Microbiological research最新文献

{"title":"Berberine ameliorates vascular dysfunction by downregulating TMAO-endoplasmic reticulum stress pathway via gut microbiota in hypertension","authors":"","doi":"10.1016/j.micres.2024.127824","DOIUrl":"10.1016/j.micres.2024.127824","url":null,"abstract":"<div><p>The gut microbial metabolite trimethylamine N-oxide (TMAO) is regarded as a novel risk factor for hypertension. Berberine (BBR) exerts cardiovascular protective effects by regulating the gut microbiota-metabolite production pathway. However, whether and how BBR alleviates TMAO-induced vascular dysfunction in hypertension remains unclear. In the present study, we observed that plasma TMAO and related bacterial abundance were significantly elevated and negatively correlated with vascular function in 86 hypertensive patients compared with 46 normotensive controls. TMAO activated endoplasmic reticulum stress (ERS) signaling pathway to promote endothelial cell dysfunction and apoptosis in vitro. BBR (100, 200 mg · kg⁻¹ ·d⁻¹) for 4 weeks ameliorates TMAO-induced vascular dysfunction and ERS activation in a choline-angiotensin II hypertensive mouse model. We found that plasma TMAO levels in 15 hypertensive patients treated with BBR (0.4 g, tid) were reduced by 8.8 % and 16.7 % at months 1 and 3, respectively, compared with pretreatment baseline. The oral BBR treatment also improved vascular function and lowered blood pressure. Faecal 16 S rDNA showed that BBR altered the gut bacterial composition and reduced the abundance of CutC/D bacteria in hypertensive mice and patients. In vitro bacterial cultures and enzyme reaction systems indicated that BBR inhibited the biosynthesis of TMAO precursor in the gut microbiota by binding to and inhibiting the activity of CutC/D enzyme. Our results indicate that BBR improve vascular dysfunction at least partially by decreasing TMAO via regulation of the gut microbiota in hypertension.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002258/pdfft?md5=48f3c1de219da59376433e3d27a0e957&pid=1-s2.0-S0944501324002258-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Small RNA-regulated expression of efflux pump affects tigecycline resistance and heteroresistance in clinical isolates of Klebsiella pneumoniae","authors":"","doi":"10.1016/j.micres.2024.127825","DOIUrl":"10.1016/j.micres.2024.127825","url":null,"abstract":"<div><p>Tigecycline and the newly Food and Drug Administration-approved tetracyclines, including eravacycline and omadacycline, are regarded as last-resort treatments for multidrug-resistant Enterobacterales<em>.</em> However, tigecycline resistance in <em>Klebsiella pneumoniae</em> has increased, especially the underlying mechanism of heteroresistance is unclear. This study aimed to elucidate the mechanisms underlying tigecycline resistance and heteroresistance in clinical <em>K. pneumoniae</em> isolates. A total of 153 clinical <em>K. pneumoniae</em> isolates were collected, and identified 15 tigecycline-resistant and three tigecycline-heteroresistant isolates using broth microdilution and population analysis profile methods, respectively. Total RNAs from <em>K. pneumoniae</em> ATCC13883 and the laboratory-induced tigecycline-resistant strain were extracted and sequenced on an Illumina platform. Differentially expressed genes and regulatory small RNAs (sRNAs) were analyzed and validated in clinical isolates of <em>K. pneumoniae</em> using quantitative real-time PCR. RNA sequencing results showed that <em>mdtABC</em> efflux pump genes were significantly upregulated in the tigecycline-resistant strains. Overexpression of <em>mdtABC</em> was observed in a clinical <em>K. pneumoniae</em> isolate, which increased tigecycline minimum inhibitory concentrations (MICs) and was involved in tigecycline heteroresistance. Sequencing analysis of sRNA demonstrated that candidate sRNA-120 directly interacted with the <em>mdtABC</em> operon and was downregulated in tigecycline-resistant strains. We generated an sRNA-120 deletion mutation strain and a complemented strain of <em>K. pneumoniae.</em> The sRNA-120 deletion strain displayed increased mRNA levels of <em>mdtA, mdtB,</em> and <em>mdtC</em> and an increase in MICs of tigecycline. The complemented strain of sRNA-120 restored the mRNA levels of these genes and the susceptibility to tigecycline. RNA antisense purification and parallel reaction monitoring mass spectrometry were performed to verify the interactions between sRNA-120 and <em>mdtABC</em>. Collectively, our study highlights that the post-transcriptional repression of <em>mdtABC</em> through sRNA-120 may provide an additional layer of efflux pump gene expression control, which is important for resistance and heteroresistance in clinical <em>K. pneumoniae</em> isolates.