Microbiological research最新文献

{"title":"More than chromosome organizers: Unique mycobacterial nucleoid-associated proteins","authors":"Kornel Milcarz,&nbsp;Joanna Hołówka,&nbsp;Agnieszka Strzałka,&nbsp;Jolanta Zakrzewska-Czerwińska","doi":"10.1016/j.micres.2025.128239","DOIUrl":"10.1016/j.micres.2025.128239","url":null,"abstract":"<div><div>Nucleoid-associated proteins (NAPs) play a fundamental role in organizing chromosomal architecture and regulating gene expression in <em>Mycobacterium</em>, enabling these bacteria to adapt to diverse environments. In <em>Mycobacterium tuberculosis</em> (Mtb), NAPs contribute to virulence, antibiotic resistance, and persistence within the host, whereas in <em>Mycobacterium smegmatis</em> (Ms), they influence growth dynamics and stress responses. Recent findings indicate that, beyond their role in DNA compaction and replication, mycobacterial NAPs exert broad regulatory effects on gene expression, highlighting their significance in cellular physiology. Differences in NAP composition between saprophytic and pathogenic <em>Mycobacterium</em> species underscore their distinct evolutionary adaptations and survival strategies. Given their central role in bacterial homeostasis and stress adaptation, NAPs have emerged as potential targets for novel antimycobacterial therapies, particularly against drug-resistant Mtb. This review explores the structural and functional diversity of mycobacterial NAPs, emphasizing their roles in chromosomal organization, transcriptional regulation, and stress adaptation, with a focus on their implications for mycobacterial pathophysiology.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128239"},"PeriodicalIF":6.1,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144166727","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":"Pathogen-activated Chaetomium globosum G3 enhances iron competition and other antagonistic mechanisms to suppress maize seedling blight causal agent Fusarium verticillioides","authors":"Chunlin Ren ,&nbsp;Shiying Li ,&nbsp;Peipei Li ,&nbsp;Yi Wang ,&nbsp;Hongxia Yuan ,&nbsp;Qingyun Zhao ,&nbsp;Hui Li ,&nbsp;Fang Li ,&nbsp;Yanlai Han","doi":"10.1016/j.micres.2025.128237","DOIUrl":"10.1016/j.micres.2025.128237","url":null,"abstract":"<div><div><em>Fusarium verticillioides</em> (<em>F. verticillioides</em>) is a prevalent soilborne fungal pathogen that seriously threatens the production of maize (<em>Zea mays</em>). Species within the <em>Chaetomium</em> genus are recognized as potential biocontrol agents for managing plant pathogens. However, the biocontrol efficacy and underlying inhibitory mechanisms of <em>Chaetomium</em> species against maize seedling blight caused by <em>F. verticillioides</em> have yet to be comprehensively evaluated and fully elucidated. This study demonstrates that <em>Chaetomium globosum</em> (<em>C. globosum</em>) G3 reduced the disease index of <em>F. verticillioides</em> on maize seedlings from 81.5 % to 37.6 % and inhibited the growth of <em>F. verticillioides</em> by 79 %. Dual transcriptomic and metabolomic analysis revealed that when co-cultured with <em>F. verticillioides, C. globosum</em> G3 upregulated the iron binding pathway and enhanced the secretion of siderophore ferrioxamine. An iron supplementation experiment further indicated that <em>C. globosum</em> G3 inhibits <em>F. verticillioides</em> through more effective competition for iron. Additionally, over 60 % of the carbohydrate-active enzymes and peptidases gene expressions in <em>C. globosum</em> G3 were induced in response to <em>F. verticillioides</em>, resulting in increased activities of cellulase, chitinase, and protease, as well as the production of antibacterial compounds. Furthermore, <em>F. verticillioides</em> downregulated genes associated with the fumonisin biosynthetic pathway, resulting in reduced fumonisin production. These findings suggest that <em>C. globosum</em> holds potential as a biocontrol agent against the maize seedlings blight pathogen <em>F. verticillioides</em> and highlight that pathogen-activated <em>C. globosum</em> G3 enhances iron competition and other antagonistic mechanisms, contributing to the suppression of <em>F. verticillioides</em>.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128237"},"PeriodicalIF":6.