":"Xin Cao, Cuihua Cao, Zefan Chen, Jialin Li, Zikun Yao, Yidong Zheng, Jinjin Wu, Zeling Li, Yueming Hu, Gaofeng Hao, Guoqiang Zhu, Wolfgang Köster, Aaron P White, Yejun Wang","doi":"10.1128/aem.00557-25","DOIUrl":"10.1128/aem.00557-25","url":null,"abstract":"<p><p>Several genes in Gram-negative bacteria encoding outer membrane proteins (OMPs) have been reported to show patterns of mosaic evolution featured by a mixture of negative selection and local recombination. Here, we improved a strategy and applied it to screen OMPs under mosaic evolution in <i>Escherichia coli</i> at the genome level. In total, 21 OMP families, including 16 new ones, were detected with the typical patterns of mosaic evolution. An absolute majority of the protein families are conserved in <i>E. coli</i> for the composition, genomic loci, and the overall structures. Highly variable regions (HVRs) can be recognized, which are frequently located extracellularly within the protruding loops. There is only a limited number of major HVR sequence types, within which positively selected sites can be detected occassionally. Based on the simulated results of multiple models, the OMPs under mosaic evolution are often with good antigenicity, with HVRs of various sequence types coinciding with the B-cell epitopes of the strongest immunogenicity. The study further broadened our understanding of the characteristics of mosaic evolution and the functions of OMPs in Gram-negative bacteria, laying an important foundation for their potential translational applications.IMPORTANCEIt is important to understand the evolutionary mechanisms of bacterial OMP-encoding genes, which would facilitate the development of anti-bacterial reagents. This study made the first genome-wide screening of bacterial OMPs under mosaic evolution and increased the list of candidate OMP families by threefold in <i>E. coli</i>, far more than we expected. The study further confirmed the hypothesis about the evolutionary, micro-evolutionary, and structural features of these OMPs and facilitated the functional theory of mosaic evolution. Moreover, the findings of limited HVR sequence types and strong immunogenicity of HVRs paved an important foundation for the application of these OMPs and their HVRs in the development of antibodies or other antibacterial treatment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0055725"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186336","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":"Longitudinal and cross-sectional sampling and whole genome sequencing of <i>Campylobacter</i> in a chicken abattoir reveal highly dynamic population structure.","authors":"Shanwei Tong, Kaidi Wang, Shenmiao Li, Michael Trimble, Yunxuan Chen, Lixue Liu, Jun Duan, Eduardo Taboada, Xiaonan Lu, William Hsiao","doi":"10.1128/aem.02369-24","DOIUrl":"10.1128/aem.02369-24","url":null,"abstract":"<p><p><i>Campylobacter</i> is a leading cause of human gastroenteritis worldwide and is commonly identified in poultry products. Current knowledge of its dissemination patterns in poultry production largely relies on the less sensitive traditional genotyping methods. In this study, whole-genome sequencing was applied to 324 <i>Campylobacter</i> isolates sampled from a chicken abattoir in the Greater Vancouver area throughout 2020. Core genome multi-locus sequence typing analysis revealed a highly diverse and dynamic <i>Campylobacter</i> population containing 27 distinct lineages. A wide range of plasmids was characterized, and a high prevalence of antibiotic resistance was observed among these isolates. Distinct subpopulations were identified in 10 lineages, suggesting that some <i>Campylobacter</i> populations may have diversified within the local agricultural environment. Some lineages were frequently reintroduced to the abattoir, suggesting the potential presence of hidden <i>Campylobacter</i> reservoirs upstream of slaughter. Comparisons between biological and environmental samples suggest a high probability of between-batch cross-contamination. Locally sourced public <i>Campylobacter</i> isolates showed strong genomic correlations with the lineages identified in this study. Notably, lineages 1629a and 1629b were identified to have persisted within the local poultry production ecosystem for several years, explaining their recurrent detection. In conclusion, this study enhances our understanding of <i>Campylobacter</i> population dynamics in the chicken abattoir environment, providing insights for controlling this foodborne pathogen in poultry production systems.IMPORTANCEUsing whole-genome sequencing, this study revealed a highly diverse and dynamic <i>Campylobacter</i> population within the chicken abattoir. The high prevalence of antibiotic resistance marked the critical need for surveillance in this region. The