Microbiological research最新文献

{"title":"Influence of environmental and agronomic variables on soil microbiome in citrus orchards: A comparative analysis of organic and conventional farming system","authors":"Sebastiano Conti Taguali ,&nbsp;Rhea Pöter ,&nbsp;Francesco Aloi ,&nbsp;Clara Fernández-Trujillo ,&nbsp;Alberto Acedo ,&nbsp;Federico La Spada ,&nbsp;Maria Giulia Li Destri Nicosia ,&nbsp;Antonella Pane ,&nbsp;Leonardo Schena ,&nbsp;Santa Olga Cacciola","doi":"10.1016/j.micres.2025.128260","DOIUrl":"10.1016/j.micres.2025.128260","url":null,"abstract":"<div><div>Crop health and productivity depend on the structure and functionality of soil microbiota associated with the root system of plants. The agricultural policy of the European Union promotes organic farming systems to ensure environmental sustainability and food safety. The objective of this study was to investigate the impact of organic farming on soil microbiome in citrus orchards. The soil microbiota of eight conventionally and seven organically managed commercial citrus orchards across eastern Sicily was characterised using Illumina sequencing and BeCrop® primers for PCR amplification. The structure (diversity and relative abundance) and functionality of soil bacterial and fungal communities depended primarily on the sampling site. Other variables influencing the soil microbiome included soil total carbon content, seasonality, rootstock genotype, soil tillage and irrigation system. The latter three exerted differential effects on either bacterial or fungal communities. Conversely, age and visible health status of the tree had negligible influence on both communities. The differences between organically and conventionally managed citrus orchards accounted for a significant proportion of the variability, indicating a relevant effect of the farming system on soil microbiome. Organically managed orchards compared to those managed conventionally exhibited higher microbial diversity and a unique composition of nutrient-cycling microbes. In particular, organic farming promoted beneficial microbial functions, such as nitrogen fixation and phosphorus solubilization. Findings provide insights into the dynamic and complex interactions between environmental variables and soil microbial communities in citrus orchards, confirming the potential of microbial diversity as an indicator of sustainability in agricultural systems.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"299 ","pages":"Article 128260"},"PeriodicalIF":6.1,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144314505","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":"Staphylococcal exotoxins in ocular infection with focus on enterotoxins","authors":"Jiawei Shen,&nbsp;Muhammad Yasir,&nbsp;Mark Willcox","doi":"10.1016/j.micres.2025.128258","DOIUrl":"10.1016/j.micres.2025.128258","url":null,"abstract":"<div><div><em>Staphylococcus aureus</em> (<em>S. aureus</em>) is one of principal etiological agents of bacterial keratitis, a blinding corneal infection. Traditional treatment strategies rely heavily on antibiotics. However, the overuse and injudicious use of these agents have significantly contributed to the emergence of multidrug-resistant bacterial strains. Therefore, understanding the role of virulence factors in the disease is important for the design of new therapeutics. This review aims to explore and summarize current research on the role of Staphylococcal toxins, especially enterotoxins (SEs), in ocular infections. The relationship between SEs and ocular infections is reviewed, as are their genomic location and regulatory mechanisms. Current research suggests that SE genes are detected in ocular isolates, with a higher frequency of specific SE genes observed in ocular isolates compared to non-ocular isolates. Additionally, several SE genes have been confirmed to confer cytotoxicity and invasion ability to <em>S. aureus</em> in animal keratitis models. Despite the progress in this area, significant knowledge gaps remain, particularly regarding the specific functions of SEs and the host response pathways. Addressing these questions may contribute to the development of effective preventive and therapeutic measures for eye damage caused by SEs.