Journal of Microbiology最新文献

{"title":"Prebiotic potential of proso millet and quinoa: Effects on gut microbiota composition and functional metabolic pathways.","authors":"Jinwoo Kim, Jiwoon Kim, Yewon Jung, Gyungcheon Kim, Seongok Kim, Hakdong Shin","doi":"10.71150/jm.2503002","DOIUrl":"https://doi.org/10.71150/jm.2503002","url":null,"abstract":"<p><p>Prebiotics are indigestible dietary components that improve host health by stimulating the growth and metabolic activity of beneficial intestinal microbes. The whole grains are rich in non-digestible carbohydrates, which may confer prebiotic potential. Among them, millet and quinoa have gained attention as dietary alternatives due to the growing popularity of gluten-free diets. In this study, we examined the effects of proso millet and quinoa on the human gut microbiota using an in vitro fecal incubation model. Both grains altered alpha diversity metrics, including microbial richness, evenness, and phylogenetic diversity. Beta diversity analysis showed that the proso millet and quinoa treatment groups exhibited distinct clustering patterns compared to the control, highlighting their impact on microbial community structure. Taxonomic analysis showed an increase in beneficial genera, including Bifidobacterium, and a decrease in taxa such as Enterobacteriaceae and Flavonifractor. To assess metabolic changes associated with microbial fermentation, short-chain fatty acid (SCFA) intensities were measured. The intensities of acetic acid, propionic acid, and butyric acid were significantly higher in the proso millet- and quinoa-treated groups compared to the control group. Spearman correlation analysis showed that the abundances of Bifidobacterium and Blautia were significantly positively associated with SCFA intensities. Furthermore, predicted functional pathway analysis identified enrichment of carbohydrate-related pathways in proso millet and quinoa treatments. Quinoa supplementation led to a broader enhancement of metabolic pathways, including glycolysis/gluconeogenesis, starch and sucrose metabolism, and pentose phosphate pathways, whereas proso millet enriched galactose metabolism, and starch and sucrose metabolism. These findings suggest that proso millet and quinoa influence gut microbial diversity, composition, and function.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 7","pages":"e2503002"},"PeriodicalIF":2.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144753634","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":"Erratum: Bacteroides celer sp. nov. and Bacteroides mucinivorans sp. nov., isolated from human feces, and the reclassification of Bacteroides koreensis Shin et al. 2017 and Bacteroides kribbi Shin et al. 2017 as later heterotypic synonyms of Bacteroides ovatus Eggerth and Gagnon 1933 (Approved Lists 1980).","authors":"Ah-In Yang, Bora Kim, Woorim Kang, Hae-In Joe, Na-Ri Shin","doi":"10.71150/jm.2507100","DOIUrl":"https://doi.org/10.71150/jm.2507100","url":null,"abstract":"","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 7","pages":"e2507100"},"PeriodicalIF":2.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144753630","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":"Targeting innate immune sensors for therapeutic strategies in infectious diseases.","authors":"Seyun Shin, Young Ki Choi, SangJoon Lee","doi":"10.71150/jm.2503009","DOIUrl":"https://doi.org/10.71150/jm.2503009","url":null,"abstract":"<p><p>The innate immune system relies on innate immune sensors, such as pattern recognition receptors (PRRs), to detect pathogens and initiate immune responses, crucial for controlling infections but also implicated in inflammatory diseases. These innate immune sensors, including Toll-like receptors (TLRs), nod-like receptors (NLRs), RIG-I-like receptors (RLRs), absent in melanoma 2 (AIM2), and Z-DNA binding protein 1 (ZBP1) trigger signaling pathways that produce cytokines, modulating inflammation and cell death. Traditional therapies focus on directly targeting pathogens; however, host-targeting therapeutic strategies have emerged as innovative approaches to modulate innate immune sensor activity. These strategies aim to fine-tune the immune response, either enhancing antiviral defenses or mitigating hyperinflammation to prevent tissue damage. This review explores innate immune sensor-based therapeutic approaches, including inhibitors, agonists, and antagonists, that enhance antiviral defense or suppress harmful inflammation, highlighting innate immune sensors as promising targets in infectious and inflammatory disease treatment.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 6","pages":"e2503009"},"PeriodicalIF":3.