Antimicrobial resistance (AMR) in marine environments remains difficult to assess under standard antimicrobial susceptibility testing conditions, which may not adequately reflect the physiological requirements of marine-derived bacteria. In this study, we applied NaCl-supplemented susceptibility testing conditions to bacterial isolates recovered from coastal environments and marine organism guts to evaluate their practical applicability and limitations. A total of 927 isolates were obtained from lagoon, seawater, soil, and gut samples of abalone, crab, eel, halibut, and salmon. Of these, 365 isolates grew on standard Mueller–Hinton (MH) medium, whereas 562 isolates were not evaluable under standard MH conditions. Taxonomic analysis showed that the isolate collection was dominated by Proteobacteria and Firmicutes, with Vibrio as the most abundant genus. Disk diffusion assays of the 365 MH-grown isolates revealed differences in screening-level reduced susceptibility profiles among sample groups, and putative multidrug resistance was frequently observed in Vibrio isolates from abalone and seawater. For isolates not evaluable under standard MH conditions, minimum inhibitory concentration (MIC) analysis was performed using 2% NaCl-supplemented MH broth. Under these conditions, 115 isolates showed stable growth and distinct antibiotic-dependent MIC profiles. Chloramphenicol and tetracycline inhibited most isolates at relatively low concentrations, whereas reduced susceptibility to penicillin was relatively high in isolates from seawater, abalone, and eel. Overall, these findings suggest that standard MH conditions alone may be insufficient for evaluating antibiotic responses in marine- and brackish-origin bacteria, and that 2% NaCl-supplemented MH broth can serve as a practical supplementary condition for selected marine-derived isolates.

Fecal microbiota transplantation (FMT) has been successfully applied on clinical aspects, but its clinical outcomes remain unpredictable due to inconsistent donor screening protocols across hospitals, institutions, and countries. Hence, a retrospective analysis of metagenomic data from published studies on FMT donors via a unified bioinformatics workflow might contribute to the understanding of the safety considerations for donor screening and the fecal microbial profiles of qualified donors. In this study, we reanalyzed metagenomic data of 475 screened donor fecal samples from 24 studies spanning China, the USA, Canada, New Zealand, and the Netherlands. The genomic safety risks were evaluated by profiling antibiotic resistance genes (ARGs) and virulence factors (VFs), the results of which showed that no major toxin-associated virulence genes, such as Shiga toxin, Shiga-like toxin, or botulinum neurotoxin (BoNTs) genes harbored in the detected Escherichia coli, Clostridium butyricum, and Streptococcus pneumoniae, but several high-risk ARGs remained insufficiently addressed. The distribution of ARG-harboring bacteria in eligible FMT donors was country-specific. The alpha-diversity and microbial community structure were comparable between donor fecal samples from China and the USA. Interestingly, the core microbiome in fecal samples from Canada, the Netherlands, and New Zealand formed a single guild, while that from China and the USA formed two guilds, with predominantly positive intra-guild and negative inter-guild correlations, indicating that the co-abundance patterns of the core microbiome were conserved among certain countries. Furthermore, an exploratory retrospective classifier was developed based on core microbiome profiles to distinguish eligible FMT donors from general healthy individuals. These results provide evidence for integrating metagenomic sequencing into future FMT donor screening strategies.

Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image.

SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.

Human adenovirus type 55 (HAdV-55) is an emerging respiratory pathogen associated with severe pneumonia, for which no licensed vaccines are currently available. The lack of physiologically relevant small-animal models has limited preclinical evaluation of vaccine candidates. In this study, we generated a transgenic mouse model co-expressing human CD46 and desmoglein-2 (DSG-2), key entry receptors for HAdV-55, and evaluated its utility for vaccine efficacy testing. A bicistronic expression system enabling simultaneous expression of CD46 and DSG-2 was constructed and functionally validated in vitro, demonstrating enhanced susceptibility to HAdV-55 infection. The transgenic mice exhibited dose-dependent weight loss, robust viral replication in lung tissues, and characteristic histopathological changes following intranasal challenge, recapitulating key features of human adenoviral pneumonia. Using this model, we assessed the immunogenicity and protective efficacy of an inactivated HAdV-55 (iHAdV-55) vaccine formulated with alum. Vaccination induced strong HAdV-55-specific IgG and neutralizing antibody responses, which increased over time following prime–boost immunization. Upon viral challenge, vaccinated mice showed significantly reduced weight loss and accelerated recovery compared to controls. Viral load analysis demonstrated effective control of viral replication and clearance in vaccinated animals. Collectively, these findings establish the CD46/DSG-2 transgenic mouse as a physiologically relevant and translationally valuable model for HAdV-55 infection and demonstrate that iHAdV-55 vaccination confers robust humoral immunity and protective efficacy. This platform provides a critical tool for the development and preclinical evaluation of adenovirus-targeted vaccines and therapeutics.

