Frontiers in Microbiology最新文献

{"title":"Microbial response under sulfate stress in a sulfur-based autotrophic denitrification system.","authors":"Yiqiang Chen, Xu Jiang, Juanjuan Zhao, Maosheng Yang, Yong Chen, Hong Ling, Yang Liu, Feng Deng, Zhu Wang","doi":"10.3389/fmicb.2025.1615317","DOIUrl":"10.3389/fmicb.2025.1615317","url":null,"abstract":"<p><p>This study investigated the responses of the bacterial community structure and metabolic pathways in a sulfur-based autotrophic denitrification filter (SADF) system to fast elevated sulfate salinity, from 0.04 to 1.2% in 30 days. Results showed that the SADF system exhibited robust sulfate salinity stress tolerance at low nitrate concentrations. In the context of sulfate scenarios, the genus <i>Thiobacillus</i> significantly proliferated and was identified as the dominant sulfur-oxidizing player in the SADF system, achieving a relative abundance of 63.79% under 1.2% sulfate salinity. Cooperative and competitive interactions were found in the SADF-related microorganisms, promoting stable denitrification performance under high salinity. Surprisingly, with a low hydraulic retention time (HRT) of 60 min, metagenomic sequencing revealed a upregulated abundance of functional genes encoding for enzymes associated with nitrogen and sulfur metabolism, while positive correlations were observed between these two pathways in response to sulfate salinity. Furthermore, global wastewater treatment plants were thoroughly explored for the distribution of the SADF-related microorganisms identified in this study. Interestingly, one-way ANOVA analysis showed that the SADF-related microorganisms were widely distributed globally, demonstrating their universality in potential engineering applications worldwide.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1615317"},"PeriodicalIF":4.0,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the origin of non-specific binders isolated in the selection of phage display peptide libraries.","authors":"Babak Bakhshinejad, Andreas Kjaer","doi":"10.3389/fmicb.2025.1571679","DOIUrl":"10.3389/fmicb.2025.1571679","url":null,"abstract":"<p><p>Over the recent decades, phage display has been used successfully to identify a variety of peptides with diagnostic and therapeutic applications. Despite the significant role of this technology in the pharmaceutical industry, the affinity selection of phage display peptide libraries through biopanning suffers from some limitations. The most significant drawback of phage display is the undesirable enrichment and isolation of phages whose displayed peptides have no binding affinity toward the target. Phages with high amplification rates constitute the most important category of non-specific binders. Amplification, which aims to increase the copy number of phages displaying target-specific peptides, acts like a double-edged blade and can also make a major contribution to the target-unrelated enrichment of non-specific binders, leading to compositional bias in the sequence content of the biopanning output. The cutting-edge breakthroughs fueled by the integration of next-generation sequencing (NGS) into phage display have led researchers to gain a deeper understanding of the information content of the phage population recovered from biopanning and how its peptide content changes during further rounds of selection and amplification. This body of vastly increasing information has shed more light on the complications encountered during library selection and opened new perspectives to obtain in-depth insights into amplification-associated bias in the selected phage display libraries, analyze biopanning data more rigorously, and devise more optimal protocols for phage display selections. This knowledge can finally provide a solid foundation for discovering promising target-specific binders in the evolutionary selection of phage display libraries.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1571679"},"PeriodicalIF":4.0,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174986/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis and prevention of microbial degradation of shadow puppetry artifacts preserved in the National Shadow Puppetry Museum in Chengdu.","authors":"Yu Wang, Yuanyuan Wang, Zhiqian Guan, Zeao Wang, Yangbo Duan, Chen Min, Yuhan Zhong, Lilong Hou, Jiao Pan","doi":"10.3389/fmicb.2025.1611451","DOIUrl":"10.3389/fmicb.2025.1611451","url":null,"abstract":"<p><p>Shadow puppetry, an integral and crucial component of China's intangible cultural heritage, currently faces the significant threat of microbial degradation. This is primarily due to the organic materials used in its artifacts. This study centers on the shadow puppets housed in the National Shadow Puppetry Museum in Chengdu. By employing Scanning Electron Microscopy (SEM) and high-throughput sequencing techniques, it has revealed a diverse array of co-existing microorganisms on the surfaces of