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540573","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":"Inhibiting kinesin family member 20A disrupts Zika virus entry by blocking internalization.","authors":"Jeonghyeon Lee, Younghyun Lim, Hyeong-Rae Kim, Yong-Bin Cho, In-Gu Lee, Young-Jin Seo","doi":"10.71150/jm.2503008","DOIUrl":"https://doi.org/10.71150/jm.2503008","url":null,"abstract":"<p><p>Zika virus, a mosquito-borne virus, is associated with congenital birth defects and neurological complications. However, despite its significant public health threat, no approved vaccines or antiviral treatments are currently available. Therefore, this study aims to identify kinesin family member 20A as a key host factor promoting Zika virus life cycle. The elevated expression of kinesin family member 20A following Zika virus infection suggests its role in the viral life cycle. Suppressing its expression through gene silencing or inhibiting its function with a small-molecule inhibitor significantly reduced viral infectivity in host cells. Furthermore, kinesin family member 20A is essential for facilitating viral internalization, a key step in the entry step. These findings suggest its significance in the Zika virus life cycle and highlight its potential as a novel therapeutic target for the Zika virus.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 6","pages":"e2503008"},"PeriodicalIF":3.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540569","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":"Phycobium rhodophyticola gen. nov., sp. nov. and Aliiphycobium algicola gen. nov., sp. nov., isolated from the phycosphere of marine red algae.","authors":"Jeong Min Kim, Woonhee Baek, Byeong Jun Choi, Hülya Bayburt, Jae Kyeong Lee, Sung Chul Lee, Che Ok Jeon","doi":"10.71150/jm.2503014","DOIUrl":"https://doi.org/10.71150/jm.2503014","url":null,"abstract":"<p><p>Two Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacteria, designated D3-12ᵀ and G2-2ᵀ, were isolated from the phycosphere of marine red algae. Both strains exhibited catalase- and oxidase-positive activities. Strain D3-12ᵀ grew optimally at 30°C, pH 7.0, and 2.0-3.0% (w/v) NaCl, while strain G2-2ᵀ showed optimal growth at 30°C, pH 7.0, and 2.0% NaCl. Ubiquinone-10 was the sole respiratory quinone in both strains. The major fatty acids (> 5%) in strain D3-12ᵀ were feature 8 (C18:1 ω7c and/or C18:1 ω6c), 11-methyl-C18:1 ω7c, and C16:0, while strain G2-2ᵀ contained summed feature 8 and C16:0. The predominant polar lipids in strain D3-12ᵀ were phosphatidylcholine, phosphatidylglycerol, and phosphatidylethanolamine, whereas strain G2-2ᵀ contained phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G + C content was 59.9% for strain D3-12ᵀ and 60.2% for strain G2-2ᵀ. Phylogenetic analyses based on 16S rRNA and whole-genome sequences placed both strains into distinct lineages within the family Roseobacteraceae, separate from previously described genera. Genome-based relatedness metrics, including average nucleotide identity, digital DNA-DNA hybridization, average amino acid identity, and percentage of conserved proteins, further confirmed that these strains represent novel genera. Based on phenotypic, chemotaxonomic, and molecular characteristics, strains D3-12ᵀ and G2-2ᵀ are proposed as novel genera: Phycobium rhodophyticola gen. nov., sp. nov. (D3-12ᵀ = KACC 22712ᵀ = JCM 35528ᵀ) and Aliiphycobium algicola gen. nov., sp. nov. (G2-2ᵀ = KACC 22602ᵀ = JCM 35752ᵀ). Additionally, metabolic features relevant to interactions with marine algae, including genes associated with carbohydrate-active enzymes, vitamin biosynthesis, phenylacetic acid production, and bacterioferritin synthesis, were bioinformatically investigated.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 6","pages":"e2503014"},"PeriodicalIF":3.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540572","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":"Bacteroides celer sp. nov. and Bacteroides mucinivorans sp. nov., isolated from human feces, and the reclassification of Bacteroides koreensis Shin et al. 2017 and Bacteroides kribbi Shin et al. 2017 as later heterotypic synonyms of Bacteroides ovatus Eggerth and Gagnon 1933 (Approved Lists 1980).","authors":"Ah-In Yang, Bora Kim, Woorim Kang, Hae-In Joe, Na-Ri Shin","doi":"10.71150/jm.2502006","DOIUrl":"10.71150/jm.2502006","url":null,"abstract":"<p><p>Two novel, Gram-stain-negative, anaerobic, and non-motile bacterial strains, designated KFT8T and CG01T, were isolated from the feces of healthy individuals without diagnosed diseases and characterized using a polyphasic approach. Phylogenetic analysis revealed that both strains belong to the genus Bacteroides, with < 99.0% similarity in their 16S rRNA gene sequences to B. facilis NSJ-77T and B. nordii JCM 12987T. Within the genus Bacteroides, strain KFT8T exhibited the highest Orthologous Average Nucleotide Identity value of 94.7% and a digital DNA-DNA hybridization value of 63.7% with B. ovatus ATCC 8483T, whereas strain CG01T showed the highest values of 95.3% and 63.3%, respectively, with B. nordii JCM 12987T. The values between the two novel strains were 74.8% and 21.4%, respectively, which are below