Protein quality control systems are increasingly recognized as a critical determinant of bacterial survival and antibiotic tolerance. Conventional antibiotics predominantly target nucleic acids, protein synthesis, or cell wall synthesis, yet bacterial adaptation and resistance emergence remain major challenges. Targeting the bacterial protein quality control machineries including molecular chaperones and proteases offers a promising strategy to overcome these limitations. Recent advances include small molecules and adaptor/degron mimetics that modulate the activities of chaperones and proteases, aggregation-prone peptides (APPs) that induce proteotoxic stress, and bacterial PROTAC (BacPROTAC) strategies that redirect endogenous proteases. Notably, persister and viable-but-non-culturable (VBNC) cells, which tolerate conventional antibiotics, remain susceptible to proteostasis-targeted approaches, thereby enabling killing in both actively dividing and dormant populations. Furthermore, synergistic strategies combining chaperone inhibition or protease activation with conventional antibiotics enhance bactericidal efficacy, suggesting a potential avenue to mitigate antimicrobial resistance. This review summarizes the mechanistic basis, recent developments, and translational potential of proteostasis-centered antibacterial strategies.

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.

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.

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.

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).

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.

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.

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 threat of antimicrobial resistance has renewed global interest in peptide-based antibiotics as adaptable and effective alternatives to conventional small molecules. Peptides possess diverse mechanisms of action, high target specificity, and structural flexibility, which collectively limit the emergence of resistance. This review outlines recent advances spanning the discovery, optimization, and application of peptide antibiotics, from their biological origins and structural classifications to emerging strategies involving artificial intelligence, synthetic biology, and modern delivery technologies. Peptide antibiotics can be categorized by origin as natural, semi-synthetic, or fully synthetic, and further organized by structural class such as α-helical, β-sheet, cyclic, and extended forms. They are also grouped by function into membrane-targeted and non-membrane-targeted types. These classification schemes are not only descriptive but also critical for understanding the therapeutic potential of peptides, as each category presents distinct advantages and engineering challenges that influence stability, specificity, and overall clinical performance. Advances in artificial intelligence, synthetic biology, and continuous manufacturing are reshaping how peptide drugs are designed and produced, while innovations in drug delivery systems are addressing critical issues of stability and bioavailability. Together, these developments are laying the foundation for a new generation of peptide-based therapeutics capable of meeting the evolving challenges of antimicrobial resistance.

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.

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.

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.

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.

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.

Antimicrobial resistance (AMR) poses an ongoing threat to global health, with the number of deaths directly attributable to AMR projected to rise to 8 million. One of the main reasons for the current crisis is the depletion of antibiotic candidates in clinical pipelines. To address this, more preclinical candidates must be advanced into development. However, the scientific challenges and limited economic incentives associated with antibiotic research have further aggravated the situation. Antibiotic hybrids, which combine two antibiotics with different modes of action, have emerged as a promising strategy to overcome AMR and are already being developed for clinical use. This approach takes advantage of the strong selective pressure exerted when two bactericidal agents act simultaneously. Importantly, because hybrids are administered as a single chemical entity, they may offer advantages over conventional combination therapies, such as simplified pharmacokinetics and dosing. Furthermore, since clinically validated antibiotics are used as the building blocks of hybrids, this strategy provides an efficient platform for generating new lead compounds. Recently, the concept of antibiotic hybrids has expanded beyond antibiotic–antibiotic conjugates to include the attachment of functional molecules designed to mitigate the disadvantages of the parent antibiotics. In this review, we summarize the definition of antibiotic hybrids, highlight representative compounds that have entered clinical evaluation, and discuss recent advances in their development.

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).

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.

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.

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.

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.

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.