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759743","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":"Sphingomonas sp. Hbc-6 alters Arabidopsis metabolites to improve plant growth and drought resistance by manipulating the microbiome","authors":"","doi":"10.1016/j.micres.2024.127852","DOIUrl":"10.1016/j.micres.2024.127852","url":null,"abstract":"<div><p>Drought significantly affects crop productivity and poses a considerable threat to agricultural ecosystems. Plant growth-promoting bacteria (PGPB) and plant microbiome play important roles in improving drought resistance and plant performance. However, the response of the rhizosphere microbiota to PGPB during the development of plants and the interaction between inoculum, microbiota, and plants under drought stress remain to be explored. In the present study, we used culturomic, microbiomic, and metabonomic analyses to uncover the mechanisms by which <em>Sphingomonas</em> sp. Hbc-6, a PGPB, promotes <em>Arabidopsis</em> growth and enhances drought resistance. We found that the rhizosphere microbiome assembly was interactively influenced by developmental stage, Hbc-6, and drought; the bacterial composition exhibited three patterns of shifts with developmental stage: resilience, increase, and decrease. Drought diminished microbial diversity and richness, whereas Hbc-6 increased microbial diversity and helped plants recruit specific beneficial bacterial taxa at each developmental stage, particularly during the bolting stage. Some microorganisms enriched by Hbc-6 had the potential to promote carbon and nitrogen cycling processes, and 86.79 % of the isolated strains exhibited PGP characteristics (for example <em>Pseudomonas</em> sp. TA9). They jointly regulated plant physiological metabolism (i.e., upregulated drought resistant-facilitating substances and reduced harmful substances), thereby stimulating the growth of <em>Arabidopsis</em> and increasing plant biomass under drought stress conditions. Collectively, these results indicate that Hbc-6 mediates plant growth and drought resistance by affecting the microbiome. The study thus provides novel insights and strain resources for drought-resistant, high-yielding crop cultivation and breeding.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141853184","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":"Exploring the journey: A comprehensive review of vaccine development against Klebsiella pneumoniae","authors":"","doi":"10.1016/j.micres.2024.127837","DOIUrl":"10.1016/j.micres.2024.127837","url":null,"abstract":"<div><p><em>Klebsiella pneumoniae</em>, a prominent nosocomial pathogen, poses a critical global health threat due to its multidrug-resistant (MDR) and hypervirulent strains. This comprehensive review focuses into the complex approaches undertaken in the development of vaccines against <em>K. pneumoniae</em>. Traditional methods, such as whole-cell and ribosomal-based vaccines, are compared with modern strategies, including DNA and mRNA vaccines, and extracellular vesicles (EVs), among others. Each method presents unique advantages and challenges, emphasising the complexity of developing an effective vaccine against this pathogen. Significant advancements in computational tools and artificial intelligence (AI) have revolutionised antigen identification and vaccine design, enhancing the precision and efficiency of developing multiepitope-based vaccines. The review also highlights the potential of glycomics and immunoinformatics in identifying key antigenic components and elucidating immune evasion mechanisms employed by <em>K. pneumoniae</em>. Despite progress, challenges remain in ensuring the safety, efficacy, and manufacturability of these vaccines. Notably, EVs demonstrate promise due to their intrinsic adjuvant properties and ability to elicit robust immune responses, although concerns regarding inflammation and antigen variability persist. This review provides a critical overview of the current landscape of <em>K. pneumoniae</em> vaccine development, stressing the need for continued innovation and interdisciplinary collaboration to address this pressing public health issue. The integration of advanced computational methods and AI holds the potential to accelerate the development of effective immunotherapies, paving the way for novel vaccines against MDR <em>K. pneumoniae</em>.