Pub Date : 2024-08-21Epub Date: 2024-07-31DOI: 10.1128/aem.01033-24
Hannah McKinnon Reish, Lindsey Dewey, Lucas J Kirschman
Pseudoreplication compromises the validity of research by treating non-independent samples as independent replicates. This review examines the prevalence of pseudoreplication in host-microbiota studies, highlighting the critical need for rigorous experimental design and appropriate statistical analysis. We systematically reviewed 115 manuscripts on host-microbiota interactions. Our analysis revealed that 22% of the papers contained pseudoreplication, primarily due to co-housed organisms, whereas 52% lacked sufficient methodological details. The remaining 26% adequately addressed pseudoreplication through proper experimental design or statistical analysis. The high incidence of pseudoreplication and insufficient information underscores the importance of methodological reporting and statistical rigor to ensure reproducibility of host-microbiota research.
{"title":"A host of issues: pseudoreplication in host-microbiota studies.","authors":"Hannah McKinnon Reish, Lindsey Dewey, Lucas J Kirschman","doi":"10.1128/aem.01033-24","DOIUrl":"10.1128/aem.01033-24","url":null,"abstract":"<p><p>Pseudoreplication compromises the validity of research by treating non-independent samples as independent replicates. This review examines the prevalence of pseudoreplication in host-microbiota studies, highlighting the critical need for rigorous experimental design and appropriate statistical analysis. We systematically reviewed 115 manuscripts on host-microbiota interactions. Our analysis revealed that 22% of the papers contained pseudoreplication, primarily due to co-housed organisms, whereas 52% lacked sufficient methodological details. The remaining 26% adequately addressed pseudoreplication through proper experimental design or statistical analysis. The high incidence of pseudoreplication and insufficient information underscores the importance of methodological reporting and statistical rigor to ensure reproducibility of host-microbiota research.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854567","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}
Wastewater treatment plants (WWTPs) are host to diverse microbial communities and receive a constant influx of microbes from influent wastewater. However, the impact of immigrants on the structure and activities of the activated sludge (AS) microbial community remains unclear. To gain insight on this phenomenon known as perpetual community coalescence, the current study utilized controlled manipulative experiments that decoupled the influent wastewater composition from the microbial populations to reveal the fundamental mechanisms involved in immigration between sewers and AS-WWTP. The immigration dynamics of heterotrophs were analyzed by harvesting wastewater biomass solids from three different sewer systems and adding to synthetic wastewater. Immigrating influent populations were observed to contribute up to 14% of the sequencing reads in the AS. By modeling the net growth rate of taxa, it was revealed that immigrants primarily exhibited low or negative net growth rates. By developing a protocol to reproducibly grow AS-WWTP communities in the lab, we have laid down the foundational principles for the testing of operational factors creating community variations with low noise and appropriate replication. Understanding the processes that drive microbial community diversity and assembly is a key question in microbial ecology. In the future, this knowledge can be used to manipulate the structure of microbial communities and improve system performance in WWTPs.IMPORTANCEIn biological wastewater treatment processes, the microbial community composition is essential in the performance and stability of the system. This study developed a reproducible protocol to investigate the impact of influent immigration (or perpetual coalescence of the sewer and activated sludge communities) with appropriate reproducibility and controls, allowing intrinsic definitions of core and immigrant populations to be established. The method developed herein will allow sequential manipulative experiments to be performed to test specific hypothesis and optimize wastewater treatment processes to meet new treatment goals.
污水处理厂(WWTPs)是多种微生物群落的栖息地,并不断接收来自废水进水的微生物。然而,移民对活性污泥(AS)微生物群落结构和活动的影响仍不清楚。为了深入了解这种被称为 "永恒群落凝聚 "的现象,本研究采用了受控操纵实验,将进水废水成分与微生物种群脱钩,以揭示下水道与活性污泥法微生物群落之间移民的基本机制。通过从三个不同的下水道系统中收集废水生物质固体并加入合成废水,分析了异养生物的迁移动态。据观察,移民进水种群贡献了 AS 中 14% 的测序读数。通过模拟类群的净增长率,发现移民主要表现出较低或负的净增长率。通过制定在实验室中可重复性地培育 AS-WWTP 群落的方案,我们为测试产生低噪声和适当复制的群落变异的操作因素奠定了基本原则。了解驱动微生物群落多样性和组装的过程是微生物生态学的一个关键问题。重要意义在生物废水处理过程中,微生物群落的组成对系统的性能和稳定性至关重要。本研究开发了一种可重复的方案,用于研究进水移民(或下水道和活性污泥群落的永久聚合)的影响,具有适当的可重复性和控制,可建立核心种群和移民种群的内在定义。本实验所开发的方法将允许进行连续操作实验,以测试特定假设并优化废水处理过程,从而实现新的处理目标。
