Antimicrobial resistance poses a major global health challenge, and infections caused by multidrug-resistant Gram-negative bacteria are associated with substantial morbidity and mortality. In contrast to many Gram-positive pathogens, Gram-negative bacteria combine intrinsic barriers with acquired determinants, including enzymatic drug inactivation, reduced outer membrane permeability, active efflux, and target modifications, which collectively compromise the efficacy of multiple antibiotic classes. Previous reviews have largely catalogued resistant pathogens or antimicrobial agents. This review provides a mechanism-focused overview of antimicrobial resistance in clinically important Gram-negative bacteria and explains how dominant resistance determinants translate into clinically relevant failure modes, such as delayed effective therapy, limited treatment options, and increased reliance on toxic last-line agents. Current and emerging therapeutic strategies are discussed through a mechanism-based lens, emphasizing newer β-lactam/β-lactamase inhibitor combinations and nontraditional approaches, including phages, antivirulence, and microbiome-based interventions. This review highlights the conceptual links between resistance mechanisms, clinical impact, and rational therapeutic choices and identifies priorities for future research aimed at mitigating antimicrobial-resistant Gram-negative infections.

Fungal extracellular vesicles (EVs) have emerged as critical mediators of fungal physiology, virulence, and host–pathogen interactions. Since their first description in Cryptococcus neoformans, EVs have been identified in several fungal species and shown to transport a broad repertoire of bioactive cargo. Increasing evidence indicates that fungal EVs participate in multiple biological processes, including cell wall remodeling, stress adaptation, biofilm formation, antifungal resistance, and modulation of host immune responses. Recent advances in cryo-electron microscopy, multi-omics approaches, and functional genetics have substantially expanded our understanding of the molecular mechanisms governing EV biogenesis, cargo selection, and extracellular trafficking. These studies have further revealed that EV cargo loading is a highly regulated process linked to intracellular proteostasis, glycosylation, lipid homeostasis, and environmental adaptation. In parallel, the intrinsic immunogenicity and structural stability of fungal EVs have highlighted their translational potential as diagnostic biomarkers, vaccine platforms, therapeutic targets, and nanoscale delivery systems. Given the increasing global burden of invasive fungal infections, this review focuses on EVs derived from clinically relevant human fungal pathogens. We summarize recent advances in EV biogenesis, cargo regulation, their roles in pathogenesis, highlight emerging translational applications, and discuss key unresolved questions and future research directions in the field.

The global rise of multidrug-resistant bacteria poses a critical threat to public health, and bacteriophage-derived endolysins have emerged as promising alternatives to conventional antibiotics. The engineered endolysin LNT113, derived from the Escherichia coli phage PBEC131 endolysin EC340, exhibits potent lytic activity against Gram-negative bacteria. This study investigated the transcriptomic responses of E. coli to sublethal LNT113 stress and identified genetic determinants required for bacterial adaptation to endolysin-induced stress. Transcriptomic analysis identified 552 differentially expressed genes (DEGs) following sublethal LNT113 exposure. Thirteen DEGs associated with stress response and envelope maintenance were individually deleted to generate thirteen mutant strains and to functionally evaluate their roles in bacterial stress tolerance. Among these, the ΔfabB and Δ(prmB–yfcL) mutants exhibited significantly reduced survival under sublethal LNT113 exposure, indicating increased susceptibility to the endolysin. Regarding the prmB–yfcL operon, individual genes were deleted to determine the gene critical for bacterial tolerance. Deletion of aroC and mepA rendered E. coli more susceptible to LNT113. Furthermore, 1-N-phenylnaphthylamine uptake assays demonstrated increased membrane permeability in the ΔfabB, ΔaroC, and ΔmepA mutants. Complementation with pWSK129::fabB, pWSK129::aroC, and pWSK129::mepA restored membrane integrity in the respective mutant strains. These findings suggest that fabB-mediated unsaturated fatty acid biosynthesis and mepA-dependent peptidoglycan remodeling are critical for maintaining envelope integrity under endolysin stress, whereas aroC may indirectly support bacterial tolerance to LNT113 via metabolic adaptation. This study provides insights into bacterial responses to LNT113 and offers a foundation for optimizing endolysin-based therapeutic strategies.