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144166550","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":"Bacteriophage therapy for critical antibiotic-resistant Gram-positive bacteria: A systematic review of clinical researches","authors":"Xinyu Nie ,&nbsp;Yigang Tong ,&nbsp;Mengzhe Li ,&nbsp;Zhenbo Ning ,&nbsp;Huahao Fan","doi":"10.1016/j.micres.2025.128231","DOIUrl":"10.1016/j.micres.2025.128231","url":null,"abstract":"<div><div>The emergence of antibiotic-resistant bacteria compromises medical interventions and poses a significant threat to global public health systems. Bacteriophage (phage) therapy offers a promising, natural, safe, and effective antimicrobial alternative, particularly advantageous for combating Gram-positive bacteria with increasing resistance. This systematic review synthesizes clinical cases published in recent 15 years, evaluating the safety and efficacy of phage therapy in treating Gram-positive bacterial infections. It details the mechanisms of action and applications of phages in treating Gram-positive bacterial infections, critically assessing phage cocktail, phage-assisted regimens, and phage-derived agents. The review further studies phage’s interaction with human host, commensal microbiota, and immune system. Through the rigorous analysis, it identifies phage therapy’s potential implementation obstacles, and provides valuable perspectives for future research and clinical treatment.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128231"},"PeriodicalIF":6.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144138752","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":"Corrigendum to \"Understanding the ternary interaction of crop plants, fungal pathogens, and rhizobacteria in response to global warming\" [Microbial. Res. 296 (2025) 128113].","authors":"Fayun Feng, Fei Du, Qiuling Li, Leigang Zhang, Xiangyang Yu, Changhong Liu","doi":"10.1016/j.micres.2025.128233","DOIUrl":"https://doi.org/10.1016/j.micres.2025.128233","url":null,"abstract":"","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":" ","pages":"128233"},"PeriodicalIF":6.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132627","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":"Synergistic potential of halophytes and halophilic/halotolerant plant growth-promoting bacteria in saline soil remediation: Adaptive mechanisms, challenges, and sustainable solutions","authors":"Huifang Jiang ,&nbsp;Charles Obinwanne Okoye ,&nbsp;Bonaventure Chidi Ezenwanne ,&nbsp;Yanfang Wu ,&nbsp;Jianxiong Jiang","doi":"10.1016/j.micres.2025.128227","DOIUrl":"10.1016/j.micres.2025.128227","url":null,"abstract":"<div><div>Salinity stress poses significant challenges to agriculture, reducing productivity and limiting arable land by causing ionic and osmotic imbalances in plants, disrupting physiological processes, and leading to soil degradation over time. Halophytes and halophilic/halotolerant (HP/HT) plant growth-promoting bacteria (PGPB) offer sustainable solutions to mitigate saline stress and improve plant growth due to their adaptation to extreme environments through various mechanisms to tolerate high salinity, including ion homeostasis, osmotic balance, and the production of compatible solutes. However, understanding their synergistic interactions and specific salt adaptation strategies remains limited, impeding their application in saline soil remediation. This review examines the salt stress tolerance mechanisms of halophytes and HP/HT PGPB, highlighting their interactions and performance in saline environments. Halophyte and HP/HT PGPB demonstrate diverse mechanisms such as ion homeostasis, osmoprotection, and phytohormone modulation to enhance plant resilience to salt stress. Their synergistic interactions, facilitated by root exudates, chemical signaling, and hormone regulation, are vital for optimizing saline soil remediation and plant growth. The review also outlined challenges in utilizing halophyte-associated HP/HT PGPB for effective plant salt tolerance, discussing potential advancements through multi-omics approaches, genetic engineering, machine learning-assisted bioinformatics, chemometrics, and synthetic biology in sustainable agriculture. These integrated strategies offer valuable insights into salt stress tolerance mechanisms, paving the way for innovative applications of halophyte-HP/HT PGPB synergy in saline soil remediation and enhanced plant resilience, highlighting their role in promoting long-term agricultural sustainability.