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"299 ","pages":"Article 128258"},"PeriodicalIF":6.1,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144307907","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 regarding incomplete Conflict of Interest statements in previously published articles.","authors":"","doi":"10.1016/j.micres.2025.128234","DOIUrl":"https://doi.org/10.1016/j.micres.2025.128234","url":null,"abstract":"","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":" ","pages":"128234"},"PeriodicalIF":6.1,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144294074","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 role of the oral microbiota in allergic diseases: Current understandings and future trends","authors":"Ran Zhang ,&nbsp;Jialu Shi ,&nbsp;Yan Xu ,&nbsp;Siyu Yao ,&nbsp;Vijaya Raghavan ,&nbsp;Jin Wang","doi":"10.1016/j.micres.2025.128254","DOIUrl":"10.1016/j.micres.2025.128254","url":null,"abstract":"<div><div>Allergic diseases, including allergic asthma, allergic rhinitis, atopic dermatitis, and food allergy, have become a growing global health concern and impose significant public health burdens. The oral microbiota, integral to the oral ecosystem, has emerged as a crucial factor associated with the pathogenesis and progression of various diseases, including allergic diseases. Studies have revealed significant distinctions in the oral microbial community structure between allergic patients and healthy counterparts, suggesting the potential pivotal role of the oral microbiota in the onset and development of allergic diseases. This review summarized the implications and the underlying mechanisms of the oral microbiota in allergic diseases, providing novel insights and potential therapeutic targets for the prevention and treatment of allergic diseases.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"299 ","pages":"Article 128254"},"PeriodicalIF":6.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144221856","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":"Host-Directed Therapeutic for the treatment of Mycobacterium tuberculosis","authors":"Pratik Mahajan ,&nbsp;Hetarth R. Gor ,&nbsp;Sushama Jadhav ,&nbsp;Manali Joshi ,&nbsp;Vijay Nema","doi":"10.1016/j.micres.2025.128253","DOIUrl":"10.1016/j.micres.2025.128253","url":null,"abstract":"<div><div>This comprehensive review examines the emerging role of Host-Directed Therapies (HDTs) as complementary approaches to conventional Tuberculosis (TB) treatment. The review focuses on diverse HDT mechanisms utilizing their modulators like small molecule, protein-based, lipid-based, vitamin-based, and polysaccharide-based therapeutics. Key mechanisms include autophagy induction through multiple pathways, including mTOR inhibition, calcium signaling modulation, and TFEB activation. Notable compounds such as dimethyl itaconate, tamoxifen, and berbamine demonstrate significant efficacy in enhancing autophagosome formation and bacterial clearance. Matrix metalloproteinase inhibitors like doxycycline show promise in reducing tissue damage and cavity formation. The review highlights the importance of metabolic modulation through compounds like metformin and ezetimibe, which target cellular energy pathways and cholesterol metabolism respectively. Immunomodulatory approaches, including phosphodiesterase inhibition and cytokine regulation, demonstrate potential in optimizing host immune responses. Novel mechanisms such as ferroptosis inhibition and pyroptosis modulation present promising therapeutic avenues. The review also examines the role of established drugs being repurposed for TB treatment, including statins and antidepressants. While preclinical evidence supports the efficacy of various HDTs, the review emphasizes the need for careful consideration of host-pathogen interactions and potential immunological approaches. The complexity of TB pathophysiology necessitates a personalized approach to HDT implementation. Future research directions should focus on clinical validation, optimal dosing strategies, and combination approaches with standard antimicrobial therapy. This review underscores the potential of HDTs to address drug resistance and persistent infections, while highlighting the importance of continued investigation into their safety and efficacy across diverse patient populations.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"299 ","pages":"Article 128253"},"PeriodicalIF":6.1,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144230583","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":"Unraveling the pathogenetic overlap of Helicobacter pylori and metabolic syndrome-related Porphyromonas gingivalis: Gingipains at the crossroads and as common denominator","authors":"Michael Doulberis ,&nbsp;Dimitrios Tsilimpotis ,&nbsp;Stergios A. Polyzos ,&nbsp;Elisabeth Vardaka ,&nbsp;Aryan Salahi-Niri ,&nbsp;Abbas Yadegar ,&nbsp;Jannis Kountouras","doi":"10.1016/j.micres.2025.128255","DOIUrl":"10.1016/j.micres.2025.128255","url":null,"abstract":"<div><div>Chronic bacterial infections exert profound systemic effects beyond their primary infection sites, influencing a range of inflammatory, metabolic, and neurodegenerative diseases. <em>Helicobacter pylori</em> (<em>Hp</em>) and <em>Porphyromonas gingivalis</em> (<em>Pg</em>) are two highly prevalent pathogens that, despite occupying distinct niches, share remarkable pathogenic similarities. Both bacteria, connected with metabolic syndrome<strong>,</strong> employ immune evasion strategies, induce chronic inflammation, and contribute to systemic diseases such as metabolic-associated steatotic liver disease, cardiovascular disease, and neurodegeneration, such as Alzheimer’s disease. A key unifying factor in their pathogenicity is the role of gingipains—cysteine proteases produced by <em>Pg</em>—which facilitate bacterial invasion, immune modulation, and tissue destruction. Emerging evidence suggests that <em>Hp</em> possesses analogous proteolytic enzymes, further supporting their potential synergistic impact on host health. Moreover, both pathogens have been implicated in metabolic syndrome-related blood-brain barrier disruption, chronic (smoldering) systemic inflammation, and lipid metabolism dysregulation, contributing to progressive neurodegenerative and cardiovascular disorders<strong>.