This study compared the rhizosphere microbial communities of two closely related Monotropastrum species (M. humile, Mh; and M. humile var. glaberrima, Mhg) and identified key soil factors associated with their assembly. Bacterial and fungal communities were profiled by Illumina high-throughput sequencing, and soil physicochemical properties were assessed across multiple sites in Zhejiang Province, China. The bacterial communities of both species were dominated by Proteobacteria and Acidobacteriota at the phylum level, while the dominant fungal groups belonged to Ascomycota and Basidiomycota. The two plants shared several dominant bacterial genera, including Serratia, Burkholderia-Caballeronia-Paraburkholderia, and Bradyrhizobium, as well as common dominant fungal genera such as Saitozyma and Podila. Despite these similarities, species-specific enrichment patterns were observed. The rhizosphere of Mhg contained higher abundances of Acidothermus and Lactarius, whereas Mh preferentially enriched Cedecea, Klebsiella, and Russula. Bacterial communities were shaped by pH, soil organic matter (SOM), available potassium (AK), and available phosphorus (AP), whereas fungal communities were primarily influenced by pH, alkali-hydrolyzable nitrogen (AN), and SOM (p < 0.05). These results suggest that both host identity and soil properties contribute to rhizosphere microbial assembly, with clear host-associated differentiation in microbial communities. Notably, the identified host-associated microbial taxa, particularly key mycorrhizal fungi, may serve as potential microbial inoculants, providing new opportunities for the conservation and cultivation of mycoheterotrophic plants.

Dual specificity phosphatases (DUSPs) are a subfamily of protein tyrosine phosphatases that regulate diverse cellular processes through dephosphorylation of phosphorylated substrates. DUSPs are commonly found in eukaryotes, bacteria, archaea, and viruses. However, structural and biochemical characterization of bacterial DUSP remains limited, as only one bacterial DUSP has been identified thus far. In this study, we investigated a novel putative bacterial DUSP from Candidatus Chlorohelix allophototropha, referred to as CCaDUSP. The crystal structure of CCaDUSP showed the presence of a well-conserved catalytic motif with a characteristic phosphate-binding loop. Biochemical analyses further confirmed that CCaDUSP exhibits phosphatase activity and contains dual general acid/base residues, both of which contribute to its enzymatic activity. These findings not only represent the first characterization of a novel bacterial DUSP with dual general acid/base residues but also provide a foundation for understanding the diversity of DUSP proteins in bacteria.

Reliable quantification of neutralizing antibodies (nAb) against human adenovirus type 55 (HAdV-55) is critical for the evaluation of emerging vaccine candidates. While the plaque reduction neutralization test (PRNT) is currently the reference standard, its utility for large-scale studies is limited by low throughput, labor-intensive plaque counting, and prolonged assay times. In this study, we established and analytically validated a microneutralization assay based on cytopathic effect (MN-CPE) as a scalable alternative for HAdV-55-specific nAb quantification. Comparative performance analysis revealed that both assays maintain high dilution linearity, with coefficients of determination (R²) of 0.988 for MN-CPE and 0.9926 for PRNT. Relative accuracy assessments using high-, middle-, and low-titer reference sera demonstrated acceptable responses across the dynamic range. Notably, the MN-CPE assay allowed for the definition of a negative-control acceptance range, providing a distinct statistical advantage over PRNT, where negative-control values were consistently zero. Furthermore, both assays successfully detected HAdV-55-specific nAbs in immunized cynomolgus macaques, with no cross-reactivity observed against other HAdV types such as HAdV-4. These findings indicate that the MN-CPE assay is analytically comparable to PRNT and serves as a practical, relatively high-capacity alternative for HAdV-55 neutralization testing in clinical and preclinical vaccine research.

Small regulatory RNAs (sRNAs) are short noncoding RNAs that can fine-control the expression of target genes in trans at the post-transcriptional level in prokaryotes. Since there is a big challenge in constructing gene-knockout libraries, synthetic sRNAs have attracted considerable interest in synthetic biology and metabolic engineering, as they enable targeted gene knockdown without requiring chromosomal modifications. However, the development of high-efficiency synthetic sRNAs remains a demanding task that requires careful consideration of multiple design factors. Here, we provide a detailed protocol for the design and construction of synthetic sRNAs, detailing key design principles and critical optimization factors, including scaffold selection, target mRNA binding affinity, target mRNA secondary structure, and Hfq expression levels. This strategy can be broadly applied across E. coli and other bacterial hosts to modulate gene expression, thereby supporting versatile applications in synthetic biology and metabolic engineering.

