Microbiological research最新文献

{"title":"Rho2 regulates granulocyte-triggered stress adaptation and cell wall remodeling in Aspergillus fumigatus","authors":"Dominik Ruf ,&nbsp;Kristina Striegler ,&nbsp;Sean Brazil ,&nbsp;Hesham Elsaman ,&nbsp;Kalpana Singh ,&nbsp;Mathieu Lepas ,&nbsp;Liyanage D. Fernando ,&nbsp;Victor Brantl ,&nbsp;Patricia Heß ,&nbsp;Karl Dichtl ,&nbsp;Vishukumar Aimanianda ,&nbsp;Tuo Wang ,&nbsp;Johannes Wagener","doi":"10.1016/j.micres.2025.128238","DOIUrl":"10.1016/j.micres.2025.128238","url":null,"abstract":"<div><div>The airborne opportunistic fungal pathogen <em>Aspergillus fumigatus</em> poses a deadly threat to immunocompromised patients. Neutrophil granulocytes play a key role in the defense against invasive infections caused by this pathogen. The mechanisms by which <em>Aspergillus</em> defends itself against attacks by the immune system are only partially understood. Here we show that human granulocytes activate the cell wall integrity (CWI) pathway of <em>A. fumigatus</em> and that key components of the CWI such as the cell wall stress sensor MidA and the Rho GTPases Rho2 and Rho4 are important for the survival of <em>Aspergillus</em> hyphae under granulocyte attacks. A more detailed investigation of the role of Rho2 revealed that a mutant lacking <em>rho2</em> is less virulent in a <em>Galleria mellonella</em> infection model. Overexpression of Rho2 increases the resistance of <em>A. fumigatus</em> hyphae to killing by granulocytes. While a mutant lacking Rho2 has a normal cell wall composition, overexpression or constitutive activation of Rho2 leads to an altered cell wall composition and impairs growths of the pathogen. The fungicidal effect of constitutive activation of Rho2 signaling, which correlates with the formation of cell wall chitin bulges, depends on the CWI MAP kinase MpkA. However, Rho2 itself does not appear to be a direct activator of the CWI MAP kinase module. Our results support a model where Rho2 in <em>A. fumigatus</em> actively counteracts granulocyte attacks by upregulating cell wall biosynthesis, thereby strengthening the cell wall and aiding the fungus in surviving the stress condition.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"299 ","pages":"Article 128238"},"PeriodicalIF":6.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144212422","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 ,&nbsp;Fei Du ,&nbsp;Qiuling Li ,&nbsp;Leigang Zhang ,&nbsp;Xiangyang Yu ,&nbsp;Changhong Liu","doi":"10.1016/j.micres.2025.128233","DOIUrl":"10.1016/j.micres.2025.128233","url":null,"abstract":"","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 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":"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":"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":"Targeting HIV-1 immune escape mechanisms: Key advances and challenges in HIV-1 vaccine design","authors":"Zhongyue Fang ,&nbsp;Wenling Jiang ,&nbsp;Pei Liu ,&nbsp;Ningshao Xia ,&nbsp;Shaowei Li ,&nbsp;Ying Gu","doi":"10.1016/j.micres.2025.128229","DOIUrl":"10.1016/j.micres.2025.128229","url":null,"abstract":"<div><div>Despite numerous efforts, a successful vaccine against HIV-1 remains elusive. An effective vaccine must overcome the virus’s sophisticated immune evasion strategies and induce the production of broadly neutralizing antibodies to counteract HIV-1’s rapid mutation, replication, and transmission within and between hosts. HIV-1 predominantly evades immune recognition and clearance through mechanisms such as genomic mutations, alterations in envelope protein affinity, the formation of latent viral reservoirs, and interference with major histocompatibility complex class I antigen presentation. Although considerable efforts have focused on generating potent HIV-1 vaccines that elicit bnAbs, the probability of achieving such antibodies remains exceedingly low given the virus’s immune-evasive tactics. This review discusses the principal mechanisms of HIV-1 immune evasion and highlights the latest progress in vaccine research, providing fresh perspectives and insights for the design of effective HIV-1 vaccines.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"299 ","pages":"Article 128229"},"PeriodicalIF":6.1,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144194892","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":"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}