Pathogenic Escherichia coli is a major cause of foodborne illness worldwide and includes strains capable of causing severe disease. To establish a genome-informed framework for foodborne outbreak surveillance, we analyzed 1,029 E. coli isolates from clinical, food, livestock, and environmental sources using whole-genome sequencing. Pathogenic isolates obtained from human clinical cases or linked to documented outbreaks were classified as epidemiologically defined high-risk (EpiHR), whereas the remaining pathogenic isolates were classified as non-EpiHR. Virulence-associated genomic features were extracted using a bioinformatics pipeline, and four machine learning (ML) algorithms, including gradient boosting machine, random forest (RF), and support vector machines with linear and radial basis function kernels, were evaluated. Among them, the RF model showed the best performance, achieving an area under the curve (AUC) of 0.98 and accuracy of 0.93 in 10-fold cross-validation. Additional leave-one-group-out validation showed retained discrimination across held-out sequence types and serotypes, although performance was reduced when isolates were grouped by isolation source. Evaluation using an independent test dataset of 1,908 publicly available pathogenic E. coli genomes showed an AUC of 0.97 and a sensitivity of 0.98. Feature importance analysis using Shapley additive explanations identified influential predictive features, including traT, etpB, and enterotoxin-associated genes. A reduced 10-feature model achieved an AUC of 0.79 in the independent test dataset, supporting its exploratory use for future simplified screening approaches. These results indicate that genome-based ML provides a sensitive framework for surveillance-oriented prioritization of EpiHR pathogenic E. coli isolates, with model predictions interpreted together with epidemiological information.

While shotgun metagenomics is often used to profile antibiotic resistome in gut microbial communities, few studies have investigated if the choice of sequencing platform and assembly strategy affect what mobile genetic elements and antimicrobial resistance genes are recovered. In this study, we compared three platforms (Illumina, Oxford Nanopore, and PacBio HiFi) and seven assembly strategies on gut metagenomes from cattle, pig, and human as case studies. Long-read assemblies recovered 5- to 7-fold more plasmid sequence than Illumina in cattle and pig (mean 17.0 Mb vs. 3.1 Mb), while Illumina performed comparably in the less diverse human gut where high per-species coverage enabled effective short-read plasmid assembly. Long reads also detected more resistance genes on plasmid contigs. Hybrid assembly results depended on the algorithm: scaffolding-based OPERA-MS preserved long-read contiguity and recovered more plasmid-borne resistance genes, while the short-read-centric metaSPAdes hybrid mode produced fragmented assemblies. After collapsing haplotype redundancy, PacBio HiFi identified 2 and 49 unique multi-drug resistance plasmid lineages in cattle and pig, respectively. On the other hand, only 2 and 4 were identified from Illumina. Long reads also placed far more ARGs in a putative mobilization context (50–73%) compared to 14–21% for short reads. Platform and assembly strategy are thus key variables in mobilome and resistome characterization and should be accounted for in antimicrobial resistance surveillance.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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

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

The oral administration of synthetic drugs can effectively reduce blood lipid levels, but adverse reactions may occur. Because of this, the hypolipidemic ability of natural products has been increasingly investigated. We evaluate the safety and hypolipidemic characteristics of a water-soluble blue pigment extracted using HPD-400 resin from the fungus Quambalaria cyanescens. Hypolipidemic ability was examined by constructing a hyperlipidemia model with different doses of blue pigment (50, 100, and 200 mg/kg. mouse body weight) for 28 d. Blue pigment purity increased from 20.32% to 70.70% following treatment with HPD-400 resin. Acute toxicity tests revealed blue pigment sourced from Q. cyanescens to have no toxic effects on mouse body weight, mortality, or behavioral characteristics. Subacute toxicity tests revealed no significant differences in food intake, body weight, or organ weights between treatment groups and controls. Histopathological examination of the liver and kidney tissues of mice administered blue pigment were normal, and serum enzyme activities and blood constituents were also within normal ranges. Blue pigment can significantly reduce the weight of mice, reduce liver and kidney damage and fat accumulation. It can also reduce total cholesterol, triglyceride and low density lipoprotein cholesterol in serum and liver tissue, and increase the level of high density lipoprotein cholesterol. Reduce the levels of alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, creatinine, urea and uric acid in serum. Increase the activities of total superoxide dismutase, glutathione peroxidase and catalase in serum and liver tissue, reduce the content of malondialdehyde, and up-regulate liver lipase and lipoprotein lipase. Our work proves that blue pigment is nontoxic, has the function of reducing blood lipid, and can alleviate obesity-related symptoms by regulating lipid metabolism and oxidative stress.