Marine dinoflagellates are gaining attention as sustainable bioresource for polyunsaturated fatty acids (PUFAs), particularly omega-3 such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). In the present study, we analyzed the FAs and transcriptomic profiles of marine dinoflagellates Amphidinium carterae (D-044) and Prorocentrum minimum (D-127) to evaluate their potential as FAs producers. Gas chromatography-FA methyl ester (GC-FAME) analysis showed that A. carterae is a superior omega-3 producer, yielding a total FA content of 67.6 mg/g DW. DHA accounted for 26.7% of the total FAME profile, which is significantly higher than that of P. minimum (18.1 mg/g DW; DHA 13.1%). Gene Ontology (GO) annotation revealed genes related to FAs and lipid metabolism in A. carterae (1,217 genes) and in P. minimum (2,317 genes), which provide a molecular basis for dinoflagellates with high lipid productivity. Notably, three lipid droplet-associated hydrolase (LDAH) genes with diverse evolutionary origins were identified from A. carterae. These findings suggest a potential expansion of the genetic repertoire related to lipid storage and metabolism, highlighting A. carterae and LDAH as candidates for future biotechnological applications and microalgal metabolic engineering.

Skin aging increases transepidermal water loss (TEWL), reduces elasticity, and perturbs the skin microbiome. Adipose tissue-derived stem cell exosomes (ASCE) show regenerative potential; however, their clinical effects on skin physiology and microbiome remain unclear. We conducted a split-face, randomized controlled trial in 16 adults aged ≥ 40 years with visible facial aging. One facial side received ultrasound-assisted transdermal delivery of a human ASCE-containing solution (HACS), whereas the other side received normal saline, at two-week intervals for three sessions. Biophysical outcomes (TEWL, stratum corneum hydration, and elasticity parameters R2/R5/R7) were assessed at baseline and week 2, 4, and 8. Wrinkles, pigmentation, and sebum levels were quantified using Mark-Vu imaging, and the Physician’s Global Aesthetic Improvement Scale (PGAIS) and patient satisfaction assessment scores were recorded. Skin swabs from ten participants were subjected to 16S rRNA and ITS1 sequencing. HACS treatment significantly reduced TEWL (p = 0.006 at week 2; p = 0.009 at week 8) and increased hydration (p < 0.001 at all time points) with a significant increase in elasticity (R2/R5/R7 values, p < 0.001). Both the PGAIS and patient satisfaction scores were significantly higher on the experimental side. Bacterial α/β-diversity remained largely unchanged, and no bacterial taxa remained significantly associated with skin parameters after FDR correction. In contrast, several fungal taxa showed significant positive associations with skin parameters after FDR correction, detectable only on the HACS-treated side. No significant adverse events were observed. HACS improved barrier function, elasticity, and aesthetic outcomes, whereas microbiome analyses suggested a modest fungal response associated with treatment-related skin changes in aging skin.

Recent advances in sequencing technologies, particularly long-read platforms, have substantially improved contiguity of bacterial genome assemblies and enabled the routine generation of near-complete or circular genomes. However, achieving a contiguous assembly does not necessarily guarantee accuracy. Assembly errors, including structural misassemblies, collapsed repeats, incorrect circularization, plasmid reconstruction errors, and nucleotide-level inaccuracies, remain prevalent and may lead to misleading biological interpretations if not properly identified. In this review, we provide a comprehensive overview of bacterial genome assembly from a validation-centered perspective and examine the underlying causes of draft genome formation and assembly uncertainty, highlighting the roles of repetitive genomic structures, platform-specific error profiles, and algorithmic limitations. We further emphasize that the central challenge in contemporary bacterial genomics is no longer simply to maximize assembly contiguity, but to determine whether apparently complete genomes are truly correct and sufficiently reliable for their intended downstream applications. We propose a practical decision-making framework that links sequencing strategy, assembly workflow, polishing, and validation rigor, and introduce a tiered confidence classification to guide the interpretation of genome assembly reliability. As bacterial genome sequencing becomes increasingly routine and large-scale, future efforts should prioritize accuracy, reproducibility, transparent reporting, and evidence-supported validation over completeness alone.

Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs), which are subsequently processed to generate single-stranded DNA (ssDNA). Replication protein A (RPA), a heterotrimeric ssDNA-binding complex, plays essential roles in DNA replication, repair, and recombination; however, the specific functions of RPA in meiotic recombination progression and chromosome morphogenesis remain unclear. Here, we investigate the role of RPA in recombination and meiotic progression by conditionally depleting Rfa1, the large subunit of the RPA complex, using an auxin-inducible degron (AID) system in Saccharomyces cerevisiae. We show that Rfa1 depletion causes severe defects in meiotic recombination, including impaired DSB processing, defective chromosome axis assembly, compromised synaptonemal complex formation, and failure of ZMM-dependent crossover recombination. Notably, inhibition of Mek1 protein kinase activity, which bypasses the recombination checkpoint, does not rescue these defects in Rfa1-depleted cells. Together, these findings identify RPA as a key factor that stabilizes recombination intermediates and coordinates prophase I events with chromosome synapsis and crossover formation during meiosis.

Postbiotics derived from lactic acid bacteria (LAB) have attracted growing interest as stable and potentially safer alternatives to probiotics for use in foods and health-related products. Comprehensive safety evaluation remains essential before their broader application. In this study, we assessed the safety profiles of RHT3201, a postbiotic preparation derived from Lacticaseibacillus rhamnosus IDCC 3201, through genomic, genotoxic, acute oral, and subchronic oral toxicity studies. Whole-genome analysis showed that IDCC 3201 lacks antimicrobial resistance genes and exhibits no hemolytic activity, supporting the genomic safety of the source strain. RHT3201 showed no genotoxic potential in either in vitro or in vivo assays, as evidenced by no structural or numerical chromosomal aberrations at concentrations up to 5,000 μg/ml in CHL/IU cells and no increase in micronucleated polychromatic erythrocytes, with no suppression of bone marrow erythropoiesis by oral administration of RHT3201 at doses up to 15,000 mg/kg/day using a mouse model. In rats, single oral doses of up to 15,000 mg/kg caused no mortality, treatment-related clinical signs, or gross pathological abnormalities, indicating an approximate lethal dose greater than 15,000 mg/kg. In a 90-day repeated-dose oral toxicity study, no adverse treatment-related effects were observed at doses up to 5,000 mg/kg/day. Mild liver and thyroid histopathological findings were considered adaptive and reversible. Accordingly, the no-observed-adverse-effect level was determined to be 5,000 mg/kg/day. Taken together, these findings support the safety of RHT3201 as a LAB-derived postbiotic ingredient.

Despite the application of H-1 parvovirus as an anticancer drug, the relationship between its specific tropism and oncolytic activity has been unknown. H-1 viral infection induced cytopathic effects in HeLa cells, whereas Kilham rat virus (KRV), similar to H-1 virus, did not. To explore which segments of the viral protein 2 (VP2) capsid protein in the H-1 virus determine susceptibility to human cancer cells, chimeric H-1 viruses with specific gene segments of H-1 VP2 were constructed. Delineation of the VP2 capsid protein revealed a minimum domain (K208–L435 in the H-1 VP2 protein) to determine infectivity in human cancer cells; however, this domain was not sufficient to maintain infectivity. To solve this problem, further construction of chimeric H-1 viruses illustrated the necessity of segments covering both M1-N87 and D104-P206 in the H-1 VP2 protein, based on chimeric H-1 viruses designated as YCH44, YCH45, and YCH46. Both the variable region 4b (VR4b) domains from KRV VP2 and VR8 from H-1 VP2 were required for the same purpose, based on chimeric H-1 viruses designated as YCH-HK8, YCH16, YCH17, YCH18, and YCH19. We confirmed that chimeric viruses carrying these segments infected human lung adenocarcinoma A549 and pancreatic cancer Panc-1 cells, whereas the parental KRV did not. Taken together, these findings indicate that specific domains of the H-1 virus VP2 capsid protein determine infectivity toward human cancer cells.