findings highlighted the likely existence of a hidden common source of <i>Campylobacter</i> upstream in the poultry production chain, which significantly contributes to the repeated introduction of the same lineages into the abattoir. Given the frequent reintroductions, the current understanding of <i>Campylobacter</i> persistence in the abattoir environment (up to 21 days) may require revision. Additionally, batch-to-batch dissemination of <i>Campylobacter</i> strains during processing is highly possible. A robust geographic association was also observed between the <i>Campylobacter</i> population in the abattoir and the local community. In sum, this study provides insights into the dynamics of <i>Campylobacter</i> contamination in the poultry production chain, offering guidance for improving prevention and control strategies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0236924"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143974460","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":"Potential pathogens and antimicrobial resistance genes in household environments: a study of soil floors and cow dung in rural Bangladesh.","authors":"Anna T Nguyen, Kalani Ratnasiri, Gabriella Barratt Heitmann, Sumaiya Tazin, Claire Anderson, Suhi Hanif, Afsana Yeamin, Abul Kasham Shoab, Ireen Sultana Shanta, Farjana Jahan, Md Sakib Hossain, Zahid Hayat Mahmud, Mohammad Jubair, Mustafizur Rahman, Mahbubur Rahman, Ayse Ercumen, Jade Benjamin-Chung","doi":"10.1128/aem.00669-25","DOIUrl":"10.1128/aem.00669-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;In low- and middle-income countries, living in homes with soil floors and animal cohabitation may expose children to fecal organisms, increasing the risk of enteric and antimicrobial-resistant infections. Our objective was to understand whether cow cohabitation in homes with soil floors in rural Bangladesh contributed to the presence and diversity of potential pathogens and antimicrobial resistance genes (ARGs) in the home. In 10 randomly selected households in rural Sirajganj District, we sampled floor soil and cow dung, which is commonly used as sealant in soil floors. We extracted DNA and performed shotgun metagenomic sequencing to explore potential pathogens and ARGs in each sample type. We detected 7 potential pathogens in soil only, 38 pathogens in cow dung only, and 182 pathogens in both soil and cow dung. Cow dung exhibited modestly higher potential pathogen genus richness compared to soil floors (Wilcoxon signed-rank test, &lt;i&gt;P&lt;/i&gt; = 0.002). Using Bray-Curtis dissimilarity, potential pathogen species community composition differed between floors and cow dung (permutational multivariate analysis of variance, &lt;i&gt;P&lt;/i&gt; &lt; 0.001). All soil floor and cow dung samples contained ARGs; detected ARGs confer resistance to antibiotic classes including sulfonamides, rifamycin, aminoglycosides, lincosamides, and tetracycline. Paired floor and cow dung samples shared ARGs against rifamycin and glycopeptides, but otherwise, there was little overlap in resistomes between sample types. Our findings contribute to the growing literature on household soil and domestic animals as potentially important contributors to disease transmission and as reservoirs of antimicrobial resistance in low-income country settings.IMPORTANCEIn low-income countries, inadequate housing materials and animal cohabitation can lead to fecal contamination of rural homes. Contaminated soil floors are difficult to clean and may harbor organisms causing illness and antibiotic resistance, especially in young children, who frequently ingest soil. We sequenced soil floor and cow dung samples from households in Sirajganj district, Bangladesh, and identified potential pathogens and antibiotic resistance genes. We detected 182 potential pathogens in both soil and cow dung; organisms present in both sample types at the highest relative abundances were &lt;i&gt;Escherichia coli&lt;/i&gt;, &lt;i&gt;Klebsiella pneumoniae, Salmonella enterica&lt;/i&gt;, and &lt;i&gt;Pseudomonas aeruginosa&lt;/i&gt;. Antibiotic resistance genes were found in all samples. In cow dung, the most common genes conferred resistance to the antibiotics lincosamide, rifamycin, cephamycin, tetracycline, and multiple antibiotics. In soil floors, the most common genes conferred resistance to rifamycin, sulfonamides, and multiple antibiotics. Household soil and cow dung may be important reservoirs of pathogens and antimicrobial resistance in low-income country settings with high levels of animal cohabitation compared to settings with finished household floo","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0066925"},"PeriodicalIF":3.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144149026","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}