Microbiological research最新文献

{"title":"An auto-excision system for rapid and efficient genetic manipulation in Glaesserella parasuis","authors":"Jing Xiao ,&nbsp;Yuxin Wang ,&nbsp;Xiaojuan Xu ,&nbsp;Hongbo Zhou","doi":"10.1016/j.micres.2025.128235","DOIUrl":"10.1016/j.micres.2025.128235","url":null,"abstract":"<div><div>Site-specific recombination systems are widely used in bacterial gene editing due to their precision and efficiency. However, traditional gene editing methods often require labor-intensive plasmid construction and multiple transformation steps, which can be time-consuming and inefficient. In this study, we developed an Auto-Excision (AE) system that overcomes these limitations by optimizing the entire process—from the preparation of targeting sequences to the screening of marker-free mutants. The AE system simplifies the knockout process by eliminating the need to construct targeting plasmids for each target gene, requiring only a single transformation, and allowing for the direct selection of markerless mutants in the presence of antibiotics. We validated the AE system's ability to enable rapid and efficient gene knockout in <em>Glaesserella parasuis</em> (<em>G. parasuis</em>), demonstrating its potential as a rapid and labor-efficient gene manipulation tool. This method reduces the overall timeline to as little as one day, with a hands-on time of less than one hour, while achieving a knockout efficiency greater than 90 %. Additionally, the system successfully performed multi-gene knockouts, targeting five genes in succession. This approach offers substantial time and labor savings, with the entire process achievable within a single bacterial colony growth cycle. This positions the AE system as a rapid bacterial genetic manipulation method currently known, with broad potential applications across diverse bacterial species.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128235"},"PeriodicalIF":6.1,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144124395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phage therapy: A novel approach to combat drug-resistant pathogens","authors":"Mengru Yao ,&nbsp;Yuan Zhu ,&nbsp;Jin-ao Duan,&nbsp;Ping Xiao","doi":"10.1016/j.micres.2025.128228","DOIUrl":"10.1016/j.micres.2025.128228","url":null,"abstract":"<div><div>Antibiotic-resistant infections, such as those caused by the overuse of antibiotics, have greatly strained healthcare systems. Among them, drug-resistant bacteria ESKAPE (<em>Enterococcus faecium</em>, <em>Staphylococcus aureus</em>, <em>Klebsiella pneumoniae</em>, <em>Acinetobacter baumannii</em>, <em>Pseudomonas aeruginosa</em>, and <em>Enterobacter</em> species) are typical and common. <em>Enterococcus faecalis</em> and <em>Escherichia coli</em> are of equal concern. These pathogens often have higher pathogenicity than the same strains, and resistance has reduced treatment options, so new treatment options are needed to address these pathogens. This review analyzes recent studies related to phage therapy for the treatment of bacterial infections in various parts of the human body (e.g., alcoholic liver disease, skin, and soft tissues, respiratory tract, gastrointestinal tract, urinary system, etc.), to better understand the potential role of phage therapy as a non-antibiotic strategy for the treatment of infections caused by drug-resistant bacteria. In addition, this review introduces a series of products related to phage therapy and points out potential research directions for phage therapy in clinical applications. This paper elucidates the basic mechanism of human infection by some drug-resistant bacteria and the therapeutic effect of phage therapy against drug-resistant bacteria. It popularizes the understanding of phage therapy and provides a reference for research on its use for drug-resistant bacterial infections.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128228"},"PeriodicalIF":6.1,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144124396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bridging phage production models and practical applications to control antibiotic-resistant bacteria","authors":"Xiaoyu Wang ,&nbsp;Song Zhang ,&nbsp;Juhee Ahn","doi":"10.1016/j.micres.2025.128230","DOIUrl":"10.1016/j.micres.2025.128230","url":null,"abstract":"<div><div>The emergence of multidrug-resistant (MDR) bacteria represents a significant global health threat, demanding urgent development of alternative treatment strategies. Bacteriophages (phages) have gained attention as promising alternatives to antibiotics due to their specificity, abundance, and minimal side effects, leading to potential applications in food safety, agriculture, aquaculture, and clinical settings. However, the practical use of phage therapy is limited by challenges in efficiently producing phages, due to the complex and dynamic interactions between bacteria and phages. Therefore, this review aims to bridge the gap between theoretical models and practical applications by examining bacteria-phage interactions, focusing on the coevolution of bacteria and phages, their resistance mechanisms, and the