Three Gram-stain-negative, strictly aerobic, motile bacterial strains, designated IMCC44359^T, IMCC44632^T, and IMCC44653, were isolated from coastal surface seawater collected near Jangbong Island in the Yellow Sea. Phylogenetic analyses based on 16S rRNA gene and whole-genome sequences assigned the isolates to the genus Aliikangiella. Strains IMCC44632^T and IMCC44653 shared identical 16S rRNA gene sequences and exhibited high genomic relatedness (99.0% average nucleotide identity and 92.0% digital DNA-DNA hybridization), indicating that they represent a single species. In contrast, strain IMCC44359^T showed low genomic relatedness to these strains and to previously validly published Aliikangiella species, supporting its recognition as a distinct species. The genome of IMCC44359^T (5.95 Mbp; 36.5 mol% G + C) is substantially larger than those of IMCC44632^T and IMCC44653 (~3.75 Mbp; 40.1–40.2 mol% G + C), and all genomes encode aerobic chemoorganotrophic metabolism and biochemical capacities consistent with adaptation to marine environments. The isolates grew under mesophilic and moderately halophilic conditions typical of coastal seawater bacteria, with growth occurring at ranges at 10–40℃, pH 6.0–9.0, and 0.5–7.5% NaCl (optimum, 30℃, pH 7.0–8.0, and 2.0–3.0% NaCl). All strains contained ubiquinone-8 (Q-8) as the sole respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were the major polar lipids. The dominant cellular fatty acids were iso-C_15:0 and summed feature 9 (iso-C_17:1 ω9c and/or C_16:0 10-methyl). Integrated phylogenetic, genomic, phenotypic evidence supported the recognition of two novel species within the genus Aliikangiella, for which the names Aliikangiella litoralis sp. nov. (type strain IMCC44359^T = KCTC 18089^T = JCM 37879^T = HNIBRBA19635^T) and Aliikangiella aequoris sp. nov. (type strain IMCC44632^T = KCTC 18090^T = JCM 37880^T = HNIBRBA19636^T) are proposed.

16S rRNA gene amplicon sequencing is the most widely used approach for characterizing microbial communities, yet analyzing such data requires navigating a fragmented landscape of bioinformatics tools with distinct installation requirements, parameter settings, and data formats. Here we present 16S-Pipeline, an open-source, web-based platform that provides a complete workflow from raw FASTQ files to publication-ready statistical analyses. 16S-Pipeline automatically detects sequencing type (paired-end, single-end, long-read), variable region, and sequencing platform (Illumina, PacBio HiFi, Nanopore), then performs quality filtering, primer trimming, amplicon sequence variant (ASV) inference via DADA2, taxonomy assignment against SILVA v138.1, phylogenetic tree construction, and optional functional prediction via PICRUSt2. Downstream analyses include alpha and beta diversity, taxonomic composition visualization, differential abundance testing using five complementary methods (ALDEx2, DESeq2, ANCOM-BC2, LinDA, MaAsLin2) with consensus reporting, and KEGG pathway mapping. Built-in NCBI SRA integration enables downloading public datasets for re-analysis and generates submission metadata spreadsheets for data deposition. The interactive web interface built on FastAPI and Plotly Dash enables researchers to perform complex microbiome analyses without command-line expertise. 16S-Pipeline is freely available at https://github.com/tatsu1207/16S-Pipeline under the MIT License.

Lymphocystis disease viruses (LCDVs), members of the Lymphocystivirus genus of the Iridoviridae family, infect various freshwater and marine fish species. They cause the chronic disease lymphocystis, which is non-fatal, but substantially reduces the commercial value of the infected fish. To date, four genotypes of LCDV (LCDV1–4) have been identified, all of which encode the viral homologue of B-cell lymphoma 2 (Bcl-2), a key inhibitor of apoptosis. In this study, we performed biochemical and structural analyses of LCDV2 Bcl-2. Binding assays revealed that LCDV2 Bcl-2 exhibits binding selectivity toward BH3 domain-containing zebrafish proteins. It interacted with zBaxA and zNoxa, but not with zBaxB, zBid, or zBeclin 1, distinguishing it from mammalian and herpesviral Bcl-2 proteins. Subsequent structural determination of LCDV2 Bcl-2 in complex with the BH3 domain of zBaxA demonstrated that they interact in a canonical manner, primarily mediated by the BH3 consensus motif residues of zBaxA. In addition, a subpocket formed by two phenylalanine residues in LCDV2 Bcl-2 plays a key role in determining binding selectivity.

