Journal of Microbiology最新文献

{"title":"SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.","authors":"Seong-In Na, Juhee Kim, So-Yeon Kim, Jin Park, Yong-Joon Cho","doi":"10.71150/jm.2606011","DOIUrl":"10.71150/jm.2606011","url":null,"abstract":"<p><p>Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":" ","pages":"e2606011"},"PeriodicalIF":3.8,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148990334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishment of a CD46 and desmoglein-2 expressing mouse model for human adenovirus type 55 vaccine evaluation.","authors":"Jung-Ah Choi, Eunji Yang, Shing Young Noh, Dae-Im Jung, Yun Jeong Park, Ji Heun Jeong, Hye Yun Jeong, Manki Song, Soon-Hwan Kwon, Sang Hwan Seo","doi":"10.71150/jm.2605005","DOIUrl":"10.71150/jm.2605005","url":null,"abstract":"<p><p>Human adenovirus type 55 (HAdV-55) is an emerging respiratory pathogen associated with severe pneumonia, for which no licensed vaccines are currently available. The lack of physiologically relevant small-animal models has limited preclinical evaluation of vaccine candidates. In this study, we generated a transgenic mouse model co-expressing human CD46 and desmoglein-2 (DSG-2), key entry receptors for HAdV-55, and evaluated its utility for vaccine efficacy testing. A bicistronic expression system enabling simultaneous expression of CD46 and DSG-2 was constructed and functionally validated in vitro, demonstrating enhanced susceptibility to HAdV-55 infection. The transgenic mice exhibited dose-dependent weight loss, robust viral replication in lung tissues, and characteristic histopathological changes following intranasal challenge, recapitulating key features of human adenoviral pneumonia. Using this model, we assessed the immunogenicity and protective efficacy of an inactivated HAdV-55 (iHAdV-55) vaccine formulated with alum. Vaccination induced strong HAdV-55-specific IgG and neutralizing antibody responses, which increased over time following prime-boost immunization. Upon viral challenge, vaccinated mice showed significantly reduced weight loss and accelerated recovery compared to controls. Viral load analysis demonstrated effective control of viral replication and clearance in vaccinated animals. Collectively, these findings establish the CD46/DSG-2 transgenic mouse as a physiologically relevant and translationally valuable model for HAdV-55 infection and demonstrate that iHAdV-55 vaccination confers robust humoral immunity and protective efficacy. This platform provides a critical tool for the development and preclinical evaluation of adenovirus-targeted vaccines and therapeutics.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":" ","pages":"e2605005"},"PeriodicalIF":3.8,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148990294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-evolutionary pathways of synthetic biology regulation: A comparative analysis of major countries and Korea's strategic legislation.","authors":"Hyeonsu Kim, Yeji Kwon, Heoung-Yeol Kim, Jiyeon Lee","doi":"10.71150/jm.2606027","DOIUrl":"10.71150/jm.2606027","url":null,"abstract":"<p><p>The convergence of synthetic biology and artificial intelligence is widening the gap between technological advancement and existing regulatory frameworks - a phenomenon known as regulatory lag. As global competition intensifies to capture a synthetic biology market projected to reach approximately $70 billion by 2030, nations are responding to this challenge through markedly different approaches. This study applies a comparative legal methodology, drawing on co-evolutionary theory and the Law 1.0/2.0/3.0 framework, to analyze the regulatory responses of the United States, United Kingdom, Japan, and South Korea. The analysis reveals that national differences stem less from institutional design choices than from the triggers that initiate regulatory change, yielding four distinct co-evolutionary pathways. In the United States, a shift in the judicial environment prompted regulatory adaptation; in the United Kingdom, a political transition created the conditions for legislative reform; and in Japan, administrative reinterpretation of existing rules enabled regulatory adjustment. South Korea represents a fundamentally different case. By enacting the world's first standalone synthetic biology legislation prior to full technological maturation, Korea has pursued a top-down co-evolutionary model in which institutional design precedes and shapes the trajectory of technological development. Three conclusions emerge from this analysis: there is no single optimal co-evolutionary pathway; institutional flexibility determines the sustainability of co-evolution; and co-evolution can itself be an object of proactive design. For Korea's preemptive model to prove effective, it requires a sufficient scientific foundation, institutional flexibility, and coherence with existing regulatory frameworks - conditions that offer a reference point for other nations confronting similar governance challenges.