Streptomyces are a crucial source of bioactive secondary metabolites with significant clinical applications. Recent studies of bacterial and metagenome-assembled genomes have revealed that Streptomyces harbors a substantial number of uncharacterized silent secondary metabolite biosynthetic gene clusters (BGCs). These BGCs represent a vast diversity of biosynthetic pathways for natural product synthesis, indicating significant untapped potential for discovering new metabolites. To exploit this potential, genome mining using comprehensive strategies that leverage extensive genomic databases can be conducted. By linking BGCs to their encoded products and integrating genetic manipulation techniques, researchers can greatly enhance the identification of new secondary metabolites with therapeutic relevance. In this context, we present a step-by-step guide for using the antiSMASH pipeline to identify secondary metabolite-coding BGCs within the complete genome of a novel Streptomyces strain. This protocol also outlines gene manipulation methods that can be applied to Streptomyces to activate cryptic clusters of interest and validate the functions of biosynthetic genes. By following these guidelines, researchers can pave the way for discovering and characterizing valuable natural products.

Protein solubility is a critical factor in the production of recombinant proteins, which are widely used in various industries, including pharmaceuticals, diagnostics, and biotechnology. Predicting protein solubility remains a challenging task due to the complexity of protein structures and the multitude of factors influencing solubility. Recent advances in computational methods, particularly those based on machine learning, have provided powerful tools for predicting protein solubility, thereby reducing the need for extensive experimental trials. This review provides an overview of current computational approaches to predict protein solubility. We discuss the datasets, features, and algorithms employed in these models. The review aims to bridge the gap between computational predictions and experimental validations, fostering the development of more accurate and reliable solubility prediction models that can significantly enhance recombinant protein production.

The increasing environmental concerns regarding conventional plastics have led to a growing demand for sustainable alternatives, such as biodegradable plastics. Yeast cell factories, specifically Saccharomyces cerevisiae and Yarrowia lipolytica, have emerged as promising platforms for bioplastic production due to their scalability, robustness, and ease of manipulation. This review highlights synthetic biology approaches aimed at developing yeast cell factories to produce key biodegradable plastics, including polylactic acid (PLA), polyhydroxyalkanoates (PHAs), and poly (butylene adipate-co-terephthalate) (PBAT). We explore recent advancements in engineered yeast strains that utilize various synthetic biology strategies, such as the incorporation of new genetic elements at the gene, pathway, and cellular system levels. The combined efforts of metabolic engineering, protein engineering, and adaptive evolution have enhanced strain efficiency and maximized product yields. Additionally, this review addresses the importance of integrating computational tools and machine learning into the Design-Build-Test-Learn cycle for strain development. This integration aims to facilitate strain development while minimizing effort and maximizing performance. However, challenges remain in improving strain robustness and scaling up industrial production processes. By combining advanced synthetic biology techniques with computational approaches, yeast cell factories hold significant potential for the sustainable and scalable production of bioplastics, thus contributing to a greener bioeconomy.

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.

The escalating antibiotic resistance crisis poses a significant challenge to global public health, threatening the efficacy of current treatments and driving the emergence of multidrug-resistant pathogens. Among the various factors associated with bacterial antibiotic resistance, small regulatory RNAs (sRNAs) have emerged as pivotal post-transcriptional regulators which orchestrate bacterial adaptation to antibiotic pressure via diverse mechanisms. This review consolidates the current knowledge on sRNA-mediated mechanisms, focusing on drug uptake, drug efflux systems, lipopolysaccharides, cell wall modification, biofilm formation, and mutagenesis. Recent advances in transcriptomics and functional analyses have revealed novel sRNAs and their regulatory networks, expanding our understanding of resistance mechanisms. These findings highlight the potential of targeting sRNA-mediated pathways as an innovative therapeutic strategy to combat antibiotic resistance, and offer promising avenues for managing challenging bacterial infections.

Obesity is increasingly recognized as a systemic pro-inflammatory condition that influences not only metabolic and cardiovascular health but also the development and exacerbation of cutaneous inflammatory diseases. This review examines the interplay between obesity, microbial dysbiosis, and two archetypal inflammatory skin disorders—hidradenitis suppurativa (HS) and psoriasis. We highlight how obesity-induced changes in immune signaling, gut permeability, and microbiota composition—both in the gut and the skin—contribute to cutaneous inflammation. Special emphasis is placed on shared pathways such as the Th17/IL-23 and IL-22 signaling axes, adipokine imbalance, and microbial metabolites like short-chain fatty acids and lipopolysaccharides. The review critically evaluates the current literature, distinguishing preclinical insights from clinical evidence, and underscores the potential of microbiota-targeted therapies and metabolic interventions as adjunctive treatment strategies. By integrating metabolic, immunologic, and microbiome data, we synthesize emerging evidence to better understand the gut–skin–obesity interplay and guide future therapeutic innovations.

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.

This review explores current advancements in microbiome functional analysis enabled by next-generation sequencing technologies, which have transformed our understanding of microbial communities from mere taxonomic composition to their functional potential. We examine approaches that move beyond species identification to characterize microbial activities, interactions, and their roles in host health and disease. Genome-scale metabolic models allow for in-depth simulations of metabolic networks, enabling researchers to predict microbial metabolism, growth, and interspecies interactions in diverse environments. Additionally, computational methods for predicting metabolite profiles offer indirect insights into microbial metabolic outputs, which is crucial for identifying biomarkers and potential therapeutic targets. Functional pathway analysis tools further reveal microbial contributions to metabolic pathways, highlighting alterations in response to environmental changes and disease states. Together, these methods offer a powerful framework for understanding the complex metabolic interactions within microbial communities and their impact on host physiology. While significant progress has been made, challenges remain in the accuracy of predictive models and the completeness of reference databases, which limit the applicability of these methods in under-characterized ecosystems. The integration of these computational tools with multi-omic data holds promise for personalized approaches in precision medicine, allowing for targeted interventions that modulate the microbiome to improve health outcomes. This review highlights recent advances in microbiome functional analysis, providing a roadmap for future research and translational applications in human health and environmental microbiology.

Pathogenic fungi pose major threats to both global food security and human health, yet the molecular basis of their virulence remains only partially understood. Beyond genetic and transcriptional control, emerging evidence highlights protein glycosylation as a key post-translational modification that governs fungal development, stress adaptation, and host interactions. Glycosylation regulates protein folding, stability, trafficking, and immune evasion, thereby shaping infection processes across diverse pathogens. While extensively studied in model organisms, our understanding of glycosylation in pathogenic fungi remains fragmented and lacks a coherent framework linking glycosylation dynamics to fungal development and pathogenicity. This review synthesizes recent advances from proteomic, transcriptomic, and glycomic studies in pathogenic fungi, focusing on interspecific variation in glycogenes and enzymes, hierarchical regulatory networks, and glycoprotein-mediated mechanisms of virulence. Finally, we outline current challenges and highlight glycosylation-targeted strategies as promising avenues for antifungal intervention.