the species delineation thresholds, supporting their classification as novel species. The major fatty acid of strain KFT8T was C18:1 ω9c, whereas strain CG01T predominantly contained summed feature 11 (comprising iso-C17:0 3OH and/or C18:2 DMA). The only respiratory quinone was MK-11, the major polar lipid was phosphatidylethanolamine. Both strains produced succinic acid and acetic acid as common metabolic end-products of fermentation, while lactic acid and formic acid were detected individually in each strain. Based on polyphasic characterization, strains KFT8T (= KCTC 15614T = JCM 36011T) and CG01T (= KCTC 15613T = JCM 36010T) represent two novel species within the genus Bacteroides, for which the names Bacteroides celer sp. nov. and Bacteroides mucinivorans sp. nov. are proposed, respectively. Additionally, genome-based analyses and phenotypic comparisons revealed that B. koreensis and B. kribbi represent the same strain, showing genomic relatedness to B. ovatus that exceeds the threshold for species delineation. Consequently, we propose the reclassification of B. koreensis Shin et al. 2017 and B. kribbi Shin et al. 2017 as later heterotypic synonyms of B. ovatus Eggerth and Gagnon 1933 (Approved Lists 1980).</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 6","pages":"e2502006"},"PeriodicalIF":2.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540567","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":"Development of a CRISPR/Cas9 RNP-mediated genetic engineering system in Paecilomyces variotii.","authors":"Hui-Gang Han, Rutuja Nandre, Hyerang Eom, Yeon-Jae Choi, Hyeon-Su Ro","doi":"10.71150/jm.2502011","DOIUrl":"https://doi.org/10.71150/jm.2502011","url":null,"abstract":"<p><p>A thermophilic strain of Paecilomyces variotii (MR1), capable of surviving temperatures above 40°C, was isolated from a paper mill and investigated as a host for heterologous protein production. To prevent environmental dissemination of spores, UV mutagenesis was employed to create a conidia-deficient strain, UM7. This strain underwent gene editing using Cas9-gRNA ribonucleoprotein (RNP) with HR donor DNA fragments, incorporating promoter sequences amplified from the genomic DNA of P. variotii (PH4, PP2, PS8, Ptub, Ptef1, and PgpdA), along with a signal sequence-tagged eGFP, flanked by 5'-upstream (336 bp) and 3'-downstream (363 bp) regions of pyrG. Co-transformation of HR donor DNA with RNP into protoplasts yielded 48 mutant pyrG transformants capable of surviving in the presence of 5-fluoroorotic acid (5-FOA). Sequence analysis identified 16 of the 48 pyrG-disrupted mutants carrying complete HR donor DNAs with the six different promoter sequences, indicating successful homology-directed repair (HDR). Evaluation of promoter strength revealed that PgpdA was the most effective for intracellular GFP production; however, it resulted in negligible extracellular GFP signal under all promoter conditions. A newly edited strain with an HDR integration module connecting PgpdA directly to eGFP, without the signal sequence, exhibited enhanced GFP expression in both mycelial cells and culture broth, suggesting that the signal peptide negatively affect protein expression and secretion. This work represents the first successful RNP-mediated gene editing in P. variotii, contributing to the application of this thermophilic fungus in protein production.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 6","pages":"e2502011"},"PeriodicalIF":3.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540568","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":"Inhibition of candidalysin production by methoxy-apo-enterobactin from Streptomyces ambofaciens CJD34 as a novel antifungal strategy against Candida albicans.","authors":"Eui-Seong Kim, Hyeongju Jeong, Mustansir Abbas, Soohyun Um, Juntack Oh, Kyuho Moon, Kyung-Tae Lee","doi":"10.71150/jm.2504019","DOIUrl":"https://doi.org/10.71150/jm.2504019","url":null,"abstract":"<p><p>Opportunistic fungal pathogens, responsible for over 300 million severe cases and 1.5 million deaths annually, pose a serious global health threat, especially in immunocompromised individuals. Among these, Candida albicans is a major cause of both superficial and invasive infections, which can progress to systemic candidiasis. One of the critical factors in C. albicans pathogenicity is the yeast-to-hyphal transition, which enables biofilm formation and promotes tissue invasion through the secretion of candidalysin, a cytolytic peptide toxin encoded by the ECE1 gene. In this study, metabolites produced by Streptomyces ambofaciens CJD34, isolated from soil samples, were screened for antifungal activity. Methoxy-apo-enterobactin (compound 1) was identified as a potential inhibitor of C. albicans virulence. Treatment with compound 1 significantly suppressed ECE1 expression and candidalysin production. In a murine subcutaneous infection model, topical application of compound 1 reduced subcutaneous colonization by C. albicans. Molecular docking analysis suggested that the inhibition of ECE1 expression was not mediated by direct binding to known upstream transcription factors, indicating an indirect mechanism of action. Collectively, these findings highlight compound 1 as a promising antivirulence agent targeting candidalysin-mediated pathogenicity in C. albicans.