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128227"},"PeriodicalIF":6.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144154710","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":"Advancements in CRISPR-Cas-based strategies for combating antimicrobial resistance","authors":"Ruiting Zhang,&nbsp;Qi Zhou,&nbsp;Siying Huang,&nbsp;Nan Zhang,&nbsp;Dongchang Sun","doi":"10.1016/j.micres.2025.128232","DOIUrl":"10.1016/j.micres.2025.128232","url":null,"abstract":"<div><div>Multidrug resistance (MDR) in bacteria presents a significant global health threat, driven by the widespread dissemination of antibiotic-resistant genes (ARGs). The CRISPR-Cas system, known for its precision and adaptability, holds promise as a tool to combat antimicrobial resistance (AMR). Although previous studies have explored the use of CRISPR-Cas to target bacterial genomes or plasmids harboring resistance genes, the application of CRISPR-Cas-based antimicrobial therapies is still in its early stages. Challenges such as low efficiency and difficulties in delivering CRISPR to bacterial cells remain. This review provides an overview of the CRISPR-Cas system, highlights recent advancements in CRISPR-Cas-based antimicrobials and delivery strategies for combating AMR. The review also discusses potential challenges for the future development of CRISPR-Cas-based antimicrobials. Addressing these challenges would enable CRISPR therapies to become a practical solution for treating AMR infections in the future.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128232"},"PeriodicalIF":6.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144154861","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":"Complete ammonia-oxidizing bacteria dominate ammonia oxidation rates and N2O emissions after vegetation restoration in subtropical karst forest soils","authors":"Chengyi Lao ,&nbsp;Teng Yu ,&nbsp;Ziwei Wan ,&nbsp;Pengpeng Duan ,&nbsp;Kongcao Xiao ,&nbsp;Dejun Li ,&nbsp;Huifang Xu","doi":"10.1016/j.micres.2025.128236","DOIUrl":"10.1016/j.micres.2025.128236","url":null,"abstract":"<div><div>Complete ammonia-oxidizing bacteria (comammox) are crucial for understanding soil N₂O emission mechanisms. Although comammox abundance and composition have been analyzed in various ecosystems, few studies have determined ammonia oxidation rates and the relative contributions of comammox, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) to N₂O emissions from subtropical karst forest soils, especially after vegetation restoration. To address this gap, we explored the total abundance, community structure, and ammonia oxidation rates of AOA, AOB, and comammox, as well as their relative contributions to N₂O emissions, in cropland (control) and subtropical forest soils in a karst ecosystem. Our findings showed that compared with cropland, the total abundance of comammox exhibited a significant increase (17.65 %) in forest at the RNA level. Moreover, the dominant genera in AOA, AOB, and comammox communities were <em>Nitrososphaera</em>, <em>Nitrosospira</em>, and <em>Nitrospira</em>, respectively, in both cropland and forest soils. Additionally, the ammonia oxidation rates of comammox increased by almost 4.4 times after vegetation restoration, which attributed to the high ammonia affinity in the low ammonia nitrogen (NH₄⁺-N) environment. The relative contribution of comammox to N₂O emissions was significantly higher in forest (40.87 %) than in cropland (11.25 %), which was attributed to soil texture differences. In conclusion, after vegetation restoration, low NH₄⁺-N increased comammox ammonia oxidation rates due to the high ammonia affinity, and coarse-textured soils stimulated more N₂O emission owing to the sluggish convective flow of slurry and limiting the redistribution of NH₄⁺. Our study highlights the important role of comammox in regulating ammonia oxidation in subtropical forest soils, which has important implications for improving soil nitrogen (N) cycling and ecosystem restoration in karst regions.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128236"},"PeriodicalIF":6.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144154709","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":"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}