{"title":"Activated sludge microbial community assembly: the role of influent microbial community immigration.","authors":"Claire Gibson, Shameem Jauffur, Bing Guo, Dominic Frigon","doi":"10.1128/aem.00598-24","DOIUrl":"10.1128/aem.00598-24","url":null,"abstract":"<p><p>Wastewater treatment plants (WWTPs) are host to diverse microbial communities and receive a constant influx of microbes from influent wastewater. However, the impact of immigrants on the structure and activities of the activated sludge (AS) microbial community remains unclear. To gain insight on this phenomenon known as perpetual community coalescence, the current study utilized controlled manipulative experiments that decoupled the influent wastewater composition from the microbial populations to reveal the fundamental mechanisms involved in immigration between sewers and AS-WWTP. The immigration dynamics of heterotrophs were analyzed by harvesting wastewater biomass solids from three different sewer systems and adding to synthetic wastewater. Immigrating influent populations were observed to contribute up to 14% of the sequencing reads in the AS. By modeling the net growth rate of taxa, it was revealed that immigrants primarily exhibited low or negative net growth rates. By developing a protocol to reproducibly grow AS-WWTP communities in the lab, we have laid down the foundational principles for the testing of operational factors creating community variations with low noise and appropriate replication. Understanding the processes that drive microbial community diversity and assembly is a key question in microbial ecology. In the future, this knowledge can be used to manipulate the structure of microbial communities and improve system performance in WWTPs.IMPORTANCEIn biological wastewater treatment processes, the microbial community composition is essential in the performance and stability of the system. This study developed a reproducible protocol to investigate the impact of influent immigration (or perpetual coalescence of the sewer and activated sludge communities) with appropriate reproducibility and controls, allowing intrinsic definitions of core and immigrant populations to be established. The method developed herein will allow sequential manipulative experiments to be performed to test specific hypothesis and optimize wastewater treatment processes to meet new treatment goals.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589492","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}
Pub Date : 2024-08-21Epub Date: 2024-07-16DOI: 10.1128/aem.01165-24
Josefina Duran-Bedolla, Juan Téllez-Sosa, Paola Bocanegra-Ibarias, Astrid Schilmann, Sugey Bravo-Romero, Fernando Reyna-Flores, Tania Villa-Reyes, Humberto Barrios-Camacho
Antibiotic resistance has emerged as a global threat to public health, generating a growing interest in investigating the presence of antibiotic-resistant bacteria in environments influenced by anthropogenic activities. Wastewater treatment plants in hospital serve as significant reservoirs of antimicrobial-resistant bacteria, where a favorable environment is established, promoting the proliferation and transfer of resistance genes among different bacterial species. In our study, we isolated a total of 243 strains from 5 hospital wastewater sites in Mexico, belonging to 21 distinct Gram-negative bacterial species. The presence of β-lactamase was detected in 46.9% (114/243) of the isolates, which belonging to the Enterobacteriaceae family. We identified a total of 169 β-lactamase genes; blaTEM in 33.1%, blaCTX-M in 25.4%, blaKPC in 25.4%, blaNDM 8.8%, blaSHV in 5.3%, and blaOXA-48 in 1.1% distributed in 12 different bacteria species. Among the 114 of the isolates, 50.8% were found to harbor at least one carbapenemase and were discharged into the environment. The carbapenemase blaKPC was found in six Citrobacter spp. and E. coli, while blaNDM was detected in two distinct Enterobacter spp. and E. coli. Notably, blaNDM-1 was identified in a 110 Kb IncFII conjugative plasmid in E. cloacae, E. xiangfangensis, and E. coli within the same hospital wastewater. In conclusion, hospital wastewater showed the presence of Enterobacteriaceae carrying a high frequency of carbapenemase blaKPC and blaNDM. We propose that hospital wastewater serves as reservoirs for resistance mechanism within bacterial communities and creates an optimal environment for the exchange of this resistance mechanism among different bacterial strains.
Importance: The significance of this study lies in its findings regarding the prevalence and diversity of antibiotic-resistant bacteria and genes identified in hospital wastewater in Mexico. The research underscores the urgent need for enhanced surveillance and prevention strategies to tackle the escalating challenge of antibiotic resistance, particularly evident through the elevated frequencies of carbapenemase genes such as blaKPC and blaNDM within the Enterobacteriaceae family. Moreover, the identification of these resistance genes on conjugative plasmids highlights the potential for widespread transmission via horizontal gene transfer. Understanding the mechanisms of antibiotic resistance in hospital wastewater is crucial for developing targeted interventions aimed at reducing transmission, thereby safeguarding public health and preserving the efficacy of antimicrobial therapies.