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 6","pages":"e2504019"},"PeriodicalIF":3.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540570","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":"The photosensitizer DH-I-180-3 regulates intracellular bacterial growth by increasing the secretion of proinflammatory cytokines via the NF-κB- and MAPK-mediated signaling pathways and promoting phagosome maturation in Salmonella-infected mouse macrophages.","authors":"Hyo-Jung Kim, Eui-Kwon Jeong, Hyo-Ji Lee, Yu-Jin Jung","doi":"10.71150/jm.2502003","DOIUrl":"https://doi.org/10.71150/jm.2502003","url":null,"abstract":"<p><p>Photodynamic therapy (PDT) is a known strategy for treating cancer; in PDT, photosensitizers are activated by light stimulation and then induce reactive oxygen species (ROS) production to damage cancer tissues. Recently evidence has shown that PDT can also be used as a novel treatment strategy to control pathogenic bacteria. In previous studies, the photosensitizer DH-I-180-3 was reported to effectively regulate multidrug-resistant Mycobacterium tuberculosis growth. Here, we confirmed the effects of DH-I-180-3 on the antibacterial activity and inflammatory response of macrophages to Salmonella. Photoactivated DH-I-180-3 regulated intracellular bacterial growth in Salmonella-infected macrophages. Moreover, DH-I-180-3 increased intracellular ROS levels in Salmonella-infected macrophages. The phosphorylation of the intracellular signaling proteins IκBα and JNK1/2 was increased in DH-I-180-3-treated Salmonella-infected macrophages. Additionally, we observed that DH-I-180-3 significantly increased the mRNA expression and protein secretion of the proinflammatory cytokine TNF-α and promoted phagosome maturation by upregulating EEA1, LAMP1, and Cathepsin D in Salmonella-infected macrophages. Overall, these results demonstrate that photoactivated DH-I-180-3 enhances the bactericidal response to intracellular bacterial infection by promoting inflammatory signaling pathways and phagosome maturation. Therefore, DH-I-180-3 has the potential to be developed into PDT for treating bacterial-infection.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 6","pages":"e2502003"},"PeriodicalIF":3.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540574","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":"Microbial signatures in oral sites of patients with primary Sjögren's syndrome: Association with salivary gland hypofunction.","authors":"Sarah Kamounah, Arjun Sarathi, Christiane Elisabeth Sørensen, Manimozhiyan Arumugam, Anne Marie Lynge Pedersen","doi":"10.71150/jm.2501030","DOIUrl":"https://doi.org/10.71150/jm.2501030","url":null,"abstract":"<p><p>This study aimed to determine if the microbiota in four different oral sites and the oral health status differ between patients with primary Sjögren's syndrome (pSS), non-pSS sicca symptoms, and healthy controls. All participants underwent an interview and clinical oral examination. Stimulated whole saliva (SWS), supragingival plaque (SGP), buccal mucosa tissue (BLM), and tongue scrape (TGS) samples from 23 pSS patients, 36 patients with sicca symptoms, not fulfilling the classification criteria for pSS (non-pSS sicca), and 21 age-matched healthy controls (HC) were analyzed using V3-V4 16S rRNA gene amplicon sequencing, and determination of amplicon sequence variants (ASVs). PSS and non-pSS sicca patients did not differ with respect to oral health status, saliva flow rates, abundance of predominant genera, relative abundance on genus level or bacterial diversity in any of the oral sites. Both patient groups differed significantly from the healthy control group in the abundance of 61 ASVs across all sites. The alpha-diversity was lower in SGP from non-pSS sicca patients (p = 0.019), and in TGS from pSS patients (p = 0.04). The proportion of variation in the beta-diversity across all four sites could be explained by the diagnosis (pSS, non-pSS sicca, and HC). However, subgrouping of patients according to their stimulated salivary flow rates (SWS > 0.7 ml/min versus SWS ≤ 0.7 ml/min), revealed significantly different abundance of three ASVs in SWS, 11 in SGP, and six in TGS. Our findings suggest that hyposalivation rather than pSS itself modifies the microbial composition in oral site-specific patterns leading to oral diseases.</p>","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 6","pages":"e2501030"},"PeriodicalIF":3.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540571","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}