The Bacillus subtilis spore crust is an exceptionally robust proteinaceous layer that protects spores under extreme environmental conditions. Among its key components, CgeA, a glycosylation-associated protein, plays a critical role in modifying crust properties through its glycosylated moiety, enhancing spore dispersal in aqueous environments. In this study, we present the high-resolution cryo-electron microscopy structure of the core region of CgeA at 3.05 Å resolution, revealing a doughnut-like hexameric assembly. The N-terminal regions are disordered, whereas the C-terminal region forms the core of the hexamer. Although the loop containing Thr112 was not resolved in the density map, its location can be inferred from surrounding residues, suggesting that Thr112 is situated on the exposed surface of the hexamer. On the opposite face, a distinct electrostatic pattern is observed, featuring a negatively charged central pore and a positively charged outer surface. Modeling and biochemical studies with the putative glycosyltransferase CgeB provide insights into how the glycosyl group is transferred to Thr112. This study offers a molecular-level understanding of the assembly, glycosylation, and environmental adaptability of the B. subtilis spore crust, with valuable implications for controlling spore formation in industrial applications.

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.

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

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.

Two novel, Gram-stain-negative, anaerobic, and non-motile bacterial strains, designated KFT8^T and CG01^T, were isolated from the feces of healthy individuals without diagnosed diseases and characterized using a polyphasic approach. Phylogenetic analysis revealed that both strains belong to the genus Bacteroides, with < 99.0% similarity in their 16S rRNA gene sequences to B. facilis NSJ-77^T and B. nordii JCM 12987^T. Within the genus Bacteroides, strain KFT8^T exhibited the highest Orthologous Average Nucleotide Identity value of 94.7% and a digital DNA-DNA hybridization value of 63.7% with B. ovatus ATCC 8483^T, whereas strain CG01^T showed the highest values of 95.3% and 63.3%, respectively, with B. nordii JCM 12987^T. The values between the two novel strains were 74.8% and 21.4%, respectively, which are below the species delineation thresholds, supporting their classification as novel species. The major fatty acid of strain KFT8^T was C_18:1 ω9c, whereas strain CG01^T predominantly contained summed feature 11 (comprising iso-C_17:0 3OH and/or C_18:2 DMA). The only respiratory quinone was MK-11, the major polar lipid was phosphatidylethanolamine. Both strains produced succinic acid and acetic acid as common metabolic end-products of fermentation, while lactic acid and formic acid were detected individually in each strain. Based on polyphasic characterization, strains KFT8^T (= KCTC 15614^T = JCM 36011^T) and CG01^T (= KCTC 15613^T = JCM 36010^T) represent two novel species within the genus Bacteroides, for which the names Bacteroides celer sp. nov. and Bacteroides mucinivorans sp. nov. are proposed, respectively. Additionally, genome-based analyses and phenotypic comparisons revealed that B. koreensis and B. kribbi represent the same strain, showing genomic relatedness to B. ovatus that exceeds the threshold for species delineation. Consequently, we propose the reclassification of B. koreensis Shin et al. 2017 and B. kribbi Shin et al. 2017 as later heterotypic synonyms of B. ovatus Eggerth and Gagnon 1933 (Approved Lists 1980).

This study aimed to determine if the microbiota in four different oral sites and the oral health status differ between patients with primary Sjögren’s syndrome (pSS), non-pSS sicca symptoms, and healthy controls. All participants underwent an interview and clinical oral examination. Stimulated whole saliva (SWS), supragingival plaque (SGP), buccal mucosa tissue (BLM), and tongue scrape (TGS) samples from 23 pSS patients, 36 patients with sicca symptoms, not fulfilling the classification criteria for pSS (non-pSS sicca), and 21 age-matched healthy controls (HC) were analyzed using V3–V4 16S rRNA gene amplicon sequencing, and determination of amplicon sequence variants (ASVs). PSS and non-pSS sicca patients did not differ with respect to oral health status, saliva flow rates, abundance of predominant genera, relative abundance on genus level or bacterial diversity in any of the oral sites. Both patient groups differed significantly from the healthy control group in the abundance of 61 ASVs across all sites. The alpha-diversity was lower in SGP from non-pSS sicca patients (p = 0.019), and in TGS from pSS patients (p = 0.04). The proportion of variation in the beta-diversity across all four sites could be explained by the diagnosis (pSS, non-pSS sicca, and HC). However, subgrouping of patients according to their stimulated salivary flow rates (SWS > 0.7 ml/min versus SWS ≤ 0.7 ml/min), revealed significantly different abundance of three ASVs in SWS, 11 in SGP, and six in TGS. Our findings suggest that hyposalivation rather than pSS itself modifies the microbial composition in oral site-specific patterns leading to oral diseases.