Adeno-associated virus (AAV) commonly infects humans and non-human primates, generally inducing mild or even asymptomatic outcomes. AAVs have been shaped and diversified by evolutionary pressures, resulting in the identification of 13 serotypes thus far. Each serotype of AAV exhibits distinct tissue tropisms, targeting various organs, including the lung, central nervous system (CNS), liver, and skeletal muscle, thereby establishing AAVs as widely utilized vectors for therapeutic gene delivery. Bioinformatics analysis of specific viruses enables the inference of evolutionary patterns and offers valuable insights for predicting the emergence of novel viruses. While DNA sequence-based analysis has effectively facilitated the observation of mutation patterns accumulating within specific genes, it often provides limited insight into the actual impact of these mutations on proteins, the fundamental functional units. Utilizing proteotyping, an amino acid sequence-based comparative analysis, we identified hypervariable regions (HVR) within the AAV Cap gene and revealed concentrated evolutionary pressures in serotypes 4, 5, 11, and 12. Furthermore, we found that AAV-5 proteins exhibited considerable amino acid sequence divergence compared to those of other serotypes. Despite divergence, all AAV-5 proteins maintained a noticeable structural similarity to their counterparts in other serotypes. Our findings provide sequence-based insights into the evolutionary processes of AAV, facilitating the efficient identification of novel viruses.

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.

Gut microbiome imbalance can induce inflammatory responses via Toll-like receptor 2 (TLR2) signaling pathways. Lactobacillus spp., popularly applied as probiotics in both humans and animals, have come into the spotlight for their strong immunomodulatory effects. We aimed to evaluate the immunomodulatory potential of live or pasteurized Lacticaseibacillus paracasei (L. paracasei) KBL382, isolated from healthy Korean individuals, in an in vitro monocytic THP-1 cell model. Live L. paracasei KBL382 significantly increased TLR2 and MyD88 expressions and induced IRAK1 expression, irrespective of lipopolysaccharide (LPS) stimulation (p < 0.05). Under LPS stimulation, THP-1 cells treated with live L. paracasei KBL382 showed significantly increased interleukin (IL)-6 and IL-10 levels (p < 0.05). Pasteurized L. paracasei exhibited a decrease in IL-12 levels (p < 0.05). Moreover, live L. paracasei KBL382 also markedly elevated A20 and SOCS1 expressions, the critical negative regulators of inflammation, regardless of LPS stimulation (p < 0.05). The expression of IRAK3, another negative regulator of inflammation, was increased in THP-1 cells with live L. paracasei KBL382 under LPS stimulation (p < 0.05). Our findings demonstrate that L. paracasei KBL382 contributes to the immunomodulation in THP-1 cells by coordinating both positive and negative regulatory signaling. L. paracasei KBL382 could be used as a promising probiotic strain for attenuating chronic inflammation through the gut-immune axis mechanisms.

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.

Fucoxanthin has gained attention for its beneficial effects, including anti-cancer, anti-obesity, and anti-inflammatory activities. A benthic marine diatom Melosira nummuloides is a promising candidate for fucoxanthin production. Nevertheless, industrial-scale cultivation remains constrained by suboptimal growth performance and the lack of species-tailored media. This study aimed to develop a cost-effective medium for enhancing biomass and fucoxanthin production in M. nummuloides by modifying the conventional F/2 medium based on species-specific intracellular nutrient stoichiometry. The cellular molar N:P:Si ratio of M. nummuloides was identified as 13:1:12.3. Despite nitrogen reduction by 36.13% relative to F/2 medium, M. nummuloides cultivated in the Melosira-Optimized Medium using Fumed Silica (MOM-FS) was well grown, achieving biomass concentration of 261 mg/L on day 4—approximately 1.21-fold higher than that obtained with F/2. In addition, MOM-FS enhanced biomass-associated fucoxanthin yield by 10.3% and biogenic silica yield by 20.8% relative to the F/2. The use of MOM-FS reduced total medium costs by 28.3%, fucoxanthin production cost by 36.8%, and bio-silica production cost by 28.3%. Overall, these findings indicate that the cost-effective medium developed here provides a practical, efficient, and economically viable framework for large-scale cultivation of M. nummuloides and the co-production of fucoxanthin and bio-silica.

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.