</strong> The role of galectins, particularly galectin-3, in modulating microglial activation and inflammatory pathways further highlights their involvement in neuroinflammatory diseases. Targeting gingipains presents a promising therapeutic avenue, with bismuth compounds and novel inhibitors showing potential in disrupting these proteases and mitigating their systemic effects. Understanding the interactions between <em>Hp</em> and metabolic syndrome-related <em>Pg</em> is crucial for developing comprehensive treatment strategies, integrating gastroenterology, periodontology, and neurology. Addressing these infections at both local and systemic levels may improve long-term health outcomes and reduce the burden of chronic inflammatory diseases linked to microbial persistence.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"299 ","pages":"Article 128255"},"PeriodicalIF":6.1,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144212419","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, metabolites, and pulmonary hypertension: Mutual regulation and potential therapies","authors":"Jie Yang ,&nbsp;Jixiang Liu ,&nbsp;Haoyu Gu ,&nbsp;Wanlu Song ,&nbsp;Hong Zhang ,&nbsp;Jing Wang ,&nbsp;Peiran Yang","doi":"10.1016/j.micres.2025.128245","DOIUrl":"10.1016/j.micres.2025.128245","url":null,"abstract":"<div><div>Pulmonary hypertension is a progressive condition characterized by increased pulmonary vascular pressure and resistance, ultimately leading to right heart failure and death. Increasing evidence has underscored the importance of the gut-lung axis in the development of respiratory and cardiovascular diseases. Notably, significant changes in the gut microbiota, including altered microbial composition and function, have been observed in pulmonary hypertension. Specifically, microbiota-derived metabolites, including short chain fatty acids, trimethylamine N-oxide, bile acids and tryptophan, play a significant role in the development of pulmonary hypertension. The identification of key bacteria and metabolites, along with recent advances in gut microbiota-targeting technologies and metabolic pathway-targeting inhibitors/agonists, holds potential for developing diagnostic, prognostic, and therapeutic strategies for pulmonary hypertension. Emerging research directions include metagenomic analysis of viruses and fungi, artificial intelligence-aided prediction models, novel metabolites and their associated enzymes, drug-microbiota interactions, selective antibiotics, and advanced microbiota transplantation. This review synthesizes clinical and experimental evidence linking the gut microbiota to pulmonary hypertension, highlighting their interplay as a promising avenue for further investigation and translational applications.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"299 ","pages":"Article 128245"},"PeriodicalIF":6.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144221855","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":"Role of R5 pyocin in the predominance of high-risk Pseudomonas aeruginosa isolates","authors":"Liyang Zhang ,&nbsp;Qi Xu ,&nbsp;Filemon C. Tan ,&nbsp;Meggie Wang ,&nbsp;Yanhan Deng ,&nbsp;Morgan Hakki ,&nbsp;Samuel A. Shelburne ,&nbsp;Natalia V. Kirienko","doi":"10.1016/j.micres.2025.128244","DOIUrl":"10.1016/j.micres.2025.128244","url":null,"abstract":"<div><div>Infections with antimicrobial-resistant pathogens, such as <em>Pseudomonas aeruginosa,</em> are a frequent occurrence in healthcare settings. Although human <em>P. aeruginosa</em> infections are predominantly caused by a small number of sequence types (ST), such as ST235 and ST111, that are frequently multidrug-resistant, the basis for this dominance remains unclear. Using a genome-wide, transposon-insertion library screen, we discovered that the production of R5 pyocins (one of 5 subtypes of R pyocins) confers a competitive advantage to ST111 strains. Competitive dominance was lost by mutants lacking R pyocin production. Analysis of 5135 <em>P. aeruginosa</em> strains revealed that several international, high-risk sequence types (including ST235 and ST111) are enriched for R5 pyocin production, indicating a correlation between R5 pyocin production and clinical dominance, suggesting a novel approach for evaluating risk from emerging <em>P. aeruginosa</em> strains. An ST235 strain also lost its competitive advantage after deletion of an R5 pyocin structural gene, corroborating these findings. Overall, our study sheds light onto mechanisms underlying predominance of particular clades of antimicrobial resistant bacteria.