The widespread use of antibiotics in aquaculture has led to the emergence of multidrug-resistant pathogens and environmental concerns, highlighting the need for sustainable, eco-friendly alternatives. In this study, we isolated and characterized three novel bacteriophages from aquaculture effluents in Korean shrimp farms that target the key Vibrio pathogens, Vibrio harveyi, and Vibrio parahaemolyticus. Bacteriophages were isolated through environmental enrichment and serial purification using double-layer agar assays. Transmission electron microscopy revealed that the phages infecting V. harveyi, designated as vB_VhaS-MS01 and vB_VhaS-MS03, exhibited typical Siphoviridae morphology with long contractile tails and icosahedral heads, whereas the phage isolated from V. parahaemolyticus (vB_VpaP-MS02) displayed Podoviridae characteristics with an icosahedral head and short tail.

Whole-genome sequencing produced complete, circularized genomes of 81,710 bp for vB_VhaS-MS01, 81,874 bp for vB_VhaS-MS03, and 76,865 bp for vB_VpaP-MS02, each showing a modular genome organization typical of Caudoviricetes. Genomic and phylogenetic analyses based on the terminase large subunit gene revealed that although vB_VhaS-MS01 and vB_VhaS-MS03 were closely related, vB_VpaP-MS02 exhibited a distinct genomic architecture that reflects its unique morphology and host specificity. Collectively, these comparative analyses demonstrated that all three phages possess genetic sequences markedly different from those of previously reported bacteriophages, thereby establishing their novelty. One-step growth and multiplicity of infection (MOI) experiments demonstrated significant differences in replication kinetics, such as burst size and lytic efficiency, among the phages, with vB_VhaS-MS03 maintaining the most effective bacterial control, even at an MOI of 0.01. Additionally, host range assays showed that vB_VhaS-MS03 possessed a broader spectrum of activity, supporting its potential use as a stand-alone agent or key component of phage cocktails. These findings highlight the potential of region-specific phage therapy as a targeted and sustainable alternative to antibiotics for controlling Vibrio infections in aquaculture.

The global rise in obesity and its associated metabolic complications underscores the urgent need for safe and effective interventions. This study investigated the anti-obesity efficacy of a probiotic mixture containing Bifidobacterium breve BR3 and Lactiplantibacillus plantarum LP3 in C57BL/6 mice with high-fat diet (HFD)-induced obesity. After obesity was established by feeding a 60% kcal HFD, the probiotic mixture was administered orally for 4 weeks. Compared with the control group, mice receiving the L. plantarum LP3 and B. breve BR3 mixture exhibited significant reductions in body weight and total fat mass, as assessed by Dual-energy X-ray Absorptiometry (DXA) and Echo Magnetic Resonance Imaging (EchoMRI). The probiotic treatment also lowered serum Aspartate Aminotransferase (AST), Alanine Aminotransferase (ALT), and glucose levels, and attenuated lipid accumulation in both hepatic and epididymal adipose tissues. Transcriptomic profiling revealed upregulation of lipolytic genes (Sirt1, Pparα) and downregulation of lipogenic genes (Srebp1c, Fas), suggesting that the probiotic mixture promotes lipid catabolism while suppressing lipid synthesis. Additionally, serum adipokine levels were favorably modulated, indicating improved metabolic homeostasis. Gut microbiota analysis demonstrated an increased relative abundance of beneficial genera, including Akkermansia and Bacteroides, highlighting a microbiome-mediated contribution to the observed metabolic benefits. Overall, our findings indicate that the combined administration of Lactiplantibacillus plantarum LP3 and Bifidobacterium breve BR3 exerts multi-faceted anti-obesity effects by enhancing lipolysis, regulating lipid metabolism, and restoring a healthy gut microbial balance. This probiotic mixture represents a promising therapeutic approach for managing obesity and related metabolic disorders.

Truncal acne significantly impairs quality of life yet remains underexplored relative to facial acne, particularly with respect to fungal ecology. The trunk represents a distinct cutaneous niche characterized by thicker epidermis, larger follicular units, and frequent occlusion, and harbors a high abundance of Malassezia species. In this study, we used internal transcribed spacer 2 (ITS2) amplicon sequencing to characterize the truncal mycobiome in patients with acne and in healthy controls and to compare fungal community features across doxycycline exposure groups. Although serial sampling was planned, seven participants contributed a single follow-up sample after doxycycline treatment, and only two participants contributed multiple follow-up samples sufficient for true within-subject longitudinal analyses; therefore, most analyses represent exposure-stratified cross-sectional comparisons rather than confirmed temporal change. At baseline, truncal acne lesions exhibited increased fungal richness and distinct community composition compared with controls. Acne lesions were more frequently enriched for Malassezia globosa, whereas healthy controls were dominated by M. sympodialis. Across doxycycline exposure groups, fungal communities remained Malassezia-dominant with substantial inter-individual variability. Doxycycline exposure was associated with partial and heterogeneous differences in Malassezia species composition without uniform normalization toward control profiles. Because only fungal sequencing was performed, bacterial–fungal interactions were inferred from prior literature and not directly measured. These findings indicate that truncal acne is associated with a distinct fungal community structure and highlight the need for integrated, longitudinal multi-omics studies to clarify treatment-associated microbial dynamics.

Methane gas is recognized as a promising carbon substrate for the biosynthesis of value-added products due to its abundance and low price. Methanotrophs utilized methane as their sole source of carbon and energy, thus they can serve as efficient biocatalysts for methane bioconversion. Methanotrophs-catalyzed microbial bioconversion offer numerous advantages, compared to chemical processes. Current indirect chemical conversions of methane suffer from their energy-intensive processes and high capital expenditure. Methanotrophs can be cell factories capable of synthesizing various value-added products from methane such as methanol, organic acids, ectoine, polyhydroxyalkanoates, etc. However, the large-scale commercial implementation using methanotrophs remains a formidable challenge, primarily due to limitations in gas-liquid mass transfer and low metabolic capacity. This review explores recent advancements in methanotroph research, providing insights into their potential for enabling methane bioconversion.

Two Gram-stain-negative, aerobic, non-motile, rod-shaped bacterial strains, designated IMCC43444^T and IMCC44478^T, were isolated from surface seawater collected off Deokjeok Island and Jangbong Island, respectively, in the Yellow Sea. The two strains shared 100% 16S rRNA gene sequence similarity with each other but exhibited ≤ 96.2% similarity to validly published species of the genus Robiginitalea. Complete whole-genome sequences of IMCC43444^T and IMCC44478^T were 3.21 Mb and 3.30 Mb in size, with DNA G + C contents of 46.5% and 46.4%, respectively. Genome-based relatedness analyses revealed average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values of 90.7% and 42.9% between the two strains, which are well below the accepted species-level thresholds. Furthermore, ANI (≤ 70.2%) and dDDH (≤ 17.8%) values relative to type strains of Robiginitalea species supported the conclusion that strains IMCC43444^T and IMCC44478^T each represent novel species within the genus. Chemotaxonomic characterization showed that iso-C_15:0, iso-C_17:0 3-OH and iso-C_15:1 G were the major fatty acids of both strains; menaquinone-6 (MK-6) was the sole isoprenoid quinone; and the major polar lipids comprised phosphatidylethanolamine, glycolipids, aminolipids, phospholipids, and other unidentified lipids. Based on phylogenetic, genomic, and phenotypic evidence, strains IMCC43444^T and IMCC44478^T are proposed as two novel species, Robiginitalea rubriflava sp. nov. and Robiginitalea insularis sp. nov., respectively. The type strains are IMCC43444^T (= KCTC 102397^T = JCM 37893^T) and IMCC44478^T (= KCTC 102398^T = JCM 37894^T).