Ribosomes are essential macromolecular machines that facilitate protein synthesis and have long been recognized as effective targets for antimicrobial agents. While structural differences between prokaryotic and eukaryotic ribosomes form the basis for selective antibiotics against bacteria, similar approaches for developing antifungal agents targeting ribosomes have remained limited due to the high sequence and structural conservation with human ribosomes. However, emerging insights into ribosome homeostasis, including ribosome biogenesis, turnover, and hibernation, have uncovered a set of ribosome-associated proteins whose function is critical yet display greater sequence divergence from their human counterparts. These observations suggest that these regulatory components may represent viable antifungal targets by disrupting fungal proteostasis. The present review aims to explore this developing concept by examining ribosome-associated factors and considering whether short ribosomal protein-derived peptides may eventually serve as druggable molecules for selectively modulating these pathways in fungal pathogens.

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.

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.

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.

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.

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.

Truncal acne represents a biologically distinct manifestation of acne vulgaris, yet its fungal ecology remains incompletely characterized. Previous work using internal transcribed spacer 2 (ITS2) sequencing suggested that truncal acne is associated with altered fungal richness and Malassezia species composition; however, fungal marker choice may influence ecological inference, particularly in sebaceous skin dominated by Malassezia. In this study, we characterized the truncal skin mycobiome of patients with truncal acne and healthy controls using internal transcribed spacer 1 (ITS1) amplicon sequencing. Skin swabs were collected from the upper back, and fungal communities were analyzed using QIIME 2 with taxonomic assignment against the UNITE v10.0 database. Baseline acne–control differences and doxycycline-associated patterns were evaluated using alpha- and beta-diversity metrics and differential abundance analyses. Doxycycline-associated patterns were assessed using paired, within-patient pre- and post-exposure comparisons. ITS1 profiling demonstrated that truncal acne was associated with altered baseline fungal ecology compared with controls, characterized by reduced alpha diversity and ASV-level differences within Malassezia-dominated communities. Beta-diversity analyses showed substantial overlap between acne and control samples, indicating limited global separation. Following doxycycline exposure, fungal communities remained Malassezia-dominant and did not demonstrate uniform convergence toward control profiles; instead, species- and ASV-level differences were heterogeneous across individuals and exposure durations. Together with prior ITS2-based findings, these results underscore the importance of marker-dependent perspectives when interpreting fungal ecology in sebaceous skin.

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.

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.

β-Lactam antibiotics marked the beginning of an era of effective and safe treatment for bacterial infections and remain the most widely prescribed antibacterial agents today. However, the emergence of antibiotic-resistant bacteria threatens a return to the pre-antibiotic era. In particular, bacterial expression of β-lactamases inactivating β-lactam antibiotics presents a challenge in antimicrobial therapy. While inhibitors against β-lactamases have been developed to protect the therapeutic efficacy of β-lactam antibiotics, the clinical use of β-lactamase inhibitors is constrained due to their limited inhibition spectrum and the emergence of inhibitor-resistant β-lactamase variants. As an effort to tackle this issue, here we reviewed the structural and mechanistic features of β-lactamases and their FDA-approved inhibitors. Moreover, mutations in clinically isolated β-lactamases that confer resistance against their inhibitors are compiled. The comprehensive overview offered in this review aims to support and stimulate the design of next-generation β-lactamase inhibitors for combating β-lactamase-mediated antibiotic resistance.

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.

Actinobacteria, a phylum of Gram-positive bacteria, are renowned for their remarkable ability to produce antibacterial natural products. The National Institute of Biological Resources (NIBR) of Korea maintains a collection of Korean native actinobacteria. In this study, we explored the phylogenetic and biosynthetic diversity of the NIBR actinobacteria collection to assess its potential as a source of new antibacterial natural products. A 16S rDNA-based phylogenetic analysis revealed a high level of genetic diversity within the collection, with a predominance of Streptomyces, along with rare actinobacterial genera such as Kitasatospora and Micromonospora. Additionally, genetic network analysis of biosynthetic gene clusters (BGCs) from 15 sequenced NIBR actinobacterial strains demonstrated extensive BGC diversity, with many clusters identified as cryptic. Screening of culture extracts for antibacterial activity, followed by dereplication of active extracts, suggested the presence of potentially novel antibacterial natural products. Activity-guided isolation and whole-genome sequencing of the active strain KU57 led to the isolation of one new and three known svetamycin congeners along with their BGC. Overall, our findings highlight the NIBR actinobacteria collection as a valuable source for the discovery of new antibacterial natural products.