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":" ","pages":"e2606027"},"PeriodicalIF":3.8,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148990360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic signatures associated with epidemiologically defined high-risk pathogenic Escherichia coli isolates identified by interpretable machine learning.","authors":"Yoojung Hwang, Woo Young Cho, Woojung Lee, Insun Joo, Jeong-Ih Shin, Mi-Ran Seo, Seung-Hun Shin, Kwan Soo Ko, Kun Taek Park, Yeun-Jun Chung, Seung-Hyun Jung","doi":"10.71150/jm.2604011","DOIUrl":"https://doi.org/10.71150/jm.2604011","url":null,"abstract":"<p><p>Pathogenic Escherichia coli is a major cause of foodborne illness worldwide and includes strains capable of causing severe disease. To establish a genome-informed framework for foodborne outbreak surveillance, we analyzed 1,029 E. coli isolates from clinical, food, livestock, and environmental sources using whole-genome sequencing. Pathogenic isolates obtained from human clinical cases or linked to documented outbreaks were classified as epidemiologically defined high-risk (EpiHR), whereas the remaining pathogenic isolates were classified as non-EpiHR. Virulence-associated genomic features were extracted using a bioinformatics pipeline, and four machine learning (ML) algorithms, including gradient boosting machine, random forest (RF), and support vector machines with linear and radial basis function kernels, were evaluated. Among them, the RF model showed the best performance, achieving an area under the curve (AUC) of 0.98 and accuracy of 0.93 in 10-fold cross-validation. Additional leave-one-group-out validation showed retained discrimination across held-out sequence types and serotypes, although performance was reduced when isolates were grouped by isolation source. Evaluation using an independent test dataset of 1,908 publicly available pathogenic E. coli genomes showed an AUC of 0.97 and a sensitivity of 0.98. Feature importance analysis using Shapley additive explanations identified influential predictive features, including traT, etpB, and enterotoxin-associated genes. A reduced 10-feature model achieved an AUC of 0.79 in the independent test dataset, supporting its exploratory use for future simplified screening approaches. These results indicate that genome-based ML provides a sensitive framework for surveillance-oriented prioritization of EpiHR pathogenic E. coli isolates, with model predictions interpreted together with epidemiological information.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"64 8","pages":"e2604011"},"PeriodicalIF":3.8,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Berberine promotes host lipolysis to enhance antimicrobial defense against hypervirulent Klebsiella pneumoniae infection.","authors":"Ju Yeong Lee, Hui-Jung Jung, Anwesha Ash, Seunghyeon Jeon, Miri Hyun, Ji Yeon Lee, Sang-Hee Lee, Hyuk Nam Kwon, Won-Ki Baek, Jichan Jang, Hyun Ah Kim, Jin Kyung Kim","doi":"10.71150/jm.2605001","DOIUrl":"https://doi.org/10.71150/jm.2605001","url":null,"abstract":"<p><p>Hypervirulent Klebsiella pneumoniae (hvKp) is an emerging pathogen that causes severe community-acquired infections; however, the immune mechanisms controlling intracellular hvKp have yet to be clearly defined. In this study, we investigated the therapeutic potential of berberine against hvKp infection and elucidated the underlying molecular mechanisms using macrophage cell models and in vivo zebrafish models. Berberine significantly reduced intracellular hvKp survival in macrophages and improved survival in hvKp-infected zebrafish. Berberine markedly attenuated proinflammatory cytokine production and inhibited the c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) signaling pathways. Notably, we found that hvKp exploited host lipid droplets (LD) biosynthesis to support its intracellular survival, and berberine effectively suppressed LD accumulation. Mechanistically, berberine promoted the nuclear translocation of transcription factor EB (TFEB), thereby enhancing lipolysis. Although berberine upregulated autophagy-related gene expression during hvKp infection, it did not induce lipophagy, the selective autophagic degradation of LD. Collectively, these findings indicate that berberine has potential as a therapeutic agent against hvKp infection by modulating host lipid metabolism to restrict bacterial intracellular survival.