these puppets. These include species from genera such as <i>Aspergillus</i>, <i>Streptomyces</i>, <i>Nocardiopsis</i>, <i>Pseudomonas</i>, and <i>Saccharopolyspora</i>, among others. Eleven microbial species were successfully isolated, wherein four were identified as predominant: <i>Pseudomonas</i> sp. WH. S-B1, <i>Streptomyces</i> sp. WH. S-B2, <i>Nocardiopsis</i> sp. WH. S-B6, and <i>Aspergillus fumigatus</i> WH. S-F2. Notably, these four strains demonstrated the ability to degrade collagen. The antimicrobial experiment results indicated that 0.3% isothiazolinone-based antimicrobial agents BC01 and 50 mg/mL carvacrol exhibited a certain degree of antimicrobial activity against these predominant strains. Overall, this research provides a robust foundation for the conservation of shadow puppet artifacts. It does so by thoroughly analyzing the mechanisms of microbial degradation and screening effective antimicrobial agents.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1611451"},"PeriodicalIF":4.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endolysins and membrane-active peptides: innovative engineering strategies against gram-negative bacteria.","authors":"Monika Wojciechowska","doi":"10.3389/fmicb.2025.1603380","DOIUrl":"10.3389/fmicb.2025.1603380","url":null,"abstract":"<p><p>Endolysins, bacteriophage-encoded peptidoglycan hydrolases, offer promising potential in antibacterial therapy, including treatments targeting gram-negative bacteria. While these enzymes naturally act primarily on gram-positive bacteria, their application against gram-negative pathogens is more challenging due to the presence of a dual-layer cell membrane, which acts as a protective barrier. However, innovative approaches, such as fusing endolysins with antimicrobial peptides (AMPs), have demonstrated increased efficacy against gram-negative bacteria. Modifying endolysins by introducing hydrophobic properties or positive charges or combining them with agents that disrupt the outer membrane enhances their bactericidal activity. Moreover, phage endolysins that exhibit activity against gram-negative bacteria are a promising source of membrane-active peptides. Identifying new peptide sequences derived from endolysins capable of penetrating the bacterial cell membrane represents a novel and increasingly explored research direction. Studying these innovative strategies had yielded promising results, though the field remains under active investigation and development. Ongoing efforts aim to optimize these approaches to improve their effectiveness against antibiotic-resistant gram-negative bacterial strains, which are particularly difficult to treat with conventional antibiotics. This review summarizes the latest advancements and solutions in the field, highlighting the potential of endolysins and membrane-active peptides as next-generation antibacterial agents.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1603380"},"PeriodicalIF":4.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170589/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of egg incubation on hemocyte recruitment and susceptibility of <i>Galleria mellonella</i> larvae to pathogens.","authors":"Paulo Henrique Fonseca Carmo, Patrícia Michelle Nagai de Lima, Fabiana Alves Silva, Jaqueline Lemes Ribeiro, Juliana Campos Junqueira, Maíra Terra Garcia","doi":"10.3389/fmicb.2025.1611104","DOIUrl":"10.3389/fmicb.2025.1611104","url":null,"abstract":"<p><strong>Introduction: </strong><i>Galleria mellonella</i> is widely used as an <i>in vivo</i> model in microbiological and toxicological studies due to its reproducibility, low cost, and ease of handling. However, maintaining homogeneous laboratory colonies presents challenges. This study evaluated whether different incubation methods influence the larval immune response against <i>Staphylococcus aureus, Candida albicans</i>, and <i>Escherichia coli</i>.</p><p><strong>Methods: </strong>Four experimental groups were established: (1) Traditional group (TG), eggs stored at 27°C; (2) Immediate group (IG), eggs stored at 16°C for 120 days before incubation at 27°C; (3) Gradual group (GG), temperature gradually reduced from 27°C to 16°C over 98 days, then increased back; and (4) Frozen group (FG), eggs stored at freezing temperatures.</p><p><strong>Results and discussion: </strong>FG eggs were non-viable, and IG and GG showed delayed development. IG larvae were more susceptible to infections, while GG larvae resembled TG. Thus, GG can serve as an effective alternative rearing method.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1611104"},"PeriodicalIF":4.