Evolution has been systematically exploited to engineer biological systems to obtain improved or novel functionalities by selecting beneficial mutations. Recent innovations in continuous targeted mutagenesis within living cells have emerged to generate large sequence diversities without requiring multiple steps. This review comprehensively introduces recent advancements in this field, categorizing them into three approaches depending on methods to create mutations: orthogonal error-prone DNA polymerases, site-specific base editors, and homologous recombination of mutagenic DNA fragments. Combined with high-throughput screening methods, these advances expedited evolution processes with significant reduction of labor and time. These approaches promise broader industrial and research applications, including enzyme improvement, metabolic engineering, and drug resistance studies.

Dengue, caused by four serotypes of dengue viruses (DENV-1 to DENV-4), is the most prevalent and widely mosquito-borne viral disease affecting humans. Dengue virus (DENV) infection has been reported in over 100 countries, and approximately half of the world's population is now at risk. The paucity of universally licensed DENV vaccines highlights the urgent need to address this public health concern. Action and attention to antibody-dependent enhancement increase the difficulty of vaccine development. With the worsening dengue fever epidemic, Dengvaxia^® (CYD-TDV) and Qdenga^® (TAK-003) have been approved for use in specific populations in affected areas. However, these vaccines do not provide a balanced immune response to all four DENV serotypes and the vaccination cannot cover all populations. There is still a need to develop a safe, broad-spectrum, and effective vaccine to address the increasing number of dengue cases worldwide. This review provides an overview of the existing DENV vaccines, as well as potential candidates for future studies on DENV vaccine development, and discusses the challenges and possible solutions in the field.

Existing microbial engineering strategies—encompassing metabolic engineering, systems biology, and systems metabolic engineering—have significantly enhanced the potential of microbial cell factories as sustainable alternatives to the petrochemical industry by optimizing metabolic pathways. Recently, systems metabolic engineering, which integrates tools from synthetic biology, enzyme engineering, omics technology, and evolutionary engineering, has been successfully developed. By leveraging modern engineering strategies within the Design-Build-Test-Learn (DBTL) cycle framework, these advancements have revolutionized the biosynthesis of valuable compounds. This review highlights recent progress in the metabolic engineering of Corynebacterium glutamicum, a versatile microbial platform, achieved through various approaches from traditional metabolic engineering to advanced systems metabolic engineering, all within the DBTL cycle. A particular focus is placed C5 platform chemicals derived from L-lysine, one of the key amino acid production pathways of C. glutamicum. The development of DBTL cycle-based metabolic engineering strategies for this process is discussed.

Next-generation sequencing (NGS) has become a powerful and efficient tool for surveying mycorrhizal mycobiome diversity, surpassing classical methods in accuracy and throughput. Long-read NGS techniques are increasingly applied under the assumption that they provide better taxonomic resolution, yet their use often lacks a balanced evaluation against the established strengths and limitations of widely used short-read NGS technologies. This study compares Illumina MiSeq and PacBio Sequel platforms in analyzing the mycorrhizal mycobiome of Pinus densiflora roots, focusing on how sequencing platforms and database choice influence taxonomic resolution and diversity patterns. Both platforms detected mycorrhizal taxa with similar taxonomic resolution, recovering nearly all taxa previously reported from pine roots. Most mycorrhizal taxa were shared between datasets, although several taxa were detected exclusively by one platform. In terms of diversity, the short-read dataset showed higher diversity due to greater sequencing depth, whereas the long-read dataset offered improved identification of rare or closely related taxa owing to longer sequence information. Moreover, supplementing reference databases with locally derived sequences enhanced taxonomic resolution and the detection of native taxa in both approaches, with a stronger effect for the long-read dataset. Overall, our results emphasize that short- and long-read sequencing each have distinct advantages for mycorrhizal community analysis, and that the use of curated local reference databases is essential to maximize taxonomic resolution and improve the detection of regionally unique taxa.

Two novel bacterial strains, designated CJ20^T and CJ99^T, belonging to the genus Sphingomonas, were isolated from the Han River in South Korea and a wetland in South Korea, respectively. Cells of both strains were Gram-stain-negative, aerobic, non-motile and yellow-pigmented. Strains were shown to grow optimally at 30˚C and pH 7 in the absence of NaCl on tryptic soy medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ20^T and CJ99^T belonged to the genus Sphingomonas and were most closely related to S. asaccharolytica Y-345^T and Sphingomonas koreensis JSS26^T with 97.87% and 97.58% 16S rRNA gene sequence similarities, respectively. Average nucleotide identity and digital DNA-DNA hybridization values of strain CJ20^T with S. asaccharolytica Y-345^T were 74.1% and 15.9%, respectively and those values of strain CJ99^T with S. koreensis JSS26^T were 73.9% and 15.6%, respectively. Both strains contained ubiquinone (Q-10) as the predominant respiratory quinone. The major polar lipids of strains CJ20^T and CJ99^T comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and sphingoglycolipid. The predominant fatty acids of both strains were summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c) and C_16:0. Based on polyphasic taxonomic analyses, strains CJ20^T and CJ99^T represent novel species of the genus Sphingomonas, for which names Sphingomonas degradans sp. nov. and Sphingomonas paludis are proposed, respectively. The type strains are CJ20^T (= KACC 23909 = JCM 37720) and CJ99^T (= KACC 24077 = JCM 37956).

Bandavirus dabieense, a single-stranded RNA virus, is the causative agent of severe fever with thrombocytopenia syndrome (SFTS), a disease associated with high fatality rates. Early and accurate diagnosis is essential for improving clinical outcomes, particularly given the limited therapeutic options and high mortality rates associated with SFTS. However, while highly sensitive, conventional diagnostic methods such as PCR and qRT-PCR require specialized laboratory facilities and trained personnel, making them impractical for rapid detection in resource-limited settings. To address these challenges, we developed a rapid and highly sensitive assay for Bandavirus dabieense detection by integrating reverse transcription loop-mediated isothermal amplification (RT-LAMP) with CRISPR/Cas12a technology. LAMP primers and guide RNA sequences were designed to target the L gene, ensuring broad detection across viral genotypes. The optimized assay demonstrated a detection limit of 5 RNA copies per reaction, showing more sensitivity than qRT-PCR, and exhibited 100% concordance with qRT-PCR results in clinical samples. Given its speed, accuracy, and field applicability, this LAMP-CRISPR/Cas12a-based assay represents a promising diagnostic tool for early SFTSV detection, particularly in resource-constrained environments where conventional molecular diagnostics are not readily available.