Actinobacillus pleuropneumoniae (APP) is the etiological agent of porcine pleuropneumoniae (PP), a high contagious respiratory disease with significant impact on the swine industry in both clinically and economically. Despite of the several attempts to control APP, the emergence of novel serotypes and antimicrobial resistance (AMR) strains highlights the importance of monitoring the genetic characteristics of APP at single nucleotide level. Despite the importance of genomic surveillance of APP to develop effective control strategies, genetic information on the recent Korean isolates of APP is not available at whole genome level. Therefore, in this study, six APP strains were isolated from porcine lungs with characteristic lesions of PP from 2022 to 2024. And their whole genomic sequences, serotypes, virulence factors, and AMR traits were investigated using combined short- and long-read sequencing methods. In silico PCR serotyping identified the isolates as serotype 1, 7, and 15, while one isolate was non-typeable. Multiple AMR genes including Hinf_PBP3_BLA, Ecol_EFTu_PLV, tet(B), tet(O), tetR, sul2, aph(3'')-Ib, aph(6)-Id, and aph(3')-Ia were detected. Also, these genes were located with adjacent to mobile genetic elements, suggesting the possibility of horizontal gene transfer. Phylogenetic comparison with 40 global APP complete genomes, presented that Korean isolates were closely related with China and Switzerland strains. This study provides the whole genome sequences based genetic characterization on the recent Korean isolates of APP, and this study emphasizes that continuous monitoring of APP genomic variation to support effective control of porcine pleuropneumoniae.

Triterpenoids are natural products widely found in the plant kingdom and have various pharmacological effects such as anti-inflammatory, antioxidant and anti-tumour. However, the content of triterpenoids in medicinal plants is low, and it is difficult to purify and isolate them due to their complex structure. The efficient production of some triterpenoids in chassis organisms has been achieved by constructing a heterologous triterpenoid synthesis pathway in engineered strains such as yeast, modifying the key enzymes in the pathway, and adjusting the metabolism of yeast. Modification of key enzymes in the synthetic pathway is currently an effective strategy to enhance the heterologous synthesis of triterpenoids. This paper reviews the current research progress on the modification of key enzymes downstream in the synthetic pathway and the design of key enzymes around them to enhance triterpenoid production in five main areas: 1) increasing the supply of triterpenoid precursors; 2) inhibition of the natural sterol pathway; 3) fusion expression of related enzymes; 4) compartmentalisation of the metabolic pathway; and 5) tapping and enhancing the triterpenoid efflux pump. Finally, recent advances and applications of artificial intelligence (AI) in enzyme engineering and pathway design for triterpenoid biosynthesis are highlighted. Challenges and perspectives for further increasing the yield of triterpenoid synthesis in Saccharomyces cerevisiae are presented.

Based on the escalating challenge of drug-resistant Aspergillus fumigatus infections, this study developed a silver ion-loaded carboxymethyl chitosan (CMCh-Ag^⁺) nanocomposite as a potent antifungal agent. The composite was successfully synthesized and characterized, revealing distinct physicochemical properties, uniform dispersion, and confirmed coordination between CMCh and Ag^⁺. In vitro evaluations, including minimum inhibitory concentration (MIC), minimum fungicidal concentration (MFC), growth curve, and plate spotting assays, demonstrated that CMCh-Ag^⁺ exhibited significantly superior antifungal efficacy against multiple A. fumigatus strains (including azole-resistant isolates) compared to CMCh or Ag^⁺ alone. In vivo experiments using a Galleria mellonella infection model confirmed the enhanced therapeutic effect and biocompatibility of CMCh-Ag^⁺. Investigations into the mechanism-related phenotypes revealed that CMCh-Ag^⁺ significantly removed fungal biofilm and was associated with a substantial accumulation of intracellular reactive oxygen species (ROS), correlating with fungal cell death. This research highlights the preliminary potential of CMCh Ag^⁺ as a candidate strategy to combat drug-resistant A. fumigatus infections, warranting further investigation in mammalian models to assess its clinical translational prospects.

I53-50 is a computationally designed, self-assembling protein nanoparticle (NP) that forms a stable icosahedral structure composed of 120 protein subunits coordinated through precise interfacial interactions. Through unique intelligent regulation, I53-50 exhibits sensitivity to environmental signals and display multimodal “nano-smart” properties. I53-50 has a variety of modifiable surface-active sites, which facilitates precise chemical modification, gene fusion, tag coupling, and other functionalizations, thereby promoting effective lymphatic uptake and optimizing the immune response. I53-50 NPs show great potential in vaccine development, drug delivery, and biomaterials, representing a model fusion of computational biology and nanomedicine and offering a versatile tool for precision medicine.

