Journal of Microbiology最新文献

Two Gram-stain-negative, obligately aerobic, non-motile, short rod-shaped bacteria, designated IMCC43871T and IMCC45206T, were isolated from coastal surface seawater collected from the Yellow Sea and the South Sea of Korea, respectively. The two strains shared 99.2% 16S rRNA gene sequence similarity with each other and exhibited ≤ 98.4% similarity to three described Rubrivirga species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between IMCC43871T and IMCC45206T were 88.5% and 36.3%, respectively, confirming that they represent two distinct species. Their ANI (≤ 77.7%) and dDDH (≤ 21.4%) values relative to the type strains of the genus Rubrivirga further supported the recognition of strains IMCC43871T and IMCC45206T as two novel species within the genus. The complete genomes of IMCC43871T (4.17 Mb, 71.8% G + C content) and IMCC45206T (4.17 Mb, 72.8% G + C content) fall within the known genomic range of the genus. Cellular fatty acid, quinone, and polar lipid profiles were consistent with the chemotaxonomic features of the genus Rubrivirga, supporting their affiliation with the genus. Based on phylogenetic, genomic, and phenotypic evidence, strains IMCC43871T and IMCC45206T are proposed as two novel species, Rubrivirga aquatilis sp. nov. and Rubrivirga halophila sp. nov., respectively. The type strains are IMCC43871T (= KCTC 102072T = NBRC 116463T) and IMCC45206T (= KCTC 92925T = NBRC 116172T = CCTCC AB 2023136T).

Akkermansia muciniphila (AKK, A. muciniphila) fortifies the intestinal barrier, inhibits the colonization of pathogenic bacteria, and protects the host's health. Nevertheless, the existing literature offers inadequate evidence to ascertain whether A. muciniphila can effectively treat Candida albicans (C. albicans) infections in vitro, and the underlying mechanisms remain ambiguous. This study, animal models were established through gavage with clinical isolates of C. albicans to induce gastrointestinal tract colonization and subsequent translocation infection. The models were subsequently administered A. muciniphila. We examined the analysis of 16S rRNA gene sequencing, metabolomics of colonic contents, and transcriptomics of colonic tissue. The intestinal barrier, inflammatory responses, and immune cell infiltration are analyzed. This study revealed that A. muciniphila markedly mitigated C. albicans translocation infection and modified the intestinal microbial community structure and metabolic attributes in model mice. After administering A. muciniphila to the translocation infection group, there was a notable increase in the prevalence of bacteria that produce short-chain fatty acids, including Eubacterium_F. Moreover, there was a significant increase in the levels of specific pathogens, including Faecalibaculum, Turicibacter, and Turicimonas. The study demonstrated that A. muciniphila treatment can improve the composition of intestinal microbiota and metabolites, augment the tight junctions of colonic tissue and diminish systemic inflammatory response. This presents an innovative therapeutic approach for the potential treatment of intestinal C. albicans infection using A. muciniphila.

Strains Mo2-6T, S9, KG4-3T, and 50Mo3-2, identified as coagulase-negative, Gram-stain-positive, halotolerant, non-motile coccoid bacteria, were isolated from traditional Korean soybean foods. Strains Mo2-6T and S9 were both catalase- and oxidase-negative, whereas KG4-3T and 50Mo3-2 were catalase-positive but oxidase-negative. The optimal growth conditions for Mo2-6T and S9 were 30°C, 2% NaCl, and pH 7.0, while KG4-3T and 50Mo3-2 grew best at 35°C, 2% NaCl, and pH 7.0. All strains contained menaquinone-7 as the predominant isoprenoid quinone, with anteiso-C15:0 and iso-C15:0 as the major cellular fatty acids (> 10%). Additionally, anteiso-C13:0 was a major fatty acid in strain KG4-3T. The DNA G + C contents of strains Mo2-6T, S9, KG4-3T, and 50Mo3-2 were 33.4%, 33.3%, 32.5%, and 32.7%, respectively. Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strains Mo2-6T and S9, as well as KG4-3T and 50Mo3-2, formed distinct lineages within the genus Staphylococcus. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses confirmed that strains Mo2-6T and S9, as well as KG4-3T and 50Mo3-2, belonged to the same species. Meanwhile, dDDH and ANI values between strains Mo2-6T and KG4-3T, as well as comparisons with other Staphylococcus type strains, were below the species delineation thresholds, indicating they represent novel species. Based on phenotypic, chemotaxonomic, and molecular data, we propose strain Mo2-6T as the type strain of Staphylococcus parequorum sp. nov. (=KACC 23685T =JCM 37038T) and strain KG4-3T as the type strain of Staphylococcus halotolerans sp. nov. (=KACC 23684T =JCM 37037T).