environmental factors that influence these interactions. Differential and stochastic mathematical models were used to analyze essential kinetic parameters in phage production and to assess strategies for optimizing phage production and their application in controlling antibiotic-resistant infections. Additionally, mathematical modeling in phage-bacteria dynamics was provided, highlighting new kinetic models that incorporated the evolutionary trade-offs between antibiotic resistance and phage resistance. These models provide valuable insights into the factors that influence bacteria-phage interactions and assist in designing effective treatment strategies to optimize the clinical use of phages by predicting phage behavior and therapeutic effects. Therefore, mathematical modeling serves as an invaluable tool in advancing phage therapy. Further study is needed to increase phage production and improve therapy consistency for establishing phage therapy as a reliable solution for multidrug-resistant infections.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128230"},"PeriodicalIF":6.1,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144135131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sources of variability for viability PCR using propidium monoazide","authors":"Kraiwut Jansriphibul ,&nbsp;Christian Krohn ,&nbsp;Andrew S. Ball","doi":"10.1016/j.micres.2025.128224","DOIUrl":"10.1016/j.micres.2025.128224","url":null,"abstract":"<div><div>The molecular detection of microorganisms in environmental samples relies on PCR-associated molecular workflows that typically cannot differentiate live from dead microbes. Understanding the microbial functions of complex communities can be significantly hindered by presence of the dead microbes. Using propidium monoazide (PMA), PMA-based viability PCR, is arguably the most convenient method to differentiate viability status apart. Errors from variabilities of non-standardized practices and a lack of understanding of the PMA mechanism deter the viability PCR approach. This review discusses the sources of variability in each of four key sequential steps: pre-analysis, PMA activation, DNA extraction and PCR. An analysis of previous literature on optimization of PMA-based viability PCR indicates that often only one source of variability is considered. However, all steps are interrelated and should be considered together when understanding and mitigating unwanted variability, especially in the PMA activation and PCR steps. Research gaps in PMA are addressed, such as the chemical mechanisms of PMA and possible by-products interferences, internal standard spiking and recommendations for future research.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128224"},"PeriodicalIF":6.1,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144166728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Brassica microgreens shape gut microbiota and functional metabolite profiles in a species-related manner: A multi-omics approach following in vitro gastrointestinal digestion and large intestine fermentation","authors":"Pascual García-Pérez ,&nbsp;Merve Tomas ,&nbsp;Gianluca Giuberti ,&nbsp;Esra Capanoglu ,&nbsp;Maria Luisa Callegari ,&nbsp;Luigi Lucini ,&nbsp;Vania Patrone","doi":"10.1016/j.micres.2025.128226","DOIUrl":"10.1016/j.micres.2025.128226","url":null,"abstract":"<div><div>Brassicaceae microgreens constitute a novel and promising source of bioactive compounds, such as polyphenols and glucosinolates. In this work, an integrative computational approach was performed to decipher the interaction between bioaccessible microgreen metabolites and human gut bacteria. To this end, in vitro gastrointestinal digestion and large intestine fermentation were performed on eight different microgreens, which were further subjected to a dual high-throughput approach that combined fecal metagenomics and untargeted metabolomics. Data reveal a significant correlation between <em>Parabacteroides merdae</em> and two isothiocyanates in arugula fermentates, suggesting a high bioaccessibility of these bioactive compounds. Meanwhile, two species of <em>Roseburia</em> were correlated with pseudooxynicotine, an anti-inflammatory catabolite of nicotine in <em>Brassica oleracea</em> fermentates (such as broccoli, Brussels sprouts, and red cabbage), coupled with an increase in short-chain fatty acid production. These findings confer evidence on the nutritional impact of microgreens consumption, revealing the most bioaccessible metabolites with associated health-promoting properties together with their participation in the shaping of gut microbial populations, possibly leading to prebiotic effects.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128226"},"PeriodicalIF":6.