Chimeric antigen receptor (CAR)-T cell therapy holds significant potential for the treatment of solid tumors. However, immune suppression and tumor-specific barriers limit its application. Claudin 18.2 (CLDN18.2), a gastric lineage-specific tight junction protein highly expressed in gastric and pancreatic cancers, is a promising therapeutic target. In this study, we aimed to develop a next-generation tri-cistronic CLDN18.2-directed CAR-T cell platform that integrates a programmed cell death protein 1 (PD-1)/CD28 chimeric switch receptor with cyclophilin A (CypA). This platform sought to counteract PD-1–mediated immunosuppression and enhance T-cell activation and persistence. We generated CLDN18.2 CAR-T cells incorporating costimulatory inducible T-cell costimulator (ICOS) domains using lentiviral vector-based recombinant engineering. We further evaluated their cytokine release, cytotoxic activity, and safety profiles. In vitro, tri-cistronic CAR-T cells exhibited markedly increased interferon γ and tumor necrosis factor α secretion and enhanced cytotoxicity against CLDN18.2-positive gastric cancer cells compared with conventional CAR-T constructs. In vivo, these cells showed superior antitumor efficacy and sustained tumor regression without observable toxicity in xenograft gastric cancer models. Collectively, these findings demonstrate that the integration of PD-1/CD28 signaling and CypA within a tri-cistronic framework significantly reinforces CAR-T cell functionality and durability. This suggests strong clinical potential as a next-generation immunotherapy for solid tumors.

Two aerobic, Gram-stain-negative, non-motile and rod-shaped bacterial strains designated GGG-R5^T and M4-18^T were isolated from flowers of golden wave (Coreopsis grandiflora) and rice paddy soil, respectively in the Republic of Korea. Both strains were pigmented and produced flexirubin-type pigments. Based on phylogenetic analysis using 16S rRNA gene sequence, both strains were placed within the genus Mucilaginibacter with M. agri R11^T and M. jinjuensis YC7004^T both being the closest relatives to GGG-R5^T (97.7%) and in case of M4-18^T, M. ginsenosidivorax KHI28^T (98.5%) was the nearest neighbor. Characteristic to genus Mucilaginibacter, the major cellular fatty acids in both strains were iso-C_15:0, iso-C_{17:0 3-OH}, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c); menaquinone-7 was the major menaquinone and phosphatidylethanolamine was the major polar lipid observed. Comparison of genome sequences with the other members of Mucilaginibacter indicated orthologous average nucleotide identity (orthoANI) at 73.3–73.5% for GGG-R5^T and 78.9–88.5% for M4-18^T. Digital DNA-DNA hybridization (dDDH) values ranged at 19.1–19.7% between GGG-R5^T and its neighbor species. In case of M4-18^T, the observed range was at 21.9–36.6%. Considering the 16S rRNA similarity, orthoANI and dDDH values as well as comparison of phenotypic and chemotaxonomic characteristics indicated that both strains belonged to genus Mucilaginibacter but were distinctly distinguishable from previously described species. The strains GGG-R5^T and M4-18^T, therefore represent distinct novel species for which names Mucilaginibacter florum GGG-R5^T and Mucilaginibacter oryzagri M4-18^T are proposed. The type strains are GGG-R5^T (= KACC 22063^T = JCM 36590^T) and M4-18^T (= KACC 22773^T = JCM 35894^T).

Precise and tunable gene expression is crucial for various biotechnological applications, including protein overexpression, fine-tuned metabolic pathway engineering, and dynamic gene regulation. Untranslated regions (UTRs) of mRNAs have emerged as key regulatory elements that modulate transcription and translation. In this review, we explore recent advances in UTR engineering strategies for bacterial gene expression optimization. We discuss approaches for enhancing protein expression through AU-rich elements, RG4 structures, and synthetic dual UTRs, as well as ProQC systems that improve translation fidelity. Additionally, we examine strategies for fine-tuning gene expression using UTR libraries and synthetic terminators that balance metabolic flux. Finally, we highlight riboswitches and toehold switches, which enable dynamic gene regulation in response to environmental or metabolic cues. The integration of these UTR-based regulatory tools provides a versatile and modular framework for optimizing bacterial gene expression, enhancing metabolic engineering, and advancing synthetic biology applications.

Collagenase and keratinase are two important proteolytic enzymes with recognized applications in biotechnology and medicine, particularly in the enzymatic removal of necrotic tissue and the control of infection. In the present work, a soil isolate of Bacillus subtilis strain AB2 (PX453297.1) was optimized for enzyme production under different nutritional and physicochemical conditions. The enzymes were recovered by ammonium sulphate precipitation and dialysis, examined by SDS-PAGE and zymography, and further assessed for pH and temperature optima, stability, the influence of metal ions, and kinetic parameters. Maximum collagenase activity (4.41 ± 0.22 U/ml) was observed at 37°C and pH 7.5 in a glucose–peptone medium, whereas keratinase production was enhanced between 37 and 40°C at pH 7.5 in lactose–peptone medium. Protein bands of approximately 55 and 33 kDa were detected, representing 6.2- and 5.5-fold purification. Collagenase showed an alkaline optimum (pH 10.0, 37–45°C) with K_m 0.31% and V_max 1.92 U/ml, while keratinase exhibited dual optima (pH 3.0 and ~7.0) with K_m 0.27% and V_max 0.84 U/ml. Biofilm assays revealed that collagenase reduced pre-formed biomass by 62–68% and viable counts by 1.1–1.7 log₁₀, clearly outperforming keratinase (41–57%, 0.7–1.2 log₁₀). When combined with conventional antibiotics, both enzymes potentiated activity, with notable synergy between collagenase and oxacillin against Staphylococcus aureus (FICI 0.31–0.37), ciprofloxacin against Pseudomonas aeruginosa (FICI 0.37–0.50), and meropenem against Klebsiella pneumoniae (FICI 0.28–0.44). These results indicate that B. subtilis AB2 produces collagenase and keratinase with distinct biochemical characteristics and strong antibiofilm properties, underscoring their promise as adjuncts in chronic wound care as well as in industrial applications.

Microbial biosynthesis using yeast species offers numerous advantages to produce industrially relevant biofuels and biochemicals. Conventional metabolic engineering approaches in yeast focus on biosynthetic pathways in the cytoplasm, but these approaches are disturbed by various undesired factors including metabolic crosstalk, competing pathways and insufficient precursors. Given that eukaryotic cells contain subcellular organelles with distinct physicochemical properties, an emerging strategy to overcome cytosolic pathway engineering bottlenecks is through repurposing these organelles as specialized microbial cell factories for enhanced production of valuable chemicals. Here, we review recent progress and significant outcomes of harnessing organelle engineering for biofuels and biochemicals production in both conventional and non-conventional yeasts. We highlight key engineering strategies for the compartmentalization of biosynthetic pathways within specific organelles such as mitochondria, peroxisomes, and endoplasmic reticulum; involved in engineering of signal peptide, cofactor and energy enhancement, organelle biogenesis and dual subcellular engineering. Finally, we discuss the potential and challenges of organelle engineering for future studies and propose an automated pipeline to fully exploit this approach.