Photodynamic therapy (PDT) is a known strategy for treating cancer; in PDT, photosensitizers are activated by light stimulation and then induce reactive oxygen species (ROS) production to damage cancer tissues. Recently evidence has shown that PDT can also be used as a novel treatment strategy to control pathogenic bacteria. In previous studies, the photosensitizer DH-I-180-3 was reported to effectively regulate multidrug-resistant Mycobacterium tuberculosis growth. Here, we confirmed the effects of DH-I-180-3 on the antibacterial activity and inflammatory response of macrophages to Salmonella. Photoactivated DH-I-180-3 regulated intracellular bacterial growth in Salmonella-infected macrophages. Moreover, DH-I-180-3 increased intracellular ROS levels in Salmonella-infected macrophages. The phosphorylation of the intracellular signaling proteins IκBα and JNK1/2 was increased in DH-I-180-3-treated Salmonella-infected macrophages. Additionally, we observed that DH-I-180-3 significantly increased the mRNA expression and protein secretion of the proinflammatory cytokine TNF-α and promoted phagosome maturation by upregulating EEA1, LAMP1, and Cathepsin D in Salmonella-infected macrophages. Overall, these results demonstrate that photoactivated DH-I-180-3 enhances the bactericidal response to intracellular bacterial infection by promoting inflammatory signaling pathways and phagosome maturation. Therefore, DH-I-180-3 has the potential to be developed into PDT for treating bacterial-infection.

Gout is an inflammatory arthritis resulting from the deposition of monosodium urate crystals. Urate-lowering therapies for gout have limitations, including side effects and limited efficacy, highlighting the need for novel therapeutic approaches to improve patient outcomes. In this context, our research team conducted a microbiome analysis of fecal samples from healthy individuals and gout patients, identifying Bifidobacterium as a key biomarker. Subsequently, we isolated and identified this strain, B. longum PMC72, and demonstrated its efficacy in a gout mouse model. In potassium oxonate (PO)-induced hyperuricemia mice, PMC72 significantly alleviated nausea, gait disturbances, ankle inflammation, and improved renal health. These effects were associated with marked reductions in oxidative stress markers, including serum uric acid, blood urea nitrogen, hepatic xanthine oxidase, and malondialdehyde (MDA) levels in serum, liver, and joint samples, as well as the downregulation of inflammation and uric acid transport-related gene expression in kidney samples. These benefits were comparable to those treated with Febuxostat, a standard urate-lowering therapy for gout. Furthermore, gut microbiome analysis revealed that PMC72 restored dysbiosis induced by hyperuricemia, contrasting with the reduced microbial diversity observed with febuxostat alone, and showed a complete recovery to eubiosis when combined with Febuxostat. These findings position PMC72 as a promising microbial therapeutic candidate for gout management, demonstrating significant development potential and serving as a benchmark for reverse translational microbiome-based therapeutic research.

Recently, floating membrane filter cultivation was adopted to simulate solid surface and enrich surface-adapted soil ammonia-oxidizing archaea (AOA) communities from agricultural soil, as opposed to the conventional liquid medium. Here, we conducted metagenomic sequencing to recover nitrifier bins from the floating membrane filter cultures and reveal their genomic properties. Phylogenomic analysis showed that AOA bins recovered from this study, designated FF_bin01 and FF_bin02, are affiliated with the Nitrososphaeraceae family, while the third bin, FF_bin03, is a nitrite-oxidizing bacterium affiliated with the Nitrospiraceae family. Based on the ANI/AAI analysis, FF_bin01 and FF_bin02 are identified as novel species within the genera “Candidatus Nitrosocosmicus” and Nitrososphaera, respectively, while FF_bin03 represents a novel species within the genus Nitrospira. The pan and core genome analysis for the 29 AOA genomes considered in this study revealed 5,784 orthologous clusters, out of which 653 were core orthologous clusters. Additionally, 90 unique orthologous clusters were conserved among the Nitrososphaeraceae family, suggesting their potential role in enhancing culturability and adaptation to diverse environmental conditions. Intriguingly, FF_bin01 and FF_bin02 harbor a gene encoding manganese catalase and FF_bin03 also possesses a heme catalase gene, which might enhance their growth on the floating membrane filter. Overall, the floating membrane filter cultivation has proven to be a promising approach for isolating distinct soil AOA, and further modifications to this technique could stimulate the growth of a broader range of uncultivated nitrifiers from diverse soil environments.