{"title":"<i>Citrobacter</i> spp. and <i>Enterobacter</i> spp. as reservoirs of carbapenemase <i>bla</i><sub>NDM</sub> and <i>bla</i><sub>KPC</sub> resistance genes in hospital wastewater.","authors":"Josefina Duran-Bedolla, Juan Téllez-Sosa, Paola Bocanegra-Ibarias, Astrid Schilmann, Sugey Bravo-Romero, Fernando Reyna-Flores, Tania Villa-Reyes, Humberto Barrios-Camacho","doi":"10.1128/aem.01165-24","DOIUrl":"10.1128/aem.01165-24","url":null,"abstract":"<p><p>Antibiotic resistance has emerged as a global threat to public health, generating a growing interest in investigating the presence of antibiotic-resistant bacteria in environments influenced by anthropogenic activities. Wastewater treatment plants in hospital serve as significant reservoirs of antimicrobial-resistant bacteria, where a favorable environment is established, promoting the proliferation and transfer of resistance genes among different bacterial species. In our study, we isolated a total of 243 strains from 5 hospital wastewater sites in Mexico, belonging to 21 distinct Gram-negative bacterial species. The presence of β-lactamase was detected in 46.9% (114/243) of the isolates, which belonging to the <i>Enterobacteriaceae</i> family. We identified a total of 169 β-lactamase genes; <i>bla</i><sub>TEM</sub> in 33.1%, <i>bla</i><sub>CTX-M</sub> in 25.4%, <i>bla</i><sub>KPC</sub> in 25.4%, <i>bla</i><sub>NDM</sub> 8.8%, <i>bla</i><sub>SHV</sub> in 5.3%, and <i>bla</i><sub>OXA-48</sub> in 1.1% distributed in 12 different bacteria species. Among the 114 of the isolates, 50.8% were found to harbor at least one carbapenemase and were discharged into the environment. The carbapenemase <i>bla</i><sub>KPC</sub> was found in six <i>Citrobacter</i> spp. and <i>E. coli</i>, while <i>bla</i><sub>NDM</sub> was detected in two distinct <i>Enterobacter</i> spp. and <i>E. coli</i>. Notably, <i>bla</i><sub>NDM-1</sub> was identified in a 110 Kb IncFII conjugative plasmid in <i>E. cloacae</i>, <i>E. xiangfangensis,</i> and <i>E. coli</i> within the same hospital wastewater. In conclusion, hospital wastewater showed the presence of <i>Enterobacteriaceae</i> carrying a high frequency of carbapenemase <i>bla</i><sub>KPC</sub> and <i>bla</i><sub>NDM</sub>. We propose that hospital wastewater serves as reservoirs for resistance mechanism within bacterial communities and creates an optimal environment for the exchange of this resistance mechanism among different bacterial strains.</p><p><strong>Importance: </strong>The significance of this study lies in its findings regarding the prevalence and diversity of antibiotic-resistant bacteria and genes identified in hospital wastewater in Mexico. The research underscores the urgent need for enhanced surveillance and prevention strategies to tackle the escalating challenge of antibiotic resistance, particularly evident through the elevated frequencies of carbapenemase genes such as <i>bla</i><sub>KPC</sub> and <i>bla</i><sub>NDM</sub> within the <i>Enterobacteriaceae</i> family. Moreover, the identification of these resistance genes on conjugative plasmids highlights the potential for widespread transmission via horizontal gene transfer. Understanding the mechanisms of antibiotic resistance in hospital wastewater is crucial for developing targeted interventions aimed at reducing transmission, thereby safeguarding public health and preserving the efficacy of antimicrobial therapies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337798/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141619121","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}
Pub Date : 2024-08-21Epub Date: 2024-07-17DOI: 10.1128/aem.00850-24
Yu He, Shiyan Zhuo, Donghao Gao, Yue Pan, Meng Li, Jie Pan, Yongguang Jiang, Yidan Hu, Jinzhi Guo, Qin Lin, Robert A Sanford, Weimin Sun, Jianying Shang, Na Wei, Shuming Peng, Zhou Jiang, Shuyi Li, Yongzhe Li, Yiran Dong, Liang Shi
Viral communities exist in a variety of ecosystems and play significant roles in mediating biogeochemical processes, whereas viruses inhabiting strongly alkaline geochemical systems remain underexplored. In this study, the viral diversity, potential functionalities, and virus-host interactions in a strongly alkaline environment (pH = 10.4-12.4) exposed to the leachates derived from the serpentinization-like reactions of smelting slags were investigated. The viral populations (e.g., Herelleviridae, Queuovirinae, and Inoviridae) were closely associated with the dominating prokaryotic hosts (e.g., Meiothermus, Trueperaceae, and Serpentinomonas) in this ultrabasic environment. Auxiliary metabolic genes (AMGs) suggested that viruses may enhance hosts' fitness by facilitating cofactor biosynthesis, hydrogen metabolism, and carbon cycling. To evaluate the activity of synthesis of essential cofactor vitamin B9 by the viruses, a viral folA (vfolA) gene encoding dihydrofolate reductase (DHFR) was introduced into a thymidine-auxotrophic strain Escherichia coli MG1655 ΔfolA mutant, which restored the growth of the latter in the absence of thymidine. Notably, the homologs of the validated vDHFR were globally distributed in the viromes across various ecosystems. The present study sheds new light on the unique viral communities in hyperalkaline ecosystems and their potential beneficial impacts on the coexisting microbial consortia by supplying essential cofactors.
Importance: This study presents a comprehensive investigation into the diversity, potential functionalities, and virus-microbe interactions in an artificially induced strongly alkaline environment. Functional validation of the detected viral folA genes encoding dihydrofolate reductase substantiated the synthesis of essential cofactors by viruses, which may be ubiquitous, considering the broad distribution of the viral genes associated with folate cycling.