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Research focus and trends of the association between gut microbiota and neuroinflammation.","authors":"Shan Wu, Nanjie Chen, Chuanchi Wang, Kwok-Fai So","doi":"10.3389/fmicb.2025.1564717","DOIUrl":"10.3389/fmicb.2025.1564717","url":null,"abstract":"<p><strong>Background: </strong>The interaction between the gut microbiota and neuroinflammation plays a crucial role in the pathogenesis of many diseases, particularly neurodegenerative diseases, and has become one of the focal points of research in recent years. Despite the large number of related studies, there is currently a lack of comprehensive analysis and prediction of these data to drive the field forward. This study aims to systematically analyze the clinical practices and research hotspots of the underlying mechanisms in this field using bibliometric and visualization methods, and to explore the future development pathways.</p><p><strong>Methods: </strong>CiteSpace, VOSviewer, GraphPad Prism and other software were used to analyze 1,404 studies on gut microbiota and neuroinflammation collected by the core of the Web of Science since 2000, to visually present the collaborative network between literatures, structure of authors and countries, co-occurrence of keywords, emerging reference literature, and research hotspots.</p><p><strong>Results: </strong>From 2000 to 2024, the number of related papers on this topic showed an overall upward trend, and the annual citation peaked in 2020, with significant contributions from China and the United States. Research focused on the relationship between gut microbiota and neuroinflammation, with a particular emphasis on investigating the mechanisms of the microbiota-gut-brain axis through both basic and clinical research. Treatment strategies include probiotic therapy, fecal microbiota transplantation and traditional Chinese medicine.</p><p><strong>Conclusion: </strong>This study comprehensively reviews the research progress on the association between gut microbiota and neuroinflammation, and discusses the current research focus and frontier directions of this relationship, so as to provide reference for the development of this field.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1564717"},"PeriodicalIF":4.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: Bacteriophages, prophages, and their products: regulating bacterial populations.","authors":"Barbara Maciejewska, Agata Dorotkiewicz-Jach, Zuzanna Drulis-Kawa, Gamaliel López-Leal","doi":"10.3389/fmicb.2025.1628912","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1628912","url":null,"abstract":"","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1628912"},"PeriodicalIF":4.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immunoprotective test and whole-genome sequencing analysis of the attenuated S02 strain of <i>Streptococcus iniae</i>.","authors":"Dandan Yi, Aiying Lei, Yu Liu, Guixiang Tong, Ting Huang, Chenyu Quan, Ming Chen, Liping Li","doi":"10.3389/fmicb.2025.1550544","DOIUrl":"10.3389/fmicb.2025.1550544","url":null,"abstract":"<p><strong>Background: </strong><i>Streptococcus iniae</i> is one of the most serious diseases threatening tilapia aquaculture, causing huge economic losses every year. Injectable attenuated vaccines are still the best choice for preventing streptococcal diseases affecting the tilapia.</p><p><strong>Objective: </strong>This study evaluated the safety, stability, immunogenicity, antibody production time, and immune dose of the attenuated S02 strain of <i>S. iniae</i> and comprehensively analyzed the possible mechanisms of its attenuated virulence at the whole-genome level.</p><p><strong>Results: </strong>After detoxification, the S02 strain completely loses its pathogenicity to tilapia and has good immunogenicity. The results of the backpropagation safety test showed that the S02 strain did not cause disease or death to tilapia after continuous passage for 50 generations. AfterS02 was injected, the immunoglobulin M (IgM) level in the serum was significantly higher than that in the GX005 infection group within 28 days and reached its peak at 14 days. An intraperitoneal injection of 10⁹ CFUs/mL of S02 at a dose of 0.2 mL per fish had the best relative protection rate of 92.58%. The whole-genome sequencing results showed that the S02 strain had two large 0.2 Mbp segments of inversion compared to its parent virulence strain GX005, encoding 372 genes, including the virulence genes of the GNAT family N-acetyltransferase and the hyaluronic acid lyase genes of the hysA, hylA, and hylB, which are related to virulence factors.</p><p><strong>Conclusion: </strong>This study provides theoretical data support for the prevention and control of the <i>S. iniae</i> infection in tilapia. The abnormal expression of important virulence genes GNAT family N-acetyltransferase and hyaluronic acid lyase genes hysA, hylA, and hylB caused by the inversion and translocation of large fragments could be the main mechanism for their attenuated virulence. This study provided theoretical support for the prevention and treatment of <i>S. iniae</i> infection in tilapia and the application of S02-attenuated vaccine.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1550544"},"PeriodicalIF":4.