Tella is a traditional beverage widely accepted by consumers, despite the lack of product consistency owing to its reliance on natural fermentation. This study aimed to identify potential industrial lactic acid bacteria (LAB) starter cultures based on their technological properties. Seven LAB strains isolated from Tella were characterized for their carbohydrate utilization, salt content, temperature, and acid tolerances, growth and acidification rates, and metabolite profiles. Most strains efficiently utilized various carbohydrates, with Lactiplantibacillus plantarum TDM41 showing exceptional versatility. The strains exhibited similar growth characteristics. Principal component analysis of stress tolerance properties revealed that L. plantarum TDM41, Pediococcus pentosaceus TAA01, and Leuconostoc mesenteroides TDB22 exhibited superior tolerance ability. Strong acidification properties were detected in the L. plantarum TDM41, P. pentosaceus TAA01, and Leuconostoc mesenteroides TDB22 strains after 24 h incubation at 30°C. L. plantarum TDM41 displayed the fastest acidification rate throughout the analysis period. All LAB strains produced significant amounts of diverse organic acids, including lactic acid, citric acid, acetic acid, malic acid, and succinic acid, with lactic acid being the primary acid produced by each strain. Overall, strains L. plantarum TDM41 and P. pentosaceus TAA01 prove to be potential candidates for Tella industrial starter cultures and similar cereal products owing to their robust technological properties.

Two Gram-stain-positive, facultatively anaerobic, rod-shaped, and non-motile lactic acid bacterial strains, designated as strains CBA3605^T and CBA3606^T, were isolated from kimchi, a traditional Korean fermented food. Both strains were oxidase- and catalase-negative, non-spore-forming, non-hemolytic, and non-gas-producing. Optimal growth conditions for the two strains were observed at 30°C, pH 5.0, and 0% NaCl. The two genomes were composed of a circular chromosome and three plasmids and the DNA G + C content of 43.0%, respectively. Strains CBA3605^T and CBA3606^T were most closely related to Lactiplantibacillus (Lp.) pingfangensis 382-1^T with 16S rRNA sequence similarity of 99.4% and 99.1%, respectively. However, the orthologous average nucleotide identities between CBA3605^T and CBA3606^T were 91.7%, and those with strain 382-1^T were 76.9% and 76.5%, respectively. Digital DNA–DNA hybridization values between CBA3605^T and CBA3606^T were 45.0%, and those with strain 382-1^T were 21.4% and 21.0%, respectively. The major fatty acids detected in both strains included C_16:0, C_18:1 ω9c, and summed features 7 (C_19:1 ω7c, C_19:1 ω6c, C_19:0 cyclo ω10c, and/or C_19:0 ω6c). The peptidoglycan of both strains CBA3605^T and CBA3606^T contained meso-diaminopimelic acid and was classified as A4α type (L-Lys–D-Asp). In polar lipid analyses, only strain CBA3605^T contained aminophosphoglycolipid, which was absent in CBA3606^T, although both strains harbored same major polar lipids (diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine). Based on phenotypic, phylogenetic, genomic, biochemical, and chemotaxonomic analyses, strains CBA3605^T and CBA3606^T represent two novel species of the genus Lactiplantibacillus, for which the names Lactiplantibacillus koreensis sp. nov. and Lactiplantibacillus kimchii sp. nov. are proposed, with CBA3605^T (= KACC 81073BP^T = JCM 37965^T), and CBA3606^T (= KACC 81074BP^T = JCM 37966^T) as the type strains.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have emerged as powerful tools for precise genome editing, leading to a revolution in genetic research and biotechnology across diverse organisms including microalgae. Since the 1950s, microalgal production has evolved from initial cultivation under controlled conditions to advanced metabolic engineering to meet industrial demands. However, effective genetic modification in microalgae has faced significant challenges, including issues with transformation efficiency, limited target selection, and genetic differences between species, as interspecies genetic variation limits the use of genetic tools from one species to another. This review summarized recent advancements in CRISPR systems applied to microalgae, with a focus on improving gene editing precision and efficiency, while addressing organism-specific challenges. We also discuss notable successes in utilizing the class 2 CRISPR-associated (Cas) proteins, including Cas9 and Cas12a, as well as emerging CRISPR-based approaches tailored to overcome microalgal cellular barriers. Additionally, we propose future perspectives for utilizing CRISPR/Cas strategies in microalgal biotechnology.

Acid mine drainage (AMD) poses a serious threat to rice paddy ecosystems, yet its impact on the composition and dynamics of soil nitrogen-fixing microorganisms remains poorly understood. In this study, a pot experiment was conducted using paddy soil collected from a mining area under three pollution treatments, to analyze changes in the structure of the nitrogen-fixing microbial community across different growth stages and treatments. The results showed that AMD irrigation led to soil acidification, sulfate accumulation, and a significant reduction in the diversity of nitrogen-fixing microorganisms in the root zone. Compared to the control, the Shannon index decreased by 11.65–24.79% in contaminated soil. LEfSe analysis indicated that AMD enriched metal-tolerant and sulfate-resistant microbial taxa. Irrigation with clean water was insufficient to fully restore the soil environment. The assembly process of the AMD soil community was governed solely by stochastic processes, indicating structural instability of the community. This study suggests that remediation strategies should prioritize neutralizing acidity and restoring nutrient balance to support the stability and recovery of nitrogen-fixing microorganisms. These findings provide new insight into how AMD disrupts diazotrophic community assembly, with direct implications for paddy soil restoration.

Marine organisms often form symbiotic relationships with various microorganisms to adapt and thrive in harsh environments. These symbiotic microbes contribute to host survival by providing nutrition, modulating the hosts’ immune system, and supporting overall physiological stability. Advances in high-throughput sequencing technologies have enabled a deeper understanding of the structure and function of symbiotic microbial communities, as well as host-microbe interactions. Notably, symbiotic bacteria associated with marine invertebrates such as corals and sponges are recognized as a potential source of useful bioactive compounds, including antibiotics and enzymes. However, obtaining high-quality microbial DNA from host tissues still remains a technical challenge due to the presence of unknown substances. This study focuses on optimizing sample preparation and DNA extraction procedures and additional purification to improve the recovery of microbial DNA while minimizing host DNA contamination. Comparison between several methods was conducted using sponge samples to evaluate DNA quality and microbial recovery. A sample designated as 2110BU-001 was collected from the east coast of the Republic of Korea and used for culture-independent microbial cell isolation. Total bacterial DNA was extracted by using a manual Phenol-Chloroform protocol and three commercial kits. DNA extracted using the standard manual method showed both the highest yield and the largest fragment size. However, PCR (Polymerase chain reaction) test showed that quality of manually extracted DNA was not enough for sequencing. Therefore, the quality of DNA was improved through additional purification steps. Briefly, host eukaryotic cells were removed by mechanical process and almost only bacterial DNA was successfully obtained by combination of manual extraction method and further purification processes. The established protocol was successfully introduced to extraction of metagenomic DNA from mussel and jellyfish microbiomes, indicating that it can be widely applied to various marine organisms.