{"title":"Viral communities in a pH>10 serpentinite-like environment: insight into diversity and potential roles in modulating the microbiomes by bioactive vitamin B<sub>9</sub> synthesis.","authors":"Yu He, Shiyan Zhuo, Donghao Gao, Yue Pan, Meng Li, Jie Pan, Yongguang Jiang, Yidan Hu, Jinzhi Guo, Qin Lin, Robert A Sanford, Weimin Sun, Jianying Shang, Na Wei, Shuming Peng, Zhou Jiang, Shuyi Li, Yongzhe Li, Yiran Dong, Liang Shi","doi":"10.1128/aem.00850-24","DOIUrl":"10.1128/aem.00850-24","url":null,"abstract":"<p><p>Viral communities exist in a variety of ecosystems and play significant roles in mediating biogeochemical processes, whereas viruses inhabiting strongly alkaline geochemical systems remain underexplored. In this study, the viral diversity, potential functionalities, and virus-host interactions in a strongly alkaline environment (pH = 10.4-12.4) exposed to the leachates derived from the serpentinization-like reactions of smelting slags were investigated. The viral populations (e.g., Herelleviridae, Queuovirinae, and Inoviridae) were closely associated with the dominating prokaryotic hosts (e.g., <i>Meiothermus</i>, Trueperaceae, and <i>Serpentinomonas</i>) in this ultrabasic environment. Auxiliary metabolic genes (AMGs) suggested that viruses may enhance hosts' fitness by facilitating cofactor biosynthesis, hydrogen metabolism, and carbon cycling. To evaluate the activity of synthesis of essential cofactor vitamin B<sub>9</sub> by the viruses, a viral <i>folA</i> (v<i>folA</i>) gene encoding dihydrofolate reductase (DHFR) was introduced into a thymidine-auxotrophic strain <i>Escherichia coli</i> MG1655 Δ<i>folA</i> mutant, which restored the growth of the latter in the absence of thymidine. Notably, the homologs of the validated vDHFR were globally distributed in the viromes across various ecosystems. The present study sheds new light on the unique viral communities in hyperalkaline ecosystems and their potential beneficial impacts on the coexisting microbial consortia by supplying essential cofactors.</p><p><strong>Importance: </strong>This study presents a comprehensive investigation into the diversity, potential functionalities, and virus-microbe interactions in an artificially induced strongly alkaline environment. Functional validation of the detected viral <i>folA</i> genes encoding dihydrofolate reductase substantiated the synthesis of essential cofactors by viruses, which may be ubiquitous, considering the broad distribution of the viral genes associated with folate cycling.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141625802","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}
Fungi compose a minority but a common component of normal oral microbiota and contribute to oral and systemic health by interacting with bacterial inhabitants. This study investigated the relationship of oral fungal profiles to health status and bacterial profiles of 159 elderly adults receiving community support and home care services. Fungal and bacterial densities and compositions were determined based on the fungal ribosomal internal transcribed spacer region and bacterial 16S rRNA gene amplicon analyses, respectively. The total fungal density of 87 individuals exceeded 5,000 copies, and their microbiota was characterized by significantly less dense bacterial populations and lower relative abundances of oral health-associated taxa, such as Neisseria perflava and Porphyromonas pasteri, compared with those with less than 5,000 copies of fungi. These individuals were significantly older, had fewer teeth, had lower physical function, and comprised more denture users and individuals with cognitive decline. Fungal compositions were classified into three profiles (Candida albicans-dominant, non-albicans Candida-dominant, and non-Candida-dominant), and individuals with a non-albicans Candida-dominant profile exhibited significantly lower physical and cognitive function than those with the Candida albicans-dominant profile. These results demonstrate that a high-density fungal population co-occurs with poor oral and systemic health status of the host and dysbiosis of the bacterial community, and particularly, the overgrowth of non-albicans Candida species may be implicated in worsening systemic conditions.
Importance: The interaction between fungal and bacterial components involved in the virulence of oral microbiota has received attention. This study demonstrates that an increase in fungal components is associated with a dysbiotic bacterial community and poor health status in elderly adults. Among individuals with a high-density fungal population, particularly, those with a non-albicans Candida-dominant profile had lower physical and cognitive functions than those with a C. albicans-dominant profile. These findings indicate that the evaluation of fungal components, in addition to the bacterial components, is important to understand the involvement of oral microbiota in oral and systemic diseases in elderly adults.
{"title":"Association of oral fungal profiles with health status and bacterial composition in elderly adults receiving community support and home care service.","authors":"Mikari Asakawa, Shinya Kageyama, Heba Shehta Said, Jiale Ma, Shino Suma, Michiko Furuta, Toru Takeshita","doi":"10.1128/aem.00857-24","DOIUrl":"10.1128/aem.00857-24","url":null,"abstract":"<p><p>Fungi compose a minority but a common component of normal oral microbiota and contribute to oral and systemic health by interacting with bacterial inhabitants. This study investigated the relationship of oral fungal profiles to health status and bacterial profiles of 159 elderly adults receiving community support and home care services. Fungal and bacterial densities and compositions were determined based on the fungal ribosomal internal transcribed spacer region and bacterial 16S rRNA gene amplicon analyses, respectively. The total fungal density of 87 individuals exceeded 5,000 copies, and their microbiota was characterized by significantly less dense bacterial populations and lower relative abundances of oral health-associated taxa, such as <i>Neisseria perflava</i> and <i>Porphyromonas pasteri</i>, compared with those with less than 5,000 copies of fungi. These individuals were significantly older, had fewer teeth, had lower physical function, and comprised more denture users and individuals with cognitive decline. Fungal compositions were classified into three profiles (<i>Candida albicans</i>-dominant, non-<i>albicans Candida</i>-dominant, and non-<i>Candida</i>-dominant), and individuals with a non-<i>albicans Candida</i>-dominant profile exhibited significantly lower physical and cognitive function than those with the <i>Candida albicans</i>-dominant profile. These results demonstrate that a high-density fungal population co-occurs with poor oral and systemic health status of the host and dysbiosis of the bacterial community, and particularly, the overgrowth of non-<i>albicans Candida</i> species may be implicated in worsening systemic conditions.