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"64 8","pages":"e2605001"},"PeriodicalIF":3.8,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148881066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temporal changes in culturable fungal community composition with their plastic degradation capacities in the marine plastisphere through mesocosm experiments.","authors":"Sumin Jo, Ji Seon Kim, Wonjun Lee, Chang Wan Seo, Young Woon Lim","doi":"10.71150/jm.2605011","DOIUrl":"https://doi.org/10.71150/jm.2605011","url":null,"abstract":"<p><p>Plastic waste in marine environments provides novel habitats for diverse organisms, forming distinct microbial ecosystems known as the 'plastisphere'. Although bacteria of the plastisphere have been widely studied, the role of fungi in plastisphere formation and plastic degradation remains largely unexplored. Thus, we investigated temporal changes in culturable fungal community composition on three common plastic types-high-density polyethylene, low-density polyethylene, and polypropylene-across the early (seven days) and mature (30 days) plastisphere developmental stages through a marine mesocosm experiment. In total, 436 fungal strains were isolated and identified as belonging to 179 taxa, with Penicillium, Cladosporium, Trichoderma, Aspergillus, and Fusarium as the dominant genera. Temporal shifts in the species richness of the dominant genera were observed: Cladosporium showed higher species richness at the early stage, whereas that of Trichoderma increased at the mature stage. Plastic degradation assays revealed that 54.6% of the strains exhibited measurable degradation capacity, with patterns varying by plastic type rather than fungal developmental stage. Scanning electron microscope observations revealed surface damage patterns including cracks, pitting, and erosion on the plastic surfaces. These findings provide novel insights into the composition and functional heterogeneity of culturable fungal communities in the marine plastisphere and suggest that plastisphere fungi play diverse ecological roles beyond direct plastic degradation.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"64 8","pages":"e2605011"},"PeriodicalIF":3.8,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From resistance mechanisms to therapy: Antimicrobial resistance in Gram-negative bacteria.","authors":"Minho Lee","doi":"10.71150/jm.2604017","DOIUrl":"https://doi.org/10.71150/jm.2604017","url":null,"abstract":"<p><p>Antimicrobial resistance poses a major global health challenge, and infections caused by multidrug-resistant Gram-negative bacteria are associated with substantial morbidity and mortality. In contrast to many Gram-positive pathogens, Gram-negative bacteria combine intrinsic barriers with acquired determinants, including enzymatic drug inactivation, reduced outer membrane permeability, active efflux, and target modifications, which collectively compromise the efficacy of multiple antibiotic classes. Previous reviews have largely catalogued resistant pathogens or antimicrobial agents. This review provides a mechanism-focused overview of antimicrobial resistance in clinically important Gram-negative bacteria and explains how dominant resistance determinants translate into clinically relevant failure modes, such as delayed effective therapy, limited treatment options, and increased reliance on toxic last-line agents. Current and emerging therapeutic strategies are discussed through a mechanism-based lens, emphasizing newer β-lactam/β-lactamase inhibitor combinations and nontraditional approaches, including phages, antivirulence, and microbiome-based interventions. This review highlights the conceptual links between resistance mechanisms, clinical impact, and rational therapeutic choices and identifies priorities for future research aimed at mitigating antimicrobial-resistant Gram-negative infections.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"64 8","pages":"e2604017"},"PeriodicalIF":3.8,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148881056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fluctuating environmental adaptation shapes antibiotic survival in Mycobacterium tuberculosis.","authors":"Eun Seon Chung","doi":"10.71150/jm.2606004","DOIUrl":"https://doi.org/10.71150/jm.2606004","url":null,"abstract":"<p><p>Mycobacterium tuberculosis (Mtb) encounters diverse and fluctuating microenvironments during infection, including changes in nutrient availability and pH. While adaptation to individual host-associated conditions has been extensively studied, the impact of repeated environmental fluctuations on bacterial physiology and antibiotic survival remains unclear. In this study, we investigated how long-term adaptation to stable or fluctuating environments influences Mtb growth and drug responses. Mtb