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141766710","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":"Antibiotic adjuvants against multidrug-resistant Gram-negative bacteria: important component of future antimicrobial therapy","authors":"","doi":"10.1016/j.micres.2024.127842","DOIUrl":"10.1016/j.micres.2024.127842","url":null,"abstract":"<div><p>The swift emergence and propagation of multidrug-resistant (MDR) bacterial pathogens constitute a tremendous global health crisis. Among these pathogens, the challenge of antibiotic resistance in Gram-negative bacteria is particularly pressing due to their distinctive structure, such as highly impermeable outer membrane, overexpressed efflux pumps, and mutations. Several strategies have been documented to combat MDR Gram-negative bacteria, including the structural modification of existing antibiotics, the development of antimicrobial adjuvants, and research on novel targets that MDR bacteria are sensitive to. Drugs functioning as adjuvants to mitigate resistance to existing antibiotics may play a pivotal role in future antibacterial therapy strategies. In this review, we provide a brief overview of potential antibacterial adjuvants against Gram-negative bacteria and their mechanisms of action, and discuss the application prospects and potential for bacterial resistance to these adjuvants, along with strategies to reduce this risk.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141729230","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":"Transcription factor AbrB regulates ROS generation and clearance in Bacillus licheniformis","authors":"","doi":"10.1016/j.micres.2024.127843","DOIUrl":"10.1016/j.micres.2024.127843","url":null,"abstract":"<div><p>Oxidative damage caused by the accumulation of reactive oxygen species (ROS) is one of the main obstacles to the improvement of microbial cell growth and fermentation characteristics under adverse environments. And the antioxidant capacity of cells will increase with the cell growth. Here, we found that a transition state transcription factor AbrB related to changes in cell growth status could regulate the accumulation of ROS and antioxidant capacity in <em>Bacillus licheniformis</em>. The results showed that the accumulation of intracellular ROS was reduced by 23.91 % and the cell survival rates were increased by 1.77-fold under 0.5 mM H₂O₂ when AbrB was knocked out. We further mapped regulatory target genes of AbrB related to ROS generation or clearance based on our previously analyzed transcriptome sequencing. It proved that AbrB could promote ROS generation via upregulating the synthesis of oxidase and siderophores, and negatively regulating the synthesis of iron chelators (pulcherriminic acid, and H₂S). Additionally, AbrB could inhibit ROS clearance by negatively regulating the synthesis of antioxidase (superoxide dismutase, catalase, peroxidase, thioredoxin, thioredoxin reductase) and cysteine. Those results illustrated that the inactivation of AbrB during the stationary phase, along with its control over ROS generation and clearance, might represent a vital self-protection mechanism during cell evolution. Overall, the systematic investigation of the multi-pathway regulation network of ROS generation and clearance highlights the important function of AbrB in maintaining intracellular redox balance.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141636528","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":"A comprehensive review on biological funnel mechanism in lignin valorization: Pathways and enzyme dynamics","authors":"","doi":"10.1016/j.micres.2024.127835","DOIUrl":"10.1016/j.micres.2024.127835","url":null,"abstract":"<div><p>Lignin, a significant byproduct of the paper and pulp industry, is attracting interest due to its potential utilization in biomaterial-based sectors and biofuel production. Investigating biological methods for converting lignin into valuable products is crucial for effective utilization and has recently gained growing attention. Several microorganisms effectively decomposed low molecular weight lignins, transforming them into intermediate compounds via upper and lower metabolic pathways. This review focuses on assessing bacterial metabolic pathways involved in the breakdown of lignin into aromatic compounds and their subsequent utilization by different bacteria through various metabolic pathways. Understanding these pathways is essential for developing efficient synthetic metabolic systems to valorize lignin and obtain valuable industrial aromatic chemicals. The concept of \"biological funneling,\" which involves examining key enzymes, their interactions, and the complex metabolic pathways associated with lignin conversion, is crucial in lignin valorization. By manipulating lignin metabolic pathways and utilizing biological routes, many aromatic compounds can be synthesized within cellular factories. Although there is insufficient evidence regarding the complete metabolism of polyaromatic hydrocarbons by particular microorganisms, understanding lignin-degrading enzymes, regulatory mechanisms, and interactions among various enzyme systems is essential for optimizing lignin valorization. This review highlights recent advancements in lignin valorization, bio-funneling, multi-omics, and analytical characterization approaches for aromatic utilization. It provides up-to-date information and insights into the latest research findings and technological innovations. The review offers valuable insights into the future potential of biological routes for lignin valorization.