The 2015 Zika virus (ZIKV) outbreak in Brazil and its global spread underscored the urgent need for effective and broadly protective vaccines. While C57BL/6 and BALB/c mice are widely used in preclinical vaccine research, direct comparisons of their ability to elicit ZIKV-specific neutralizing antibodies (nAbs) remain limited. This study aimed to systematically evaluate and compare the immunogenic potential of these two common mouse strains across diverse vaccine platforms, focusing on their capacity to generate functional neutralizing antibody responses. We assessed nAb and IgG responses following four vaccination strategies: (1) DNA vaccine encoding prMEΔTM followed by E protein domain III boost, (2) recombinant EΔTM protein expressed using baculovirus system, (3) formalin-inactivated ZIKV, and (4) live ZIKV. Although both strains generated detectable ZIKV- and E protein-specific IgG, the magnitude and quality of responses varied by vaccine platform and strain. Notably, C57BL/6 mice consistently mounted significantly higher nAb titers than BALB/c mice across all immunization groups, including subunit- and whole-virus-based vaccines. In contrast, BALB/c mice showed lower or undetectable nAb responses, despite comparable or higher total IgG levels in some cases. These findings show that host genetic background is a critical determinant of vaccine-induced neutralization and underscore the importance of selecting appropriate animal models in ZIKV vaccine development. C57BL/6 mice, due to their robust nAb responses, represent a reliable model for evaluating vaccine immunogenicity. Conversely, the limited nAb responses in BALB/c mice position them as a potential low-responder model, offering a stringent system to test the potency and breadth of protective immunity under suboptimal conditions.

CRISPR-Cas technologies have emerged as powerful and versatile tools in gene therapy. In addition to the widely used SpCas9 system, alternative platforms including modified amino acid sequences, size-optimized variants, and other Cas enzymes from diverse bacterial species have been developed to apply this technology in various genetic contexts. In addition, base editors and prime editors for precise gene editing, the Cas13 system targeting RNA, and CRISPRa/i systems have enabled diverse and adaptable approaches for genome and RNA editing, as well as for regulating gene expression. Typically, CRISPR-Cas components are transported to the target in the form of DNA, RNA, or ribonucleoprotein complexes using various delivery methods, such as electroporation, adeno-associated viruses, and lipid nanoparticles. To amplify therapeutic efficiency, continued developments in targeted delivery technologies are required, with increased safety and stability of therapeutic biomolecules. CRISPR-based therapeutics hold an inexhaustible potential for the treatment of many diseases, including rare congenital diseases, by making permanent corrections at the genomic DNA level. In this review, we present various CRISPR-based tools, their delivery systems, and clinical progress in the CRISPR-Cas technology, highlighting its innovative prospects for gene therapy.

Human papillomaviruses (HPVs) cause abnormal cellular proliferation, leading to malignant or benign lesions, such as cervical cancer and warts. The genome of HPV16, the most prevalent high-risk oncogenic genotype within the Alphapapillomavirus genus, encodes two oncoproteins. One of these proteins, E7, interacts with multiple host proteins and modulates their functions through distinct pathways. The CR2 domain of HPV16 E7 was recently reported to interact with the μ2 subunit of clathrin-adaptor protein 2 (AP2-μ2), an adaptor complex involved in cargo internalization during clathrin-mediated endocytosis. In this study, to provide molecular insights into their intermolecular interactions, we determined the crystal structures of AP2-μ2 in complex with the HPV16 E7-derived peptides. Subsequent biochemical analyses revealed that this interaction is primarily maintained by the Y-x-x-Φ motif and further supported by acidic cluster residues of HPV16 E7. Finally, sequence alignment of the E7 CR2 domains from various HPV genotypes showed that the AP2-μ2-binding motif is largely conserved in Alpha-, Beta-, and Mupapillomaviruses, but not in Nu- and Gammapapillomaviruses.