</p><p><strong>Importance: </strong>The interaction between fungal and bacterial components involved in the virulence of oral microbiota has received attention. This study demonstrates that an increase in fungal components is associated with a dysbiotic bacterial community and poor health status in elderly adults. Among individuals with a high-density fungal population, particularly, those with a non-<i>albicans Candida</i>-dominant profile had lower physical and cognitive functions than those with a <i>C. albicans</i>-dominant profile. These findings indicate that the evaluation of fungal components, in addition to the bacterial components, is important to understand the involvement of oral microbiota in oral and systemic diseases in elderly adults.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854570","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}
Pub Date : 2024-08-21Epub Date: 2024-07-12DOI: 10.1128/aem.00075-24
Le Li, Qiang Li, Yuting Xiao, Jiangshan Ma, Gao-Qiang Liu
Glycerol dehydratase is the key and rate-limiting enzyme in the 1,3-propanediol synthesis pathway of Klebsiella pneumoniae, which determined the producing rate and yield of 1,3-propanediol. However, the expression regulation mechanism of glycerol dehydratase gene dhaB remains poorly unknown. In this study, a histone-like nucleoid-structuring (H-NS) protein was identified and characterized as the positive transcription regulator for dhaB expression in K. pneumoniae 2e, which exhibited high tolerance against crude glycerol in our previous study. Deletion of hns gene significantly decreased the transcription level of dhaB in K. pneumoniae 2e, which led to a remarkable defect on strain growth, glycerol dehydratase activity, and 3-hydroxypropanal production during glycerol fermentation. The transcription level of dhaB was significantly up-regulated in crude glycerol relative to pure glycerol, while the inactivation of H-NS resulted in more negative effect for transcription level of dhaB in the former. Though the H-NS expression level was almost comparable in both substrates, its multimer state was reduced in crude glycerol relative to pure glycerol, suggesting that the oligomerization state of H-NS might have contributed for positive regulation of dhaB expression. Furthermore, electrophoretic mobility shift and DNase I footprinting assays showed that H-NS could directly bind to the upstream promoter region of dhaB by recognizing the AT-rich region. These findings provided new insight into the transcriptional regulation mechanism of H-NS for glycerol dehydratase expression in K. pneumoniae, which might offer new target for engineering bacteria to industrially produce 1,3-propanediol.IMPORTANCEThe biological production of 1,3-propanediol from glycerol by microbial fermentation shows great promising prospect on industrial application. Glycerol dehydratase catalyzes the penultimate step in glycerol metabolism and is regarded as one of the key and rate-limiting enzymes for 1,3-propanediol production. H-NS was reported as a pleiotropic modulator with negative effects on gene expression in most studies. Here, we reported for the first time that the expression of glycerol dehydratase gene is positively regulated by the H-NS. The results provide insight into a novel molecular mechanism of H-NS for positive regulation of glycerol dehydratase gene expression in K. pneumoniae, which holds promising potential for facilitating construction of engineering highly efficient 1,3-propanediol-producing strains.
{"title":"H-NS involved in positive regulation of glycerol dehydratase gene expression in <i>Klebsiella pneumoniae</i> 2e.","authors":"Le Li, Qiang Li, Yuting Xiao, Jiangshan Ma, Gao-Qiang Liu","doi":"10.1128/aem.00075-24","DOIUrl":"10.1128/aem.00075-24","url":null,"abstract":"<p><p>Glycerol dehydratase is the key and rate-limiting enzyme in the 1,3-propanediol synthesis pathway of <i>Klebsiella pneumoniae</i>, which determined the producing rate and yield of 1,3-propanediol. However, the expression regulation mechanism of glycerol dehydratase gene <i>dhaB</i> remains poorly unknown. In this study, a histone-like nucleoid-structuring (H-NS) protein was identified and characterized as the positive transcription regulator for <i>dhaB</i> expression in <i>K. pneumoniae</i> 2e, which exhibited high tolerance against crude glycerol in our previous study. Deletion of <i>hns</i> gene significantly decreased the transcription level of <i>dhaB</i> in <i>K. pneumoniae</i> 2e, which led to a remarkable defect on strain growth, glycerol dehydratase activity, and 3-hydroxypropanal production during glycerol fermentation. The transcription level of <i>dhaB</i> was significantly up-regulated in crude glycerol relative to pure glycerol, while the inactivation of H-NS resulted in more negative effect for transcription level of <i>dhaB</i> in the former. Though the H-NS expression level was almost comparable in both substrates, its multimer state was reduced in crude glycerol relative to pure glycerol, suggesting that the oligomerization state of H-NS might have contributed for positive regulation of <i>dhaB</i> expression. Furthermore, electrophoretic mobility shift and DNase I footprinting assays showed that H-NS could directly bind to the upstream promoter region of <i>dhaB</i> by recognizing the AT-rich region. These findings provided new insight into the transcriptional regulation mechanism of H-NS for glycerol dehydratase expression in <i>K. pneumoniae</i>, which might offer new target for engineering bacteria to industrially produce 1,3-propanediol.IMPORTANCEThe biological production of 1,3-propanediol from glycerol by microbial fermentation shows great promising prospect on industrial application. Glycerol dehydratase catalyzes the penultimate step in glycerol metabolism and is regarded as one of the key and rate-limiting enzymes for 1,3-propanediol production. H-NS was reported as a pleiotropic modulator with negative effects on gene expression in most studies. Here, we reported for the first time that the expression of glycerol dehydratase gene is positively regulated by the H-NS. The results provide insight into a novel molecular mechanism of H-NS for positive regulation of glycerol dehydratase gene expression in <i>K. pneumoniae</i>, which holds promising potential for facilitating construction of engineering highly efficient 1,3-propanediol-producing strains.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589493","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}