Antimicrobial resistance (AMR) poses a serious threat to public health, with the emergence of extended-spectrum beta-lactamases (ESBLs) in Enterobacteriaceae, particularly Escherichia coli, raising significant concerns. This study aims to elucidate the drivers of antimicrobial resistance, and the global spread of cefotaxime-resistant E. coli (CREC) strains. Whole-genome sequencing (WGS) was performed to explore genome-level characteristics, and phylogenetic analysis was conducted to compare twenty CREC strains from this study, which were isolated from broiler chicken farms in Bangladesh, with a global collection (n = 456) of CREC strains from multiple countries and hosts. The MIC analysis showed over 70% of strains isolated from broiler chickens exhibiting MIC values ≥ 256 mg/L for cefotaxime. Notably, 85% of the studied farms (17/20) tested positive for CREC by the end of the production cycle, with CREC counts increasing from 0.83 ± 1.75 log10 CFU/g feces on day 1 to 5.24 ± 0.72 log10 CFU/g feces by day 28. WGS revealed the presence of multiple resistance genes, including bla_CTX-M, which was found in 30% of the strains. Phylogenetic comparison showed that the Bangladeshi strains were closely related to strains from diverse geographical regions and host species. This study provides a comprehensive understanding of the molecular epidemiology of CREC. The close phylogenetic relationships between Bangladeshi and global strains demonstrate the widespread presence of cefotaxime-resistant bacteria and emphasize the importance of monitoring AMR in food-producing animals to mitigate the spread of resistant strains.

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

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.

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.

Bacteria-free reverse genetics techniques are crucial for the efficient generation of recombinant viruses, bypassing the need for labor-intensive bacterial cloning. These methods are particularly relevant for studying the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19. This study compared the efficiency of three bacteria-free approaches—circular polymerase extension reaction (CPER) with and without nick sealing and infectious sub-genomic amplicons (ISA)—to bacterial artificial chromosome (BAC)-based technology for rescuing SARS-CoV-2. Significant differences in viral titers following transfection were observed between methods. CPER with nick sealing generated virus titers comparable to those of the BAC-based method and 10 times higher than those of the standard CPER. In contrast, ISA demonstrated extremely low efficiency, as cytopathic effects were detected only after two passages. All rescued viruses exhibited replication kinetics consistent with those of the original strain, with no significant deviation in replication capacity. Furthermore, the utility of CPER and ISA in genetically modifying SARS-CoV-2 was demonstrated by successfully inserting the gene encoding green fluorescent protein into the genome. Overall, this study underscores the potential of bacteria-free methods, such as CPER and ISA, in advancing SARS-CoV-2 research while highlighting their significant differences in efficiency.

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.

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.

With the advent of whole-genome sequencing, opportunities to investigate the population structure, transmission patterns, antimicrobial resistance profiles, and virulence determinants of Streptococcus pneumoniae at high resolution have been increasingly expanding. Consequently, a user-friendly bioinformatics tool is needed to automate the analysis of Streptococcus pneumoniae whole-genome sequencing data, summarize clinically relevant genomic features, and further guide treatment options. Here, we developed PneusPage, a web-based tool that integrates functions for species prediction, molecular typing, drug resistance determination, and data visualization of Streptococcus pneumoniae. To evaluate the performance of PneusPage, we analyzed 80 pneumococcal genomes with different serotypes from the Global Pneumococcal Sequencing Project and compared the results with those from another platform, PathogenWatch. We observed a high concordance between the two platforms in terms of serotypes (100% concordance rate), multilocus sequence typing (100% concordance rate), penicillin-binding protein typing (88.8% concordance rate), and the Global Pneumococcal Sequencing Clusters (98.8% concordance rate). In addition, PneusPage offers integrated analysis functions for the detection of virulence and mobile genetic elements that are not provided by previous platforms. By automating the analysis pipeline, PneusPage makes whole-genome sequencing data more accessible to non-specialist users, including microbiologists, epidemiologists, and clinicians, thereby enhancing the utility of whole-genome sequencing in both research and clinical settings. PneusPage is available at https://pneuspage.minholee.net/.

Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (≥ 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.