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"299 ","pages":"Article 128244"},"PeriodicalIF":6.1,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144205678","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":"Kynureninase from Botrytis cinerea regulates the growth, development, pathogenicity, and stress response of B. cinerea through the kynurenine pathway","authors":"Bai Li ,&nbsp;Kang Zhang ,&nbsp;Jialin Wang ,&nbsp;Siqi Zhai ,&nbsp;Hongzhe Cao ,&nbsp;Helong Si ,&nbsp;Jinping Zang ,&nbsp;Jihong Xing ,&nbsp;Jingao Dong","doi":"10.1016/j.micres.2025.128243","DOIUrl":"10.1016/j.micres.2025.128243","url":null,"abstract":"<div><div>The kynurenine pathway was first identified in mammals. It is the main pathway for tryptophan catabolism, participates in many important biological processes, and is a target for the treatment of neurodegenerative diseases. However, this pathway and its function have not been reported in <em>Botrytis cinerea</em>. In this study, the kynurenine pathway-related genes <em>BcIDO</em>, <em>BcKFA</em>, <em>BcHAO</em>, <em>BcKYN</em>, <em>BcKMO,</em> and <em>BcKAT</em> were obtained by bioinformatics analysis. The <em>BcKYNL1</em> and <em>BcKYNL2</em> gene mutants positively regulated the growth and pathogenicity of <em>Botrytis cinerea</em> and the stress response. Analysis of the key metabolites of the kynurenine pathway in the mutants △<em>BcKYNL1</em> and △<em>BcKYNL2</em> revealed that the significantly changed contents of tryptophan metabolism-related products in the mutants. The exogenous addition of quinolinic acid partially restored the pathogenicity of the mutants. These results indicate that <em>BcKYNL1</em> and <em>BcKYNL2</em> regulate pathogenicity by affecting the metabolite content of the kynurenine pathway. In addition, molecular docking and surface ion resonance analyses determined that the kynurenine enzymes BcKYNL1 and BcKYNL2 directly act on kynurenine and 3-hydroxykynurenine of the kynurenine pathway, respectively, and that the branch regulated by BcKYNL2 and BcKMO is the main branch of the kynurenine pathway. These results provide new insights into the mechanism by which the kynurenine pathway regulates the growth and pathogenicity of <em>Botrytis cinerea</em> and the development and application of new targets for the prevention and treatment of <em>B. cinerea</em>.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"299 ","pages":"Article 128243"},"PeriodicalIF":6.1,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144184830","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":"Illuminating prospects of probiotic Akkermansia muciniphila in intestinal inflammation and carcinogenesis","authors":"Kexin Zhang ,&nbsp;Yue Dong ,&nbsp;Yiyun Ding ,&nbsp;Xin Wang,&nbsp;Tianyu Liu,&nbsp;Weilong Zhong,&nbsp;Hailong Cao","doi":"10.1016/j.micres.2025.128240","DOIUrl":"10.1016/j.micres.2025.128240","url":null,"abstract":"<div><div><em>Akkermansia muciniphila</em> (<em>A. muciniphila</em>) is portrayed as an advantageous enteric bacterium with a particular property of mucin utilization. Emerging data suggest <em>A. muciniphila</em> can reshape gut chronic inflammation, enhance intestinal epithelial tight junctions, and sensitize toll-like receptors 2 (TLR2) and TLR4 to restrain the infiltrating cytotoxic T lymphocytes and macrophages. As well, analogous role is detected in surface <em>A. muciniphila</em>-coated pili, outer-membrane protein Amuc_1100, β-galactosidase enzyme Amuc_2172, and extracellular vesicles. We rendered insights into empirical evidence on molecular mechanisms mediated by <em>A. muciniphila</em> in inflammatory bowel disease and intestinal cancers which include colitis-associated colorectal cancer and colorectal cancer. We discussed its potential preventive and therapeutic benefits on immune checkpoint inhibitors therapy. <em>A. muciniphila</em> supplementation through diet, probiotics-prebiotics, fecal microbiota transplantation, and certain drugs, would be a promising therapeutic strategy. Nevertheless, data profiles decipher <em>A. muciniphila</em> is linked to multiple sclerosis and Parkinson's disease occurrence and evolvement. Thus, how to avoid the deleterious effects triggered by <em>A. muciniphila</em> warrants further exploration. It ought to be considered to conduct a critical and cautious analysis of the next-generation beneficial microbe manipulation ahead of clinical application.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"299 ","pages":"Article 128240"},"PeriodicalIF":6.1,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144194893","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}