Following the global spread of SARS-CoV-2 Omicron (B.1.1.529), its subvariants KP.3.1.1, LP.8.1, and NB.1.8.1 disseminated worldwide. By April 2025, the epidemiological landscape of these subvariants had become distinct, with LP.8.1 emerging as the predominant variant, KP.3.1.1 persisting as a co-circulating variant under monitoring (VUM), and NB.1.8.1 exhibiting a significant increase in prevalence. Despite their epidemiological prominence, the functional consequences of spike mutations defining these emerging subvariants remain poorly understood. Here, we systematically dissected the entry properties conferred by their receptor-binding domain (RBD) mutations using a pseudovirus system. Our results demonstrate that all three subvariants exhibited substantially higher infectivity than ancestral Omicron. Unexpectedly, this enhanced infectivity occurred despite reduced ACE2 binding affinity. Rather, increased viral entry consistently correlated with elevated spike cleavage efficiency and fusogenicity, suggesting a compensatory evolutionary strategy in which enhanced spike processing and fusion contribute to enhanced entry despite reduced receptor engagement. These findings provide a virological explanation for the accelerated global spread of these subvariants and highlight the importance of monitoring functional shifts in spike-mediated entry that may influence SARS-CoV-2 transmission dynamics.

Antibiotic resistance poses a serious challenge to public health worldwide; however, the development of new antibiotic classes for combating bacterial infections, especially those caused by Gram-negative pathogens, has slowed in recent years. Dual-acting hybrid antibiotics with a metabolically non-cleavable covalent bond represent an emerging strategy for developing novel antibiotic classes to overcome antibiotic resistance. The covalent connection between two antibiotics results in a fixed pharmacokinetic profile of a single molecule and can impede bacterial efflux. However, as most antibiotics do not have membrane-destabilizing activity, the resulting increase in molecular weight by connection of two antibiotics could limit their activity against Gram-negative bacteria, whose outer membrane forms a strong barrier blocking the penetration of high-molecular weight antibiotics. Here, we review recent developments in dual-acting hybrid antibiotics targeting Gram-negative bacteria, with a focus on their antibacterial efficacy. We also discuss combination therapy strategies in which the underlying molecular mechanisms of synergy have been characterized. Finally, we outline future directions for the rational design of hybrid antibiotics against Gram-negative pathogens.

Antibiotic resistance has become a critical global health challenge due to the decreased efficacy of existing antibiotics and the emergence of multidrug-resistant pathogens. In particular, the rapid horizontal transfer of resistance genes and the diverse mechanisms by which bacteria acquire resistance have significantly undermined the effectiveness of conventional therapeutic strategies, revealing fundamental limitations in current infectious disease management. In this context, synthetic biology provides a promising framework to overcome the limitations of conventional antibiotics by integrating engineering principles with bioengineering approaches, thereby enabling precise and programmable control of biological processes. These synthetic biology-based approaches offer substantial potential for developing sustainable and highly specific antimicrobial strategies. This review comprehensively examines recent advances in synthetic biology-assisted antimicrobial strategies, including CRISPR-Cas systems, bacteriophage engineering, microbiome engineering, and metabolic engineering-driven antibiotic discovery. Collectively, these approaches represent a precision antimicrobial paradigm that enables selective targeting of resistant bacteria while preserving microbiome homeostasis. These strategies also provide new directions for limiting resistance dissemination and guiding the development of next-generation therapeutics.

This study presents the first investigation of acetyl-11-keto-β-boswellic acid (AKBA)’s anti-human cytomegalovirus (HCMV) activity in vitro and elucidates its underlying mechanisms. In HCMV Towne strain-infected WI-38 cells, AKBA (1-12 μM) exhibited negligible cytotoxicity while significantly suppressing virus-induced cytopathic effects (CPE) at 6–10 μM, with dose-dependent reduction of viral proteins (IE1/2 and p52) expression, viral DNA copy number (UL123, UL44, and UL32), and infectious viral progeny titer (TCID₅₀). Time-of-addition experiments demonstrated the primary antiviral activity of AKBA during post-entry phase, along with direct virion inactivation. Transcriptome analysis revealed that AKBA significantly downregulated the expression of the host factor NR4A1 induced by HCMV, a finding further validated by Western blotting. Further gene knockdown experiments confirmed that silencing NR4A1 significantly reduced the expression of viral proteins IE1/2, thereby validating NR4A1 as a key host factor for HCMV infection. These findings indicate that AKBA has a potent and dose-dependent inhibitory effect on HCMV replication in WI-38 cells, and proves that this effect is mediated through two different mechanisms: one is the downregulation of the expression of the key host factor NR4A1, and the other is the direct inactivation of HCMV viral particles.