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144138753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacillus amyloliquefaciens application alleviated the stimulation of organic fertilizer on soil denitrification rate in acidic soils","authors":"Lin Luo ,&nbsp;Nannan Zhang ,&nbsp;Entao Wang ,&nbsp;Chunzhang Zhao ,&nbsp;Qinghua Liu ,&nbsp;Xueyong Pang ,&nbsp;Chunying Yin","doi":"10.1016/j.micres.2025.128216","DOIUrl":"10.1016/j.micres.2025.128216","url":null,"abstract":"<div><div>Denitrification is important in regulating soil nitrogen (N) availability and greenhouse gas emissions. Whereas, how different fertilization strategies affect soil denitrification rate and denitrifying microbial community remains contradictory. Here, four fertilization strategies including no fertilizer (F0), biostimulant: <em>Bacillus amyloliquefaciens</em> (BA), organic fertilizer (OF), and both of them together (BAOF) application were conducted in a pot experiment to study the changes in denitrification process and its regulation factors in acidic soils. Compared with F0, treatment with BA, OF, and BAOF significantly increased denitrification rate by 400 %, 619 %, and 331 %, respectively; increased nitrate concentration and <em>nirS</em> abundance, while decreased <em>nosZ</em> abundance. Soil nitrite reductase activity and <em>nirK</em> abundance were significantly increased by OF and BAOF treatments. BA and OF treatments significantly decreased <em>nirS</em> Chao1 index. The composition of <em>nirS</em> denitrifying community, but not <em>nirK</em>, was significantly altered by all treatments; it was mainly affect by soil pH, total N, and nitrate. The increase in soil nitrate concentration, nitrite reductase activity, and <em>nirK</em> abundance, as well as the reduction in <em>nirS</em> α diversity and <em>nosZ</em> abundance, jointly lead to a higher denitrification rate in fertilization treatments. The denitrifying genes explained more denitrification rate variation than soil environmental properties. These results revealed that the stimulation effect of OF on denitrification was alleviated by BA application, and <em>nirS</em> microbial composition was more sensitive to fertilization than <em>nirK</em>. Therefore, our study suggests that in future organic agricultural practices, the combination of organic fertilizer with <em>B. amyloliquefaciens</em> can reduce N losses caused by the soil denitrification process in acidic soils.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128216"},"PeriodicalIF":6.1,"publicationDate":"2025-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144135132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gut microbiota in epilepsy: How antibiotics induce dysbiosis and influence seizure susceptibility","authors":"Shangnan Zou ,&nbsp;Xiaofeng Yang ,&nbsp;Liemin Zhou","doi":"10.1016/j.micres.2025.128225","DOIUrl":"10.1016/j.micres.2025.128225","url":null,"abstract":"<div><div>Epilepsy, a widespread chronic neurological disorder, has recently come under scrutiny for its potential association with the intricate dynamics of gut microbiota. Numerous investigations into the microbiota-gut-brain axis have revealed a close relationship between gut microbiota and epilepsy, suggesting gut microbiota as a potential treatment strategy. In clinical practice, a longstanding correlation has been observed between some kinds of antibiotics and the potential to induce seizures. Consequently, we have conceived a hypothesis that antibiotics might impact seizure activity by modulating the gut microbiota and influencing the physiological processes within the microbiota-gut-brain axis. In this review, our primary objective is to present the existing evidence and theoretical foundations supporting the hypothesis that dysbiosis within the gut microbiota may play a significant role in the pathophysiology of epilepsy. Furthermore, we aim to summarize the possible mechanisms between microbiota-gut-brain axis and epilepsy, offering insights into the selection of appropriate antibiotics for long-term epilepsy management and enhancing therapeutic efficacy through modulation of the gut microbiota. Further research is necessary to fully elucidate the intricate relationship between gut microbiota ecosystem and epilepsy. Exploring these connections holds promise for advancing our understanding of epilepsy pathogenesis and improving patient treatment and care.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128225"},"PeriodicalIF":6.1,"publicationDate":"2025-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144090130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The relationship between tryptophan metabolism and gut microbiota: Interaction mechanism and potential effects in infection treatment","authors":"Tongchao Pei ,&nbsp;Wenweiran Li ,&nbsp;Ziyang Zhou ,&nbsp;Qinyu Zhang ,&nbsp;Guohong Yu ,&nbsp;Sokun Yin ,&nbsp;Hui Chen ,&nbsp;Jianguo Tang","doi":"10.1016/j.micres.2025.128211","DOIUrl":"10.1016/j.micres.2025.128211","url":null,"abstract":"<div><div>Human health is influenced by the gut microbiota, particularly in aspects of host immune homeostasis and intestinal immune response. Tryptophan (Trp) not only acts as a nutrient enhancer but also plays a critical role in the balance between host immune tolerance and gut microbiota maintenance. Both endogenous and bacterial metabolites of Trp, exert significant effects on gut microbial composition, microbial metabolism, the host immunity and the host-microbiome interface.