Pub Date : 2024-08-21Epub Date: 2024-07-18DOI: 10.1128/aem.00516-24
James Larson, Monika Tokmina-Lukaszewska, Devon Payne, Rachel L Spietz, Hunter Fausset, Md Gahangir Alam, Brooklyn K Brekke, Jordan Pauley, Ethan J Hasenoehrl, Eric M Shepard, Eric S Boyd, Brian Bothner
Methanogens often inhabit sulfidic environments that favor the precipitation of transition metals such as iron (Fe) as metal sulfides, including mackinawite (FeS) and pyrite (FeS2). These metal sulfides have historically been considered biologically unavailable. Nonetheless, methanogens are commonly cultivated with sulfide (HS-) as a sulfur source, a condition that would be expected to favor metal precipitation and thus limit metal availability. Recent studies have shown that methanogens can access Fe and sulfur (S) from FeS and FeS2 to sustain growth. As such, medium supplied with FeS2 should lead to higher availability of transition metals when compared to medium supplied with HS-. Here, we examined how transition metal availability under sulfidic (i.e., cells provided with HS- as sole S source) versus non-sulfidic (cells provided with FeS2 as sole S source) conditions impact the metalloproteome of Methanosarcina barkeri Fusaro. To achieve this, we employed size exclusion chromatography coupled with inductively coupled plasma mass spectrometry and shotgun proteomics. Significant changes were observed in the composition and abundance of iron, cobalt, nickel, zinc, and molybdenum proteins. Among the differences were alterations in the stoichiometry and abundance of multisubunit protein complexes involved in methanogenesis and electron transport chains. Our data suggest that M. barkeri utilizes the minimal iron-sulfur cluster complex and canonical cysteine biosynthesis proteins when grown on FeS2 but uses the canonical Suf pathway in conjunction with the tRNA-Sep cysteine pathway for iron-sulfur cluster and cysteine biosynthesis under sulfidic growth conditions.IMPORTANCEProteins that catalyze biochemical reactions often require transition metals that can have a high affinity for sulfur, another required element for life. Thus, the availability of metals and sulfur are intertwined and can have large impacts on an organismismal biochemistry. Methanogens often occupy anoxic, sulfide-rich (euxinic) environments that favor the precipitation of transition metals as metal sulfides, thereby creating presumed metal limitation. Recently, several methanogens have been shown to acquire iron and sulfur from pyrite, an abundant iron-sulfide mineral that was traditionally considered to be unavailable to biology. The work presented here provides new insights into the distribution of metalloproteins, and metal uptake of Methanosarcina barkeri Fusaro grown under euxinic or pyritic growth conditions. Thorough characterizations of this methanogen under different metal and sulfur conditions increase our understanding of the influence of metal availability on methanogens, and presumably other anaerobes, that inhabit euxinic environments.
{"title":"Impact of mineral and non-mineral sources of iron and sulfur on the metalloproteome of <i>Methanosarcina barkeri</i>.","authors":"James Larson, Monika Tokmina-Lukaszewska, Devon Payne, Rachel L Spietz, Hunter Fausset, Md Gahangir Alam, Brooklyn K Brekke, Jordan Pauley, Ethan J Hasenoehrl, Eric M Shepard, Eric S Boyd, Brian Bothner","doi":"10.1128/aem.00516-24","DOIUrl":"10.1128/aem.00516-24","url":null,"abstract":"<p><p>Methanogens often inhabit sulfidic environments that favor the precipitation of transition metals such as iron (Fe) as metal sulfides, including mackinawite (FeS) and pyrite (FeS<sub>2</sub>). These metal sulfides have historically been considered biologically unavailable. Nonetheless, methanogens are commonly cultivated with sulfide (HS<sup>-</sup>) as a sulfur source, a condition that would be expected to favor metal precipitation and thus limit metal availability. Recent studies have shown that methanogens can access Fe and sulfur (S) from FeS and FeS<sub>2</sub> to sustain growth. As such, medium supplied with FeS<sub>2</sub> should lead to higher availability of transition metals when compared to medium supplied with HS<sup>-</sup>. Here, we examined how transition metal availability under sulfidic (i.e., cells provided with HS<sup>-</sup> as sole S source) versus non-sulfidic (cells provided with FeS<sub>2</sub> as sole S source) conditions impact the metalloproteome of <i>Methanosarcina barkeri</i> Fusaro. To achieve this, we employed size exclusion chromatography coupled with inductively coupled plasma mass spectrometry and shotgun proteomics. Significant changes were observed in the composition and abundance of iron, cobalt, nickel, zinc, and molybdenum proteins. Among the differences were alterations in the stoichiometry and abundance of multisubunit protein complexes involved in methanogenesis and electron transport chains. Our data suggest that <i>M. barkeri</i> utilizes the minimal iron-sulfur cluster complex and canonical cysteine biosynthesis proteins when grown on FeS<sub>2</sub> but uses the canonical Suf pathway in conjunction with the tRNA-Sep cysteine pathway for iron-sulfur cluster and cysteine biosynthesis under sulfidic growth conditions.IMPORTANCEProteins that catalyze biochemical reactions often require transition metals that can have a high affinity for sulfur, another required element for life. Thus, the availability of metals and sulfur are intertwined and can have large impacts on an organismismal biochemistry. Methanogens often occupy anoxic, sulfide-rich (euxinic) environments that favor the precipitation of transition metals as metal sulfides, thereby creating presumed metal limitation. Recently, several methanogens have been shown to acquire iron and sulfur from pyrite, an abundant iron-sulfide mineral that was traditionally considered to be unavailable to biology. The work presented here provides new insights into the distribution of metalloproteins, and metal uptake of <i>Methanosarcina barkeri</i> Fusaro grown under euxinic or pyritic growth conditions. Thorough characterizations of this methanogen under different metal and sulfur conditions increase our understanding of the influence of metal availability on methanogens, and presumably other anaerobes, that inhabit euxinic environments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632448","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}