Phytoplasmas are wall-less obligate parasites of plants and insects. Several phytoplasma strains within the Peanut Witches’ Broom (PWB; 16SrII) group are associated with significant disease losses across diverse crops and weeds. We present complete, single contig genome assemblies for two Indian parthenium phyllody strains, ‘Candidatus Phytoplasma asiaticum’ PR34 and ‘Ca. P. australasiaticum’ PR08, generated through host DNA depletion and hybrid Illumina–Nanopore sequencing. Both genomes display characteristic features of reductive evolution (∼614 kb and 589 kb, respectively) but show notable differences from previously sequenced PWB phytoplasmas. In contrast to most of PMU-rich phytoplasma genomes, neither PR34 nor PR08 retains intact Potential Mobile Units. Instead, both harbor numerous open reading frames encoding group II intron reverse transcriptase/ maturase proteins, predominantly of the mitochondrial-like type, with PR34 containing 52 and PR08 28 such loci that together constitute > 4% of each genome. These observations support the hypothesis that intron-associated processes may contribute to genome variability in the absence of canonical PMUs. Comparative analyses support the classification of PR34 as a distinct species within the PWB complex and reveal both conserved Sec-dependent effectors (SAP05, SAP11, and SAP54/PHYL1) and lineage-specific secreted proteins with predicted nuclear localization. Additional retained features include functional sodA genes and multiple truncated HlyB-like transporters. Collectively, these high-quality genomes illustrate a genomic configuration in which extensive genome reduction and loss of PMUs coexist with the retention of core virulence factors and an expanded repertoire of group II introns, providing a framework for future investigation of genome plasticity in phytoplasmas.

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.

Synthetic rescue (SR) describes a genetic interaction in which the deleterious effect of a primary mutation is compensated by a second mutation, restoring cellular function or viability. In Saccharomyces cerevisiae, SR complements synthetic lethality (SL) by revealing compensatory mechanisms that maintain essential biological processes. Classical studies established SR as a fundamental principle of genetic robustness in yeast. Subsequent development of high-throughput genetic tools, including Synthetic Genetic Array (SGA), Epistatic Miniarray Profile (E-MAP), and CRISPR interference (CRISPRi), has enabled systematic identification of SR interactions across pathways of genome maintenance, proteostasis, and metabolism. Integration of these experimental datasets with computational and network-based analyses has transformed SR research from descriptive genetics into a predictive framework. Databases such as BioGRID, TheCellMap, and Mslar further support SR inference and link yeast genetic networks to human disease models. Understanding SR has important translational implications. The same compensatory logic that restores viability in yeast can explain therapeutic resistance in cancer cells. Together, these insights reveal SR as a powerful concept connecting microbial genetics with systems medicine, emphasizing that robustness and resilience are dynamic properties of living systems.

Two novel bacterial species, designated as CJ85^T and CJ88^T, were isolated from the agricultural soil and the Han River, South Korea, respectively. Cells of both strains were Gram-staining-positive, short rod-shaped, non-motile, and yellow-pigmented. Strain CJ85^T exhibited optimal growth in tryptic soy broth at 37°C and pH 7.0 in the absence of NaCl. Strain CJ88^T showed optimal growth in lysogeny broth at 30°C and pH 7.0 in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CJ85^T belonged to the genus Paramicrobacterium, showing the highest sequence similarity to Paramicrobacterium fandaimingii HY82^T (97.6%). Strain CJ88^T was assigned to the genus Microbacterium, with the highest sequence similarity to Microbacterium azadirachtae DSM 23848^T (98.5%). The DNA G + C content was 64.8% for strain CJ85^T and 70.5% for strain CJ88^T. The genome-based analyses, including phylogenomic tree, digital DNA-DNA hybridization, and average nucleotide identity, clearly indicated that these strains represent novel species within their respective genera. The major fatty acids of both strains were anteiso-C_15:0, anteiso-C_17:0, and iso-C_16:0. Based on the polyphasic taxonomy study, strains CJ85^T and CJ88^T represent novel species of the genera Paramicrobacterium and Microbacterium, respectively, for which names Paramicrobacterium salitolerans sp. nov. and Microbacterium fluminis sp. nov. are proposed. The type strains CJ85^T (= KACC 23064^T = JCM 36217^T) and CJ88^T (= KACC 24080^T = JCM 38050^T).

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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 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).

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.

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.

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.

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.

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.

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).

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.

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.

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.