Two rod-shaped, Gram-positive, spore-forming, motile, and strictly anaerobic bacteria, FM7315T and FM7330T were isolated from Myeolchi-jeot, a traditional Korean fermented anchovy. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene and genome sequences revealed that strains FM7315T and FM7330T represent novel species within the genus Haloimpatiens. The genome sizes of strains FM7315T and FM7330T were 3,052,517 bp and 4,194,114 bp, respectively, with G + C contents of 29.7 mol% and 28.0 mol%, respectively. Strain FM7315T exhibited growth at 20-37°C, 0-2% NaCl, and pH range of 5.0-8.0, whereas strain FM7330T grew at 25-45°C, 0-4% NaCl, and pH range of 5.0-9.0. Strain FM7315T contains C14:0, C16:0, C18:1 ω9c, Summed Feature 3 (C16:1 ω7c/C16:1 ω6c), and Summed Feature 8 (C18:1 ω7c/C18:1 ω6c) as major fatty acids, along with diphosphatidylglycerol, phosphatidylglycerol, glycolipid, two aminophospholipids, and five unidentified lipids. Strain FM7330T contains C16:0, C17:1 ω8c, and C18:1 ω9c as major fatty acids, along with diphosphatidylglycerol, two phosphatidylglycerols, four aminophospholipids, and six unidentified lipids. Based on their phenotypic, chemotaxonomic, and molecular characteristics, strains FM7315T and FM7330T represent two novel species of the genus Haloimpatiens, for which the names Haloimpatiens sporogenes sp. nov. (FM7315T = KCTC 25939T = JCM 37574T) and Haloimpatiens myeolchijeotgali sp. nov. (FM7330T = KCTC 25938T = JCM 37575T) have been proposed.

Pectin-rich biomass, derived from fruit and citrus processing waste, presents a promising yet underutilized resource for sustainable biofuel and biochemical production. Its low lignin content and high concentrations of fermentable sugars, including D-galacturonic acid, L-arabinose, and D-xylose, make it an attractive feedstock. Unlike lignocellulosic biomass, pectin-rich hydrolysates require milder pretreatment, improving sugar recovery efficiency. However, industrial strains such as Saccharomyces cerevisiae exhibit strong glucose preference, limiting the efficient co-fermentation of mixed sugars. While prior reviews have broadly addressed lignocellulosic biomass utilization, this mini-review uniquely centers on the specific metabolic challenges and opportunities associated with pectin-rich feedstocks. In addition to incorporating established strategies for the co-utilization of cellobiose and xylose, we highlight recent advances that allow S. cerevisiae to metabolize carbon sources specifically from pectin-rich biomass, such as L-arabinose and D-galacturonic acid-monomers not prevalent in traditional lignocellulosic biomass. By integrating discussions on sugar transport engineering, redox balancing, and pathway optimization, this review offers a comprehensive framework to overcome glucose repression and support efficient co-fermentation of carbon sources from conventional and pectin-rich biomass. Drawing on these advances, we outline practical strategies to enhance fermentation performance and expand the valorization of food processing residues in biomanufacturing.

The global spread of COVID-19 has underscored the urgent need for advanced tools to study emerging coronaviruses. Reverse genetics systems have become indispensable for dissecting viral gene functions, developing live-attenuated vaccine candidates, and identifying antiviral targets. In this study, we describe a robust and efficient reverse genetics platform for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The system is based on the assembly of a full-length infectious cDNA clone from seven overlapping fragments, each flanked by homologous sequences to facilitate seamless assembly using the Gibson assembly method. Individual cloning of each fragment into plasmids enables modular manipulation of the viral genome, allowing rapid site-directed mutagenesis by fragment exchange. Infectious recombinant virus was successfully recovered from the assembled cDNA, exhibiting uniform plaque morphology and genetic homogeneity compared to clinical isolates. Additionally, fluorescent reporter viruses were generated to enable real-time visualization of infection, and the effects of different mammalian promoters on viral rescue were evaluated. This reverse genetics platform enables efficient generation and manipulation of recombinant SARS-CoV-2, providing a valuable resource for virological research and the development of preventive and therapeutic antiviral measures.

Extracellular vesicles derived from probiotics have received considerable attention for their pivotal role in bacterial‒host communication. These nanosized, bilayer-encapsulated vesicles carry diverse bioactive molecules, such as proteins, lipids, nucleic acids, and metabolites. Currently, ample evidence has emerged that probiotic extracellular vesicles may modulate several processes of host physiological hemostasis and offer therapeutic benefits. This review examines the biogenesis, composition, and immunomodulatory functions of probiotic-derived extracellular vesicles in probiotic-host interactions, highlighting the therapeutic potential of probiotic extracellular vesicles in the diagnosis and treatment of conditions such as cancer and inflammatory bowel disease. We further summarize the techniques for the separation and purification of extracellular vesicles, providing a methodological foundation for future research and applications. Although the field of probiotic extracellular vesicle research is still in its infancy, the prospects for their application in the biomedical field are broad, potentially emerging as a novel therapeutic approach.