Pub Date : 2024-08-21Epub Date: 2024-07-26DOI: 10.1128/aem.00862-24
Shan Shan Sun, Tian Tian He, Shu Ya Zhang, Xiu-Jun Yu, Chang Chen, Zubair Ahmed Laghari, Pin Nie, Hai Xia Xie
Type 1 fimbria, the short hair-like appendage assembled on the bacterial surface, plays a pivotal role in adhesion and invasion in Edwardsiella piscicida. The type III secretion system (T3SS), another bacterial surface appendage, facilitates E. piscicida's replication in vivo by delivering effectors into host cells. Our previous research demonstrated that E. piscicida T3SS protein EseJ inhibits adhesion and invasion of E. piscicida by suppressing type 1 fimbria. However, how EseJ suppresses type 1 fimbria remains elusive. In this study, a lacI-like operator (nt -245 to -1 of fimA) upstream of type 1 fimbrial operon in E. piscicida was identified, and EseJ inhibits type 1 fimbria through the lacI-like operator. Moreover, through DNA pull-down and electrophoretic mobility shift assay, an AraC-type T3SS regulator, EsrC, was screened and verified to bind to nt -145 to -126 and nt -50 to -1 of fimA, suppressing type 1 fimbria. EseJ is almost abolished upon the depletion of EsrC. EsrC and EseJ impede type 1 fimbria expression. Intriguingly, nutrition and microbiota-derived indole activate type 1 fimbria through downregulating T3SS, alleviating EsrC or EseJ's inhibitory effect on lacI-like operator of type 1 fimbrial operon. By this study, it is revealed that upon entering the gastrointestinal tract, rich nutrients and indole downregulate T3SS and thereof upregulate type 1 fimbria, stimulating efficient adhesion and invasion; upon being internalized into epithelium, the limit in indole and nutrition switches on T3SS and thereof switches off type 1 fimbria, facilitating effector delivery to guarantee E. piscicida's survival/replication in vivo.IMPORTANCEIn this work, we identified the lacI-like operator of type 1 fimbrial operon in E. piscicida, which was suppressed by the repressors-T3SS protein EseJ and EsrC. We unveiled that E. piscicida upregulates type 1 fimbria upon sensing rich nutrition and the microbiota-derived indole, thereof promoting the adhesion of E. piscicida. The increase of indole and nutrition promotes type 1 fimbria by downregulating T3SS. The decrease in EseJ and EsrC alleviates their suppression on type 1 fimbria, and vice versa.
{"title":"T3SS protein EsrC binds to the <i>lacI</i>-like operator of type 1 fimbrial operon to suppress adhesion of <i>Edwardsiella piscicida</i>.","authors":"Shan Shan Sun, Tian Tian He, Shu Ya Zhang, Xiu-Jun Yu, Chang Chen, Zubair Ahmed Laghari, Pin Nie, Hai Xia Xie","doi":"10.1128/aem.00862-24","DOIUrl":"10.1128/aem.00862-24","url":null,"abstract":"<p><p>Type 1 fimbria, the short hair-like appendage assembled on the bacterial surface, plays a pivotal role in adhesion and invasion in <i>Edwardsiella piscicida</i>. The type III secretion system (T3SS), another bacterial surface appendage, facilitates <i>E. piscicida</i>'s replication <i>in vivo</i> by delivering effectors into host cells. Our previous research demonstrated that <i>E. piscicida</i> T3SS protein EseJ inhibits adhesion and invasion of <i>E. piscicida</i> by suppressing type 1 fimbria. However, how EseJ suppresses type 1 fimbria remains elusive. In this study, a <i>lacI</i>-like operator (nt -245 to -1 of <i>fimA</i>) upstream of type 1 fimbrial operon in <i>E. piscicida</i> was identified, and EseJ inhibits type 1 fimbria through the <i>lacI</i>-like operator. Moreover, through DNA pull-down and electrophoretic mobility shift assay, an AraC-type T3SS regulator, EsrC, was screened and verified to bind to nt -145 to -126 and nt -50 to -1 of <i>fimA</i>, suppressing type 1 fimbria. EseJ is almost abolished upon the depletion of EsrC. EsrC and EseJ impede type 1 fimbria expression. Intriguingly, nutrition and microbiota-derived indole activate type 1 fimbria through downregulating T3SS, alleviating EsrC or EseJ's inhibitory effect on <i>lacI</i>-like operator of type 1 fimbrial operon. By this study, it is revealed that upon entering the gastrointestinal tract, rich nutrients and indole downregulate T3SS and thereof upregulate type 1 fimbria, stimulating efficient adhesion and invasion; upon being internalized into epithelium, the limit in indole and nutrition switches on T3SS and thereof switches off type 1 fimbria, facilitating effector delivery to guarantee <i>E. piscicida</i>'s survival/replication <i>in vivo</i>.IMPORTANCEIn this work, we identified the <i>lacI</i>-like operator of type 1 fimbrial operon in <i>E. piscicida</i>, which was suppressed by the repressors-T3SS protein EseJ and EsrC. We unveiled that <i>E. piscicida</i> upregulates type 1 fimbria upon sensing rich nutrition and the microbiota-derived indole, thereof promoting the adhesion of <i>E. piscicida</i>. The increase of indole and nutrition promotes type 1 fimbria by downregulating T3SS. The decrease in EseJ and EsrC alleviates their suppression on type 1 fimbria, and <i>vice versa</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756763","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}
Pub Date : 2024-08-21Epub Date: 2024-07-31DOI: 10.1128/aem.00936-24
A R Prave
The geological record of stable carbon isotopes preserved in marine carbonate rocks spans nearly 4 billion years. Numerous perturbations mark this record, but one stands out for its magnitude, the Lomagundi-Jatuli Event, which spanned the transition of the Earth's surface from an anoxic to an oxic state. An Applied and Environmental Microbiology article by D. Y. Sumner (90:e00093-24, 2024, https://doi.org/10.1128/aem.00093-24) provides, for the first time, a biological explanation for its initiation, cessation, environmental specific restriction, and geological singularity.