</div><div>Trp metabolites regulate host immunity by activating aryl hydrocarbon receptor (AhR), thereby contributing to immune homeostasis. Among Trp metabolites, AhR ligands include endogenous metabolites (such as kynurenine), and bacterial metabolites (such as indole and its derivatives). Here, we present a comprehensive analysis of the relationships between Trp metabolism and 14 key microbiota, encompassing fungi (e.g., <em>Candida albicans</em>, <em>Aspergillus</em>), bacteria (e.g., <em>Ruminococcus gnavus</em>, <em>Bacteroides, Prevotella copri</em>, <em>Clostridium difficile</em>, <em>Escherichia coli</em>, lactobacilli, <em>Mycobacterium tuberculosis</em>, <em>Pseudomonas aeruginosa</em>, <em>Staphylococcus aureus</em>, <em>Helicobacter. Pylori</em>), and viruses (e.g., SARS-CoV-2, influenza virus). This review clarifies how the gut microbiota regulates Trp metabolism and uncovers the underlying mechanisms of these interactions. And increased mechanistic insight into how the microbiota modulate the host immune system through Trp metabolism may allow for the identification of innovative therapies that are specifically designed to target Trp absorption, Trp metabolites, the gut microbiota, or interactions between Trp and gut microbiota to treat both intestinal and extra-intestinal inflammation as well as microbial infections.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128211"},"PeriodicalIF":6.1,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144090446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular mechanism whereby Bacillus nematocida BN16 activates the “Trojan Horse” response against nematodes","authors":"Lin Zhang ,&nbsp;Keyan Chen ,&nbsp;Wei Liu ,&nbsp;Zhuo Tian ,&nbsp;Mingshen Yin ,&nbsp;Baolin Sun ,&nbsp;Qiuhong Niu","doi":"10.1016/j.micres.2025.128212","DOIUrl":"10.1016/j.micres.2025.128212","url":null,"abstract":"<div><div>This study determined the molecular mechanisms by which <em>Bacillus nematocida</em> BN16 responds to nematode predation. The spores generated by BN16 act as a defense against nematodes, employing a “Trojan horse” strategy. The metabolite 6-methyl-2-heptanone triggers the defense response. To mount an effective defense, BN16 employs transcriptional regulators, including SigA, NtdR, and PksA, that modulate the expression of genes such as <em>mtnD</em> and <em>pycA</em> to enhance the synthesis of 2-heptanone. Subsequently, the enzymes YxjG and YdaC convert 2-heptanone to 6-methyl-2-heptanone, stimulating spore formation via Spo0M. Under nematode predation, <em>B. subtilis</em> BS168 activates metabolic pathways associated with environmental adaptation. However, these responses are generally inadequate to prevent the physical damage inflicted by nematode mouthparts. This study has deepened our understanding of species-specific defense strategies within the genus <em>Bacillus</em> and has advanced the development of pesticide-free pest control methods. The results have identified a novel interaction between microbe and their hosts.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128212"},"PeriodicalIF":6.1,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144107087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Faecalibacterium Prausnitzii extracellular vesicles regulating macrophage differentiation via homologous recombination repair in colitis model","authors":"Yinya Pan ,&nbsp;Xinlu Zhao ,&nbsp;Qiongyun Chen ,&nbsp;Tao Zhao ,&nbsp;Yichun Ma ,&nbsp;Hai Wu ,&nbsp;Ying Xiang ,&nbsp;Ping Jiang ,&nbsp;Wenjun Li ,&nbsp;Qiong Yan ,&nbsp;Shangtao Mao ,&nbsp;Yufei Tao ,&nbsp;Lei wang ,&nbsp;Yun Zhu ,&nbsp;Guifang Xu","doi":"10.1016/j.micres.2025.128217","DOIUrl":"10.1016/j.micres.2025.128217","url":null,"abstract":"<div><div>Inflammatory Bowel Disease (IBD) is characterized by chronic inflammation influenced by the depletion of beneficial gut microbiota, a critical factor in disease onset and progression. This study investigates the therapeutic potential of extracellular vesicles (EVs) derived from <em>Faecalibacterium prausnitzii</em> (<em>F.p</em> EVs), a commensal bacterium whose reduction is linked to IBD. Our research demonstrates that <em>F.p</em> EVs are preferentially taken up by macrophages, where they exert their anti-inflammatory effects through the enhancement of homologous recombination (HR) repair mechanisms. Specifically, <em>F.p</em> EVs upregulate the expression of key proteins involved in HR repair, such as BRCA1 and BRCA2, thereby reducing DNA damage and inhibiting the cGAS-STING pathway, which is central to the inflammatory response. This modulation of macrophage function results in decreased pro-inflammatory cytokine production and enhanced intestinal barrier integrity. By elucidating these mechanisms, our study provides a clear understanding of how <em>F.p</em> EVs can be used to target fundamental aspects of IBD pathology, laying the groundwork for the development of more effective and targeted therapies.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128217"},"PeriodicalIF":6.1,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144090445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}