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.

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 COVID-19 pandemic highlighted the critical role of reliable molecular diagnostics in outbreak response and the vulnerabilities of existing systems to delays and reagent instability. Armored RNA technology, which packages RNA within bacteriophage-derived capsids, offers a robust solution by combining nuclease resistance, safety, and versatility into a single platform. Armored RNA has become a trusted internal and external control for RT-qPCR and RT-LAMP, enabling accurate detection across a wide range of viral pathogens. Also, recent advances in alternative expression systems, such as plant-based and cell-free platforms, as well as the use of more stable scaffolds from bacteriophage Qβ, are enhancing yield, stability, and accessibility of armored RNA. Engineering innovations, including capsid polymorphism and optimized downstream purification, further improve efficiency and broaden possible applications. Looking ahead, armored RNA holds promise not only as a diagnostic standard but also as a delivery vehicle for vaccines and therapeutics. Encapsulation of self-amplifying RNA, small interfering RNA, or microRNA could open new pathways for rapid-response vaccines and targeted therapies, aligning this technology with the future of precision medicine. By uniting stability, scalability, and adaptability, armored RNA represents a critical component of global health preparedness, with the potential to strengthen diagnostic resilience and accelerate biomedical countermeasures in future pandemics.

Sarcopenia is an age-related condition marked by a reduction in muscle mass and strength, and it is associated with impaired muscle regeneration and differentiation. While diseases like cardiovascular and chronic liver disease can induce sarcopenia, there is limited evidence regarding the specific diseases and mechanisms responsible for its development. In skeletal muscle, the loss of muscle mass is accompanied by a decrease in myofilament proteins and the inhibition of muscle differentiation in satellite cells. Bioactive compounds obtained from natural products have been traditionally used as therapeutics for diverse conditions. In this report, we investigated the effect of cinchonidine (CD) extracted from Cinchona tree on muscle differentiation of mouse satellite cells, and myoblast cell lines. CD significantly inhibited muscle differentiation by suppressing myotube formation and gene expression of myogenesis markers. In addition, CD reduced muscle differentiation by blocking phosphorylation of insulin receptor substrate 1 (IRS-1) during insulin-induced signal transduction. Therefore, the results show that CD, an antimalarial agent, inhibited muscle differentiation through the suppression of IRS-1 phosphorylation, suggesting that sarcopenia can be induced by CD.

Bladder cancer is the most common malignancy of the urinary tract and is a major health burden globally. Recent advances in microbiome research have revealed that the urinary tract harbors a resident microbial community, overturning the long-held belief in its sterility. Increasing evidence suggests that microbial dysbiosis and microbially derived metabolites contribute to bladder cancer carcinogenesis, progression, and therapeutic responses. Distinct microbial signatures have been observed in bladder cancer patients, with notable differences across disease stages and between primary and recurrent cases. Mechanistic studies have demonstrated that microbe-associated metabolites and toxins can drive DNA damage, chronic inflammation, extracellular matrix remodeling, and epithelial–mesenchymal transition. In addition, biofilm formation allows bacteria to evade immune responses and promotes persistent inflammation, creating a tumor-permissive niche. Beyond pathogenesis, microbial activity also influences therapeutic outcomes; for instance, some microbial pathways can inactivate frontline chemotherapy, while others generate metabolites with anti-tumor properties. Collectively, these patterns define a microbiota–metabolite–immunity axis, presenting opportunities for precision oncology. Targeting microbial pathways, profiling urinary microbiota, and harnessing beneficial metabolites offer promising advancements in biomarker discovery, prognostic refinement, and the development of novel therapeutic strategies for bladder cancer.

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.

Minicells, which are anucleate cells generated by irregular cell division, are emerging as promising drug delivery systems owing to advances in synthetic biology. However, their development is largely limited to a few model bacteria, highlighting the need to explore minicell platforms in alternative hosts. Lactiplantibacillus plantarum (L. plantarum), a probiotic bacterium classified as Generally Recognized as Safe, is an ideal candidate for such exploration. Minicell-producing L. plantarum was engineered by deleting the putative minD gene via plasmid-mediated homologous recombination, which inactivates cell division to form spherical minicells. Anucleate cells were isolated through differential centrifugation and filtration, followed by additional drug treatment to completely eliminate progenitor cells. Microscopy and flow cytometry analyses of the purified sample confirmed the absence of progenitor cells by DAPI staining. This protocol effectively produces bacterial minicells from L. plantarum for use in various biotechnological applications, including therapeutic agent delivery.

Merkel cell polyomavirus (MCPyV) is the primary causative agent of Merkel cell carcinoma, a rare but highly aggressive neuroendocrine skin cancer. Large T antigen (LT), one of two oncoproteins encoded by MCPyV, sustains the proliferation of MCPyV-infected tumor cells. LT contains multiple protein-binding motifs that mediate interactions with diverse host proteins essential for its function. Among these, ubiquitin-specific protease 7 (Usp7), a deubiquitinase that regulates the stability of multiple substrates, including p53, is a recently identified LT-interacting protein. In the present study, we characterized the intermolecular interaction between Usp7 and MCPyV LT using biochemical analyses and AlphaFold-based structural modeling. Our results demonstrate that MCPyV LT directly interacts with the TRAF domain of Usp7 via a unique binding motif that is distinct from the canonical sequence. Moreover, MCPyV LT attenuates the p53-deubiquitinating activity of Usp7, providing insights into the molecular function of this viral oncoprotein.

Streptococcus pneumoniae is a conditionally pathogenic bacteria that colonizes the nasopharynx of 27% to 65% of children and 10% of adults. Capsular polysaccharides are the most critical virulence factor of S. pneumoniae, and nonencapsulated strains are usually non-pathogenic. Previous studies have shown that glucose regulates capsule synthesis. To investigate the mechanism of carbon metabolism regulatory factors CcpA and HPr regulating capsule synthesis in the presence of glucose as the sole carbon source, we constructed deletion mutants (D39ΔccpA and ΔptsH) and complemented strains (D39ΔccpA::ccpA and ΔptsH::ptsH). In this study, we found that the promoting effect of capsule synthesis by glucose disappeared after the deletion of ccpA and ptsH, and demonstrated that the protein CcpA regulates capsule synthesis by binding to the cps promoter and altering the transcription level of the cps gene cluster. Increased glucose concentration up-regulated the level of HPr-Ser46~P, which enhanced the binding ability of CcpA to the DNA sequence of the cps promoter, thus promoting capsule synthesis. HPr also has a regulatory effect on capsule synthesis. These insights reveal a new synthesis mechanism of capsular polysaccharide and provide a new strategy of antibacterial drugs for S. pneumoniae.