populations were serially passaged for six consecutive passages under combinations of different carbon sources and pH conditions that were either maintained consistently or altered across passages. Environmental history significantly affected bacterial growth dynamics and antibiotic survival. Notably, under identical final condition with cholesterol as a sole carbon source, populations adapted to a stable environment exhibited higher survival following bedaquiline and rifampicin treatment than populations exposed to fluctuating environments. These findings suggest that stable environments promote the optimization of growth and stress-response programs, whereas environmental fluctuations limit such optimization despite potentially increasing phenotypic heterogeneity and a possibility of survival. Together, our results identify environmental history as an important determinant of antibiotic survival in Mtb and highlight the need to consider dynamic host-like environments when investigating tuberculosis physiology and drug responses.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"64 8","pages":"e2606004"},"PeriodicalIF":3.8,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long-read sequencing reveals putatively mobilizable resistance genes and multi-drug resistance plasmids underestimated by short-read metagenomics.","authors":"Dabin Jeon, Tatsuya Unno","doi":"10.71150/jm.2605007","DOIUrl":"https://doi.org/10.71150/jm.2605007","url":null,"abstract":"<p><p>While shotgun metagenomics is often used to profile antibiotic resistome in gut microbial communities, few studies have investigated if the choice of sequencing platform and assembly strategy affect what mobile genetic elements and antimicrobial resistance genes are recovered. In this study, we compared three platforms (Illumina, Oxford Nanopore, and PacBio HiFi) and seven assembly strategies on gut metagenomes from cattle, pig, and human as case studies. Long-read assemblies recovered 5- to 7-fold more plasmid sequence than Illumina in cattle and pig (mean 17.0 Mb vs. 3.1 Mb), while Illumina performed comparably in the less diverse human gut where high per-species coverage enabled effective short-read plasmid assembly. Long reads also detected more resistance genes on plasmid contigs. Hybrid assembly results depended on the algorithm: scaffolding-based OPERA-MS preserved long-read contiguity and recovered more plasmid-borne resistance genes, while the short-read-centric metaSPAdes hybrid mode produced fragmented assemblies. After collapsing haplotype redundancy, PacBio HiFi identified 2 and 49 unique multi-drug resistance plasmid lineages in cattle and pig, respectively. On the other hand, only 2 and 4 were identified from Illumina. Long reads also placed far more ARGs in a putative mobilization context (50-73%) compared to 14-21% for short reads. Platform and assembly strategy are thus key variables in mobilome and resistome characterization and should be accounted for in antimicrobial resistance surveillance.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"64 8","pages":"e2605007"},"PeriodicalIF":3.8,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148881058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design guide for synthetic small regulatory RNAs for high-efficiency gene knockdown in bacteria.","authors":"Jun Ren, Yubin Kim, Hyun Jung Nam, Hyang-Mi Lee, Dokyun Na","doi":"10.71150/jm.2603026","DOIUrl":"https://doi.org/10.71150/jm.2603026","url":null,"abstract":"<p><p>Small regulatory RNAs (sRNAs) are short noncoding RNAs that can fine-control the expression of target genes in trans at the post-transcriptional level in prokaryotes. Since there is a big challenge in constructing gene-knockout libraries, synthetic sRNAs have attracted considerable interest in synthetic biology and metabolic engineering, as they enable targeted gene knockdown without requiring chromosomal modifications. However, the development of high-efficiency synthetic sRNAs remains a demanding task that requires careful consideration of multiple design factors. Here, we provide a detailed protocol for the design and construction of synthetic sRNAs, detailing key design principles and critical optimization factors, including scaffold selection, target mRNA binding affinity, target mRNA secondary structure, and Hfq expression levels. This strategy can be broadly applied across E. coli and other bacterial hosts to modulate gene expression, thereby supporting versatile applications in synthetic biology and metabolic engineering.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"64 7","pages":"e2603026"},"PeriodicalIF":3.8,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148663660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}