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.

Alcohol consumption can lead to the accumulation of harmful metabolites, such as acetaldehyde, contributing to various adverse health effects, including hangovers and liver damage. This study presents a comprehensive genomic and functional analysis of Leuconostoc suionicum VITA-PB2, a lactic acid bacterial strain isolated from kimchi, to elucidate its role in enhancing alcohol and acetaldehyde metabolism. Genomic characterization revealed key genes encoding alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH), providing insights into the metabolic capabilities of strain VITA-PB2. Phylogenomic analyses confirmed its taxonomic classification and genetic similarity to other Leuconostoc species. Functional validation through in vitro and in vivo experiments demonstrated superior ethanol and acetaldehyde decomposition abilities of strain VITA-PB2, with significant reductions in blood ethanol and acetaldehyde levels observed in rats administered with the strain. Further analysis indicated that while hepatic ADH activity did not significantly increase; however, ALDH expression was elevated. This suggests that the microbial ADH of strain VITA-PB2 contributed to ethanol breakdown, while both microbial and host ALDH facilitated acetaldehyde detoxification. These findings highlight the potential of strain VITA-PB2 as a functional probiotic for mitigating the toxic effects of alcohol consumption.

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

Salmonella enterica is a clinically significant oro-fecal pathogen that causes a wide variety of illnesses and can lead to epidemics. S. enterica expresses a lot of virulence factors that enhance its pathogenesis in host. For instance, S. enterica employs a type three secretion system (T3SS) to translocate a wide array of effector proteins that could change the surrounding niche ensuring suitable conditions for the thrive of Salmonella infection. Many antimicrobials have been recently introduced to overcome the annoying bacterial resistance to antibiotics. Enoxacin is member of the second-generation quinolones that possesses a considerable activity against S. enterica. The present study aimed to evaluate the effect of enoxacin at sub-minimum inhibitory concentration (sub-MIC) on S. enterica virulence capability and pathogenesis in host. Enoxacin at sub-MIC significantly diminished both Salmonella invasion and intracellular replication within the host cells. The observed inhibitory effect of enoxacin on S. enterica internalization could be attributed to its ability to interfere with translocation of the T3SS effector proteins. These results were further confirmed by the finding that enoxacin at sub-MIC down-regulated the expression of the genes encoding for T3SS-type II (T3SS-II). Moreover, enoxacin at sub-MIC lessened bacterial adhesion to abiotic surface and biofilm formation which indicates a potential anti-virulence activity. Importantly, in vivo results showed a significant ability of enoxacin to protect mice against S. enterica infection and decreased bacterial colonization within animal tissues. In nutshell, current findings shed light on an additional mechanism of enoxacin at sub-MIC by interfering with Salmonella intracellular replication. The outcomes presented herein could be further invested in conquering bacterial resistance and open the door for additional effective clinical applications.

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/.

Korean Red ginseng has emerged as a potent candidate in the fight against various viral infections, demonstrating significant efficacy both in vitro and in vivo, particularly against influenza A viruses. Despite substantial evidence of its antiviral properties, the detailed molecular mechanisms through which it reduces viral lethality remain insufficiently understood. Our investigations have highlighted the superior effectiveness of Korean Red ginseng against influenza viruses, outperforming its effects on numerous other viral strains. We aim to uncover the specific mechanisms by which Korean Red ginseng exerts its antiviral effects, focusing on influenza A viruses. Our prior studies have identified the role of Z-DNA-binding protein 1 (ZBP1), a signaling complex involved in inducing programmed cell death in response to influenza virus infection. Given the critical role of ZBP1 as a sensor for viral nucleic acid, we hypothesize that Korean Red ginseng may modulate the ZBP1-derived cell death pathway. This interaction is anticipated to enhance cell death while concurrently suppressing viral protein expression, offering novel insights into the antiviral mechanism of Korean Red ginseng against influenza A viruses.

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