The increase of sequence data in public nucleotide databases has made DNA sequence-based identification an indispensable tool for fungal identification. However, the large proportion of mislabeled sequence data in public databases leads to frequent misidentifications. Inaccurate identification is causing severe problems, especially for industrial and clinical fungi, and edible mushrooms. Existing species identification pipelines require separate validation of a dataset obtained from public databases containing mislabeled taxonomic identifications. To address this issue, we developed FunVIP, a fully automated phylogeny-based fungal validation and identification pipeline (https://github.com/Changwanseo/FunVIP). FunVIP employs phylogeny-based identification with validation, where the result is achievable only with a query, database, and a single command. FunVIP command comprises nine steps within a workflow: input management, sequence-set organization, alignment, trimming, concatenation, model selection, tree inference, tree interpretation, and report generation. Users may acquire identification results, phylogenetic tree evidence, and reports of conflicts and issues detected in multiple checkpoints during the analysis. The conflicting sample validation performance of FunVIP was demonstrated by re-iterating the manual revision of a fungal genus with a database with mislabeled sequences, Fuscoporia. We also compared the identification performance of FunVIP with BLAST and q2-feature-classifier with two mass double-revised fungal datasets, Sanghuangporus and Aspergillus section Terrei. Therefore, with its automatic validation ability and high identification performance, FunVIP proves to be a highly promising tool for achieving easy and accurate fungal identification.

Antarctic fungi can effectively adapt to extreme environments, which leads to the production of unique bioactive compounds. Studies on the discovery of fungi in the diverse environments of Antarctica and their potential applications are increasing, yet remain limited. In this study, fungi were isolated from various substrates on the Fildes Peninsula in Antarctica and screened for their antibiosis activity against two significant plant pathogenic fungi, Botrytis cinerea and Fusarium culmorum. Phylogenetic analysis using multiple genetic markers revealed that the isolated Antarctic fungal strains are diverse, some of which are novel, emphasizing the underexplored biodiversity of Antarctic fungi. These findings suggest that these fungi have potential for the development of new antifungal agents that can be applied in agriculture to manage fungal plant pathogens. Furthermore, the antibiosis activities of the isolated Antarctic fungi were evaluated using a dual-culture assay. The results indicated that several strains from the genera Cyathicula, Penicillium, and Pseudeurotium significantly inhibited pathogen growth, with Penicillium pancosmium showing the highest inhibitory activity against Botrytis cinerea. Similarly, Aspergillus and Tolypocladium strains exhibited strong antagonistic effects against Fusarium culmorum. This study enhances our understanding of Antarctic fungal diversity and highlights its potential for biotechnological applications.

This study aims to examine the mechanism by which vitamin D mitigates bronchiolitis caused by respiratory syncytial virus (RSV) through the regulation of RSV nonstructural protein 1 (NS1)-TUFM-mediated mitophagy in bronchial epithelial cells. Clinical serum and PBMC samples from RSV-infected children and healthy controls were analyzed for vitamin D, mitochondrial DNA, mitophagy markers (LC3, ATG5, VDAC1, TOMM20, and COXIV), TUFM, and inflammatory cytokines (IL-6, IL-8, and TNF-α). In vitro, human bronchial epithelial cells Beas-2B were transfected with RSV-NS1 plasmid and TUFM silencing or overexpression constructs. Vitamin D (0.1–10 μM) was administered to evaluate mitophagy inhibition using Western blot, immunofluorescence, and JC-1 staining. NS1-TUFM interaction was confirmed by co-immunoprecipitation. RSV-positive patients exhibited reduced serum vitamin D, elevated TUFM and mitophagy markers, impaired mitochondrial mass, and increased inflammation. Vitamin D inversely correlated with LC3 and TUFM. RSV-NS1 overexpression induced mitochondrial translocation of NS1, TUFM-dependent mitophagy activation, and mitochondrial dysfunction (JC-1 depolarization). Vitamin D (10 μM) suppressed mitophagy by redistributing NS1 to the cytosol and reducing mitochondrial TUFM. TUFM overexpression abolished the protective effects of vitamin D on mitophagy and inflammation. In conclusion, vitamin D inhibits mitophagy in bronchial epithelial cells infected with RSV by disrupting NS1-TUFM interaction, suggesting that the vitamin D-TUFM axis may serve as a potential therapeutic target.

Synbiotics have become a new-age treatment tool for limiting the progression of metabolic dysfunction-associated steatotic liver disease; however, inclusive comparisons of various synbiotic treatments are still lacking. Here, we have explored and evaluated multiple synbiotic combinations incorporating three distinctive prebiotics, lactitol, lactulose and fructooligosaccharides. Of the synbiotic treatments evaluated, a combination of fructooligosaccharides and probiotics (FOS+Pro) exhibited superior protection against western diet-induced liver degeneration. This synbiotic (FOS+Pro) combination resulted in the lowest body weight gains, liver weights and liver/body weight ratios. The FOS+Pro synbiotic combination substantially alleviated liver histopathological markers and reduced serum AST and cholesterol levels. FOS+Pro ameliorated hepatic inflammation by lowering expression of proinflammatory markers including TNF-α, IL-1β, IL-6, and CCL2. FOS+Pro significantly improved steatosis by restricting the expression of lipid metabolic regulators (ACC1, FAS) and lipid transporters (CD36) in the liver. These findings are critical in suggesting that synbiotic treatments are capable of restraining western diet-induced metabolic dysfunction in the liver. Additionally, this study demonstrated that adding probiotic strains amplified the effectiveness of fructooligosaccharides but not all prebiotics.

Basal cell carcinoma (BCC) is the most common form of skin cancer, with ultraviolet radiation recognized as the primary environmental driver; however, the potential contribution of alterations in the skin microbiota remains incompletely understood, particularly in Asian populations. This exploratory pilot study describes bacterial community patterns in BCC lesions compared with contralateral clinically normal skin in 20 Korean patients. Lesional and contralateral samples were obtained using paired skin swabs and punch biopsies and analyzed by full-length 16S rRNA gene sequencing, with targeted quantitative PCR (qPCR) of the roxP antioxidant gene of Cutibacterium acnes. Given the low-biomass nature of skin samples and the exploratory design, analyses focused on descriptive trends rather than confirmatory inference. Across available samples, C. acnes was the dominant taxon, with a trend toward lower relative abundance in BCC lesions, particularly in biopsy-derived datasets. Microbial evenness appeared higher in lesions than controls. Predictive functional profiling suggested reduced representation of vitamin B6 metabolism pathways in lesions, while qPCR analysis of swab samples showed a trend toward lower roxP/16S rRNA ratios in BCC-associated microbiota. These findings should be interpreted cautiously in light of methodological constraints, including sample heterogeneity, lidocaine exposure prior to biopsy, absence of sequencing-based negative controls, and reliance on predictive functional inference. Overall, this pilot study highlights potential differences in skin bacterial community structure between BCC lesions and contralateral skin in a Korean cohort. Larger, methodologically optimized studies incorporating metagenomic and functional validation will be required to determine whether these microbiota shifts contribute to, or result from, BCC-associated changes in the cutaneous environment.