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were thought to be carried-out by anaerobic bacteria constrained to anoxic conditions as they use nitrate (NO₃^-) as a terminal electron acceptor instead of molecular O₂. Three soil bacilli, Neobacillus spp. strains PS2-9 and PS3-12 and Bacillus salipaludis PS3-36, were isolated from rice paddy field soil in Korea. The bacterial strains were selected as possible candidates performing aerobic denitrification and DNRA as they were observed to reduce NO₃^- and produce extracellular NH₄⁺ regardless of oxygen presence at the initial screening. Whole genome sequencing revealed that these strains possessed all the denitrification and DNRA functional genes in their genomes, including the nirK, nosZ, nirB, and nrfA genes, which were simultaneously cotranscribed under aerobic condition. The ratio between the assimilatory and dissimilatory NO₃^- reduction pathways depended on the availability of a nitrogen source for cell growth, other than NO₃^-. Based on the phenotypic and transcriptional analyses of the NO₃^- reductions, all three of the facultative anaerobic strains reduced NO₃^- likely in both assimilatory and dissimilatory pathways under both aerobic and anoxic conditions. To our knowledge, this is the first report that describes coexistence of NO₃^- assimilation, denitrification, and DNRA in a Bacillus or Neobacillus strain under aerobic condition. These strains may play a pivotal role in the soil nitrogen cycle.

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.

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.

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.

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.

Dual specificity phosphatases (DUSPs), a subfamily of the protein tyrosine phosphatase (PTP) family, dephosphorylate not only phosphotyrosine but also phosphoserine and phosphothreonine residues. Beyond the 26 members of this family in humans, DUSPs represent the only type of PTPs found across a wide range of microorganisms, including bacteria, archaea, and viruses. This review presents a comprehensive structural analysis of human and microbial DUSPs. These proteins commonly share core features, such as a typical DUSP fold, shallow active site pocket, signature active site motif known as the P-loop, and conserved aspartate residue that acts as a general acid/base. However, DUSPs from diverse microorganisms also display unique structural and functional characteristics. Pseudomonas aeruginosa TpbA is the only bacterial DUSP identified to date, while a second candidate was proposed in this review. Archaeal DUSPs are hyperthermostable, contain a unique motif in their P-loops, and employ dual general acid/base residues. Poxviral DUSPs are characterized by the formation of domain-swapped homodimers. The presence of DUSPs across all domains of life and viruses, along with their low specificity for phosphorylated amino acids and structural similarity to classical PTPs, suggests that DUSPs represent the ancestral form of PTPs.

Strains Mo2-6^T, S9, KG4-3^T, and 50Mo3-2, identified as coagulase-negative, Gram-stain-positive, halotolerant, non-motile coccoid bacteria, were isolated from traditional Korean soybean foods. Strains Mo2-6^T and S9 were both catalase- and oxidase-negative, whereas KG4-3^T and 50Mo3-2 were catalase-positive but oxidase-negative. The optimal growth conditions for Mo2-6^T and S9 were 30°C, 2% NaCl, and pH 7.0, while KG4-3^T 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-C_15:0 and iso-C_15:0 as the major cellular fatty acids (> 10%). Additionally, anteiso-C_13:0 was a major fatty acid in strain KG4-3^T. The DNA G + C contents of strains Mo2-6^T, S9, KG4-3^T, 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 Mo2-6^T and S9, as well as KG4-3^T and 50Mo3-2, formed distinct lineages within the genus Staphylococcus. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses confirmed that strains Mo2-6^T and S9, as well as KG4-3^T and 50Mo3-2, belonged to the same species. Meanwhile, dDDH and ANI values between strains Mo2-6^T and KG4-3^T, 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 Mo2-6^T as the type strain of Staphylococcus parequorum sp. nov. (=KACC 23685^T =JCM 37038^T) and strain KG4-3^T as the type strain of Staphylococcus halotolerans sp. nov. (=KACC 23684^T =JCM 37037^T).

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.

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.

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.