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence, genetic diversity, and molecular detection of the apple hammerhead viroid in Germany.","authors":"Kerstin Zikeli, Constanze Berwarth, Ute Born, Thomas Leible, Wilhelm Jelkmann, Michael Helmut Hagemann","doi":"10.3389/fmicb.2025.1592572","DOIUrl":"10.3389/fmicb.2025.1592572","url":null,"abstract":"<p><strong>Introduction: </strong>Apple hammerhead viroid (AHVd) is an emerging plant pathogen infecting apple orchards worldwide. Its genetic variability and geographical distribution remain poorly understood, limiting effective diagnostics and management strategies.</p><p><strong>Methods: </strong>In this study, 192 samples from German apple orchards were analyzed using reverse transcription (RT) and real-time PCR, one-step RT real-time PCR, and Sanger sequencing. Next-generation sequencing (NGS) was employed on pooled RNA extracts to explore genetic diversity. Phylogenetic relationships were inferred using maximum likelihood methods, and viroid-derived small RNAs (vd-sRNAs) were identified from small RNA sequencing data.</p><p><strong>Results and discussion: </strong>AHVd was detected in 78% of samples, with prevalence varying by region: southern (82%), eastern (90%), northern (72%), and western (70%) states of Germany. Phylogenetic analysis revealed distinct clusters linked to geographical origins, indicating isolated evolutionary pathways. NGS analysis uncovered 39% inter-sample variability and 169 polymorphic positions, while Sanger sequencing of RT real-time PCR products derived from the same samples showed only 3% variability, reflecting dominant quasispecies populations. Small RNA analysis mapped 128,388 reads to the AHVd genome, identifying hotspots within and outside the rod-like structure, suggesting structural and regulatory functions of vd-sRNAs. These findings underline AHVd's genetic diversity. The complex relationship between AHVd genetic variability and symptom expression necessitates the development of highly sensitive diagnostic tools and adaptive management strategies to effectively monitor and control its spread in apple production.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1592572"},"PeriodicalIF":4.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics using long-read sequencing identifies nearly identical TAL effector regions in two <i>Xanthomonas oryzae</i> pv. <i>Oryzae</i> isolates collected from the basmati rice-growing region of Pakistan.","authors":"Khansa Ejaz, Muhammad Zakria, Peiqi Zhang, Jose Huguet Tapia, Muhammad Arif, Frank White, Sumera Yasmin","doi":"10.3389/fmicb.2025.1560969","DOIUrl":"10.3389/fmicb.2025.1560969","url":null,"abstract":"<p><p>The emergence of hostile and novel plant pathogenic strains poses a serious threat to global food security, which renders the strategies for disease management in modern agriculture ineffective. Preventing the consequences of these emerging phytopathogens requires accurate genetic information about the pathogen population to formulate effective management strategies. Bacterial leaf blight (BLB), caused by <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> (<i>Xoo</i>), is the foremost reason for substantial yield losses in rice crops worldwide, especially in Asia. The genetic information regarding the Pakistani <i>Xoo</i> population is still unexplored. To bridge this gap, two representative Pakistani <i>Xoo</i> isolates, namely PkXoo1 and PkXoo2, were sequenced using long-read Oxford Nanopore Technology (ONT). Both isolates were obtained from the Basmati rice-growing region of Pakistan, with substantially high virulence on certain susceptible rice varieties. The final assembly of PkXoo1 and PkXoo2 yielded a circular chromosome of approximately 4.9 MB with a G + C content of 64%. Genome annotation of both strains revealed the presence of key genes associated with hypersensitivity and virulence in <i>Xoo</i>. The AnnoTALE analysis showed that both strains contained 18 transcription activator-like (TAL) effectors, three of which were predicted to be pseudoTALes. A phylogenomic analysis grouped PkXoo1 and PkXoo2 with strains belonging to India and Thailand, placing them far apart from other major Asian <i>Xoo</i> strains. The present study revealed significant findings about the conservation of repeat variable di-residues (RVDs) in major TAL effectors and the utility of high-throughput sequencing technologies for TAL effector analysis and pathogen tracking. The complete genome sequence of <i>Xoo</i> isolates from Pakistan will enhance sequence resources for the global comparison of <i>Xoo</i> diversity across the region. This information is also of great significance for launching effective and durable breeding programs.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1560969"},"PeriodicalIF":4.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144316330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}