Keratinase kerZJ is a multifunctional protease with potential as a feed additive and functional ingredient. Here we performed an integrated multi‑omics evaluation of its biosafety and impact on gut homeostasis in mice. Our findings confirm that kerZJ is well-tolerated, with no evidence of systemic toxicity or intestinal epithelial damage. Integrated transcriptomic and proteomic analyses revealed that kerZJ reinforces intestinal barrier integrity by upregulating extracellular matrix components, including collagen IV, and modulates mucosal immunity by enhancing B-cell activation and antimicrobial peptide defenses without inducing inflammation. Furthermore, kerZJ administration led to a significant upregulation of digestive enzymes and a dose-dependent increase in short-chain fatty acids production. Microbiome analysis showed that while high-dose kerZJ altered community composition, it enriched for beneficial taxa like Lactobacillaceae and did not induce dysbiosis. These results demonstrate that kerZJ safely enhances gut barrier function, promotes a favorable immune and metabolic environment, and fosters a resilient gut ecosystem, supporting its development as a safe feed additive and nutraceutical component.

A Gram-stain-negative, aerobic, non-motile, rod-shaped, and orange-pigmented bacterium, designated CJ426^T, was isolated from ginseng soil in Anseong, Korea. Strain CJ426^T grew optimally on Reasoner’s 2A agar at 30°C and pH 7.0 in the absence of NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CJ426^T belonged to the family Chitinophagaceae and had the highest sequence similarity with Niabella hibiscisoli KACC 18857^T (98.7%). The 16S rRNA gene sequence similarities with other members of the genus Niabella ranged from 92.3% to 98.1%. Phylogenomic analyses and overall genomic relatedness indices, including average nucleotide identity, average amino acid identity, and the percentage of conserved proteins values, supported the classification of strain CJ426^T as a representative of a novel genus within the family Chitinophagaceae. Furthermore, genome-based analyses suggested that five members of the genus Niabella, including N. aquatica, N. defluvii, N. ginsengisoli, N. hibiscisoli, and, N. yanshanensis, should be separated from other Niabella species and be assigned as a novel genus. The major isoprenoid quinone of strain CJ426^T was menaquinone-7 (MK-7). The predominant polar lipids were phosphatidylethanolamine and six unidentified aminolipids. The major fatty acids were iso-C_15:0, iso-C_15:1 G, and iso-C_17:0 3-OH. The genome of strain CJ426^T was 6.3 Mbp in size, consisting of three contigs, with a G + C content of 41.9%. Based on a polyphasic taxonomic approach, strain CJ426^T represents a novel genus and species within the family Chitinophagaceae, for which the name Paraniabella aurantiaca gen. nov., sp. nov. is proposed. The type strain is CJ426^T (= KACC 23908^T = JCM 37728^T).

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 ATCC 43894 (also known as EDL932) has been widely used as a reference strain for studying the pathophysiology of EHEC. To elucidate the role of a large virulence plasmid pO157 and its relationship with acid resistance, for example, both EHEC ATCC 43894 and its pO157-cured derivative strain 277 were well studied. However, it is unclear whether or not these two strains are isogenic and share the same genetic background. To address this question, we analyzed the whole genome sequences of ATCC 43894 and 277. As expected, three and two closed contigs were identified from ATCC 43894 and 277, respectively; two contigs shared in both strains were a chromosome and a small un-identified plasmid, and one contig found only in ATCC 43894 was pO157. Surprisingly, our pan-genome analyses of the two sequences revealed several genetic variations including frameshift, substitution, and deletion mutations. In particular, the deletion mutation of hdeD and gadE in ATCC 43894 was identified, and further PCR analysis also confirmed their deletion of a 2.5-kb fragment harboring hdeD, gadE, and mdtE in ATCC 43894. Taken together, our findings demonstrate that EHEC ATCC 43894 harbors genetic mutations affecting glutamate-dependent acid resistance system and imply that the pO157-cured EHEC 277 may not be isogenic to ATCC 43894. This is the first report that such genetic differences between both reference strains of EHEC should be considered in future studies on pathogenic E. coli.

Mycobacterium avium complex (MAC) organisms are widespread environmental pathogens associated with chronic pulmonary infections. Although M. avium is known to invade epithelial cells, the molecular mechanisms underlying this process remain incompletely understood. In this study, we identified a novel role for MAVRS09815 (formerly MAV2054), a family 2A encapsulin nanocompartment shell protein, in mediating bacterial adhesion, epithelial cell invasion, and in vivo virulence. We engineered a recombinant M. smegmatis strain expressing MAV2054 (Ms_2054) and an M. avium MAV2054 deletion mutant (Δ2054). Ms_2054 exhibited enhanced epithelial invasion, whereas Δ2054 showed reduced intracellular survival. Recombinant MAV2054 protein was bound directly to human epithelial cells in a dose-dependent manner. Pretreatment of host cells with cytochalasin D or vinblastine significantly inhibited bacterial internalization, indicating that MAV2054-mediated invasion is cytoskeleton-dependent. Confocal and scanning electron microscopy revealed MAV2054-dependent membrane rearrangements during infection. Pull-down assays demonstrated that MAV2054 activates Cdc42, a key regulator of actin polymerization, with reduced activation observed in Δ2054-infected cells. In a murine intratracheal infection model, the Δ2054 exhibited significantly reduced bacterial burdens and lung inflammation compared to the wild type. These findings demonstrate that MAV2054 enhances M. avium virulence by promoting epithelial cell invasion through Cdc42-dependent cytoskeletal remodeling. This study reveals a previously unrecognized role for an encapsulin-like protein in host-pathogen interactions and highlights its potential as a therapeutic target in MAC infections.

Atopic dermatitis (AD) is a widespread inflammatory skin condition that affects the population worldwide. Given the implication of microbiota in AD pathogenesis, we investigated whether human-derived Lactobacillus strains could modulate AD. In this study, we identified Lactobacillus crispatus KBL693 as a probiotic candidate for AD treatment. In vitro, KBL693 suppressed mast cell degranulation and IL-4 production by T cells, suggesting its ability to attenuate key type 2 immune responses. Consistent outcomes were observed in a murine AD model, where oral administration of KBL693 alleviated disease symptoms and reduced hallmark type 2 immune markers, including plasma IgE as well as IL-4, IL-5, and IL-13 levels in skin lesions. In addition to downregulating these AD-associated immune responses, KBL693 promoted regulatory T cell (Treg) expansion in mesenteric lymph nodes, indicating its potential to restore immune balance. Collectively, these findings highlight the therapeutic potential of KBL693 for AD through enhancement of Tregs and suppression of type 2 immune responses.