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141729229","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 “Dynamic patterns of carbohydrate metabolism genes in bacterioplankton during marine algal blooms” [Microbiol. Res. 286 (2024) 127785]","authors":"","doi":"10.1016/j.micres.2024.127820","DOIUrl":"10.1016/j.micres.2024.127820","url":null,"abstract":"","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002210/pdfft?md5=d427fd969919091ae9ce943eaa295bf3&pid=1-s2.0-S0944501324002210-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141723899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biocontrol efficacy of Pseudomonas mediterranea PVCT 3C against Plenodomus tracheiphilus: In vitro and in planta mechanisms at early disease stages","authors":"","doi":"10.1016/j.micres.2024.127833","DOIUrl":"10.1016/j.micres.2024.127833","url":null,"abstract":"<div><p>In this study, we investigated the biocontrol activity of the <em>P. mediterranea</em> strain PVCT 3C against Mal secco, a severe disease of citrus caused by the vascular fungus <em>Plenodomus tracheiphilus</em>. <em>In vitro</em>, bacterial diffusible compounds, volatile organic compounds and culture filtrates produced by PVCT 3C reduced the mycelial growth and conidial germination of <em>P. tracheiphilus</em>, also affecting the mycelial pigmentation. The application of bacterial suspensions by leaf-spraying before the inoculation with the pathogen on plants of the highly susceptible species sour orange and lemon led to an overall reduction in incidence and disease index, above all during the early disease stage. PVCT 3C genome was subjected to whole-genome shotgun sequencing to study the molecular mechanisms of action of this strain. <em>In silico</em> annotation of biosynthetic gene clusters for secondary metabolites revealed the presence of numerous clusters encoding antimicrobial compounds (e.g. cyclic lipopeptides, hydrogen cyanide, siderophores) and candidate novel products. During the asymptomatic disease phase (seven days post-inoculation), bacterial treatments interfered with the expression of different fungal genes, as assessed with an NGS and <em>de novo</em> assembly RNA-seq approach. These results suggest that <em>P. mediterranea</em> PVCT 3C or its secondary metabolites may offer a potential effective and sustainable alternative to contain <em>P. tracheiphilus</em> infections via integrated management.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002349/pdfft?md5=883961c8db78c727a8cd517ff1cace51&pid=1-s2.0-S0944501324002349-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141693533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Technological modes and processes to enhance the Rhodosporidium toruloides based lipid accumulation","authors":"","doi":"10.1016/j.micres.2024.127840","DOIUrl":"10.1016/j.micres.2024.127840","url":null,"abstract":"<div><p><em>Rhodosporidium toruloides</em> has emerged as an excellent option for microbial lipid production due to its ability to accumulate up to 70 % of lipids per cell dry weight, consume multiple substrates such as glucose and xylose, and tolerate toxic compounds. Despite the potential of <em>Rhodosporidium toruloides</em> for high lipid yields, achieving these remains is a significant hurdle. A comprehensive review is essential to thoroughly evaluate the advancements in processes and technologies to enhance lipid production in <em>R. toruloides.</em> The review covers various strategies for enhancing lipid production like co-culture, adaptive evolution, carbon flux analysis, as well as different modes of fermentation. This review will help researchers to better understand the recent developments in technologies for sustainable and scalable lipid production from <em>R. toruloides</em> and simultaneously emphasize the need for developing an efficient and sustainable bioprocess.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002416/pdfft?md5=46a09d68896ba94b7ff01503b5067334&pid=1-s2.0-S0944501324002416-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141729228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}