保存在海洋碳酸盐岩中的稳定碳同位素的地质记录跨越了近 40 亿年。在这一记录中发生了无数次扰动,但有一次扰动的程度最为严重,这就是洛马昆迪-贾图利事件,它跨越了地球表面从缺氧状态向缺氧状态的转变。D. Y. Sumner发表的《应用与环境微生物学》(90:e00093-24, 2024, https://doi.org/10.1128/aem.00093-24)一文首次从生物学角度解释了这一事件的开始、停止、特定环境限制和地质奇点。
{"title":"Environmental microbiology explains the largest positive carbon isotope excursion in Earth history, the Lomagundi-Jatuli Event.","authors":"A R Prave","doi":"10.1128/aem.00936-24","DOIUrl":"10.1128/aem.00936-24","url":null,"abstract":"<p><p>The geological record of stable carbon isotopes preserved in marine carbonate rocks spans nearly 4 billion years. Numerous perturbations mark this record, but one stands out for its magnitude, the Lomagundi-Jatuli Event, which spanned the transition of the Earth's surface from an anoxic to an oxic state. An <i>Applied and Environmental Microbiology</i> article by D. Y. Sumner (90:e00093-24, 2024, https://doi.org/10.1128/aem.00093-24) provides, for the first time, a biological explanation for its initiation, cessation, environmental specific restriction, and geological singularity.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854571","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}
Pub Date : 2024-08-21Epub Date: 2024-07-31DOI: 10.1128/aem.00749-24
Yezhi Fu, Erin M Nawrocki, Nkuchia M M'ikanatha, Edward G Dudley
Enterotoxigenic Escherichia coli (ETEC) are significant pathogen in both cattle and pigs, causing diarrhea in these animals and leading to economic losses in the livestock industry. Understanding the dissimilarity in genotype, antimicrobial resistance (AMR), and virulence between bovine and swine ETEC is crucial for development of targeted preventive and therapeutic approaches for livestock. However, a comprehensive study on this area remains lacking. Here, we performed whole-genome sequencing-based analyses of bovine (n = 554) and swine (n = 623) ETEC collected in the United States over a 53-year period. We identified distinct ETEC genotypes (fimH type, O antigen, H antigen, sequence type) in cattle and pigs. Furthermore, specific AMR and virulence profiles were associated with bovine and swine ETEC. Compared to swine ETEC, bovine ETEC were less diverse in genotypes and had a significantly (P < 0.001) lower number of AMR genes per isolate but higher co-occurrence of Shiga toxin and enterotoxin genes. Our results provide an overview of the key genomic differences between bovine and swine ETEC in the United States, which might be attributed to host adaptation and antibiotic usage practice. Ongoing surveillance and research are essential to monitor the genetic diversity and AMR patterns of ETEC in different host species.
Importance: Enterotoxigenic Escherichia coli (ETEC)-associated diarrhea represent one of the most economically important diseases in the livestock industry. By analyzing over a thousand livestock-derived ETEC samples in the United States, our study unveiled a clear distinction in ETEC's genetic traits (i.e., genotypes, antimicrobial resistance [AMR], and virulence profiles) that might be tied to the different use of antibiotics in cattle and pigs, and the bacteria's adaptation to their specific animal hosts. This understanding is crucial for tailoring preventive and therapeutic strategies. It also highlights the significance of ongoing surveillance and research into the evolution of bacterial pathogens like ETEC in livestock by using advanced techniques such as whole-genome sequencing.
{"title":"Host species shapes genotype, antimicrobial resistance, and virulence profiles of enterotoxigenic <i>Escherichia coli</i> (ETEC) from livestock in the United States.","authors":"Yezhi Fu, Erin M Nawrocki, Nkuchia M M'ikanatha, Edward G Dudley","doi":"10.1128/aem.00749-24","DOIUrl":"10.1128/aem.00749-24","url":null,"abstract":"<p><p>Enterotoxigenic <i>Escherichia coli</i> (ETEC) are significant pathogen in both cattle and pigs, causing diarrhea in these animals and leading to economic losses in the livestock industry. Understanding the dissimilarity in genotype, antimicrobial resistance (AMR), and virulence between bovine and swine ETEC is crucial for development of targeted preventive and therapeutic approaches for livestock. However, a comprehensive study on this area remains lacking. Here, we performed whole-genome sequencing-based analyses of bovine (<i>n</i> = 554) and swine (<i>n</i> = 623) ETEC collected in the United States over a 53-year period. We identified distinct ETEC genotypes (<i>fimH</i> type, O antigen, H antigen, sequence type) in cattle and pigs. Furthermore, specific AMR and virulence profiles were associated with bovine and swine ETEC. Compared to swine ETEC, bovine ETEC were less diverse in genotypes and had a significantly (<i>P</i> < 0.001) lower number of AMR genes per isolate but higher co-occurrence of Shiga toxin and enterotoxin genes. Our results provide an overview of the key genomic differences between bovine and swine ETEC in the United States, which might be attributed to host adaptation and antibiotic usage practice. Ongoing surveillance and research are essential to monitor the genetic diversity and AMR patterns of ETEC in different host species.</p><p><strong>Importance: </strong>Enterotoxigenic <i>Escherichia coli</i> (ETEC)-associated diarrhea represent one of the most economically important diseases in the livestock industry. By analyzing over a thousand livestock-derived ETEC samples in the United States, our study unveiled a clear distinction in ETEC's genetic traits (i.e., genotypes, antimicrobial resistance [AMR], and virulence profiles) that might be tied to the different use of antibiotics in cattle and pigs, and the bacteria's adaptation to their specific animal hosts. This understanding is crucial for tailoring preventive and therapeutic strategies. It also highlights the significance of ongoing surveillance and research into the evolution of bacterial pathogens like ETEC in livestock by using advanced techniques such as whole-genome sequencing.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11337801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854572","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}