Monascus sp. NP1 is a significant filamentous fungus with valuable properties for food industries. Initially isolated from the fermented rice product ang-kak, this strain is known for its ability to produce natural pigments. In this study, we therefore sequenced its genome together with the 26S rRNA D1/D2 domain and ITS fragment for identifying species of Monascus sp. NP1, and further conducted functional annotations of its overall genes related to metabolic capability and growth adaptation using comparative genomics. As a result, promisingly, the NP1 strain was identified as Monascus purpureus with the genome sequences, which was shown to be 23.54 Mb with a GC content of 49.01%. Genome annotation predicted 8031 protein-encoding genes. Comparative genomics between NP1 and 11 other related strains revealed 6024 core groups, 2204 accessory groups, and 5 strain-specific groups. Metabolic pathway analysis promisingly showed carbohydrate metabolism as the most enriched category, particularly central carbon metabolism involving key precursors, e.g., acetyl-CoA and pyruvate that support energy generation and the biosynthesis of pigments, fatty acids, and lipids. These findings highlighted the metabolic versatility and adaptive growth potential of M. purpureus NP1. This study provides key genetic insights into the cellular functions of M. purpureus NP1, laying the groundwork for exploring metabolic properties. It offers a comprehensive understanding for developing targeted applications of M. purpureus NP1 as an alternative fungal cell factory in food and nutrition.

Equine melanocytic neoplasms (EMN) are aggressive tumours characterised by high metastatic potential and limited therapeutic options available. However, the molecular mechanisms underlying their progression remain poorly understood. This study therefore presents the integrative phosphoproteomic analysis of EMN tissue, with the aim of elucidating stage-specific alterations in signalling pathways and metabolism. Nineteen tissue samples from grey horses were categorised as normal-stage (n = 6), early-stage EMN (n = 7), and severe-stage EMN (n = 6) and subjected to in-depth analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 2035 phosphoproteins were identified, of which 219 were differentially expressed across the disease stages. Interestingly, early-stage EMN showed dysregulation of inositol phosphate metabolism and activation of the PI3K-Akt pathway which involved INPP5F and PKN2. In severe-stage EMN, upregulation of SYNJ1, STRN4 and VIM indicated enhanced membrane trafficking, cytoskeletal remodelling, and MAPK signalling. Additionally, ASPM and GNAO1 upregulation reflected heightened proliferation and altered Rap1 signalling, while UBR5 dysregulation suggested aberrant protein homeostasis. Metabolic reprogramming was also noticed, with elevated TKT and GAPDH expression supporting glycolysis and NADPH production. Observably, the severe-stage EMN exhibited a higher expression of Dickkopf-3 (DKK3) which suggests a role in aberrant Wnt/β-catenin activation and tumour progression. These findings reveal stage-specific molecular mechanisms in EMN pathogenesis and highlight potential biomarkers and therapeutic targets for equine melanoma.

Limosilactobacillus fermentum KUB-D18 is a probiotic strain with significant potential in food fermentation and health promotion, yet the systems-level mechanisms underlying its physiological robustness remain elusive. To elucidate the metabolic remodeling strategies operating across growth phases, we developed an integrated framework combining genome-scale metabolic modeling (GSMM) with transcriptomics. A high-quality metabolic model for L. fermentum KUB-D18, designated iYH640 and comprising 640 genes, 1530 metabolites, and 1922 reactions, was constructed and validated against experimental growth data. Specifically, in vitro assays measuring biomass and glucose concentrations showed a maximum specific growth rate of 0.2696 h−1 and a glucose uptake rate of 11.75 mmol gDCW−1 h−1, providing physiological constraints for the model. Using transcriptome-regulated flux balance analysis (TR-FBA), gene expression profiles from the logarithmic phase (L-phase) and stationary phase (S-phase) were integrated to quantify growth phase-specific metabolic flux distributions. These simulations revealed a distinct transcription-driven metabolic shift, in which the organism moves from a proliferation-oriented metabolic state with active central carbon metabolism and macromolecule synthesis to a maintenance-oriented state. This S-phase is characterized by reduced flux through anabolic pathways together with the selective preservation of redox balance and nucleotide homeostasis. Collectively, these results provide a quantitative explanation of how L. fermentum KUB-D18 balances growth and maintenance, offering a mechanistic basis for improving its stability and functional performance in industrial probiotic applications.

The impact of diet on gut microbial metabolism is essential for advancing microbiome-based health interventions. This study introduces a novel systems biology pipeline that integrates genome-scale metabolic models (GSMMs) with Thai dietary intake data to simulate gut microbiome metabolism and assess prebiotic responses. Utilizing metagenomic data from healthy Thai adults and an average Thai diet derived from national surveys, community-scale metabolic models (CSMMs) were developed and simulated under both typical dietary and prebiotic-supplemented condition. Flux variability analysis was employed to assess metabolic capacities, short-chain fatty acids (SCFAs) production in relation to microbial taxonomy. The results promisingly revealed inter-individual variability in SCFA profiles, with Bacteroides and Phocaeicola notably linked to isobutyrate production and Bifidobacterium emerged as a key responder to prebiotic supplementation. This integrative framework offers biological insights into diet-gut microbiome interactions and provides a foundation for the development of precision nutrition strategies tailored to the Thai population.

The gut microbiome plays a crucial role in maintaining health by supporting digestion, immunity, and overall well-being. Disruptions to the gut microbiome can result in dysbiosis, which is correlated with disease states. Recent advances in engineering the gut microbiome, functional ingredients designed through prebiotics, probiotics, and synbiotics have progressed together with synthetic microbial communities (SynComs), which influence the modulation of microbiome composition and functional role, offering a promising strategy to restore balance and enhance health. This field is rapidly advancing with broad applications focused on improving animal and human health. This review explores the significance and current applications of the engineering microbiome and its impact on gut health, as well as the challenges and sustainable future.

Studies have demonstrated significant alterations in ovarian oxidative stress levels, ovarian degeneration, and follicular atresia during the broody period in geese. The results of this study showed that during the broody period, geese exhibited degraded ovarian tissues, disrupted follicular development, a thinner granulosa cell layer, and lower levels of ovarian hormones E2, P4, and AMH. Antioxidant activity (GSH, CAT, SOD, T-AOC, and the content of H2O2) and the mRNA expression levels of antioxidant genes (GPX, SOD-1, SOD-2, CAT, COX-2, and Hsp70) were significantly higher in pre-broody geese compared to laying geese, while the expression of apoptosis-related genes (p53, Caspase-3, and Caspase-9) increased and the anti-apoptotic gene Bcl-2 decreased. Additionally, proteomic analysis identified 703 differentially expressed proteins (DEPs), primarily concentrated in the GO categories of the biological process (biological regulation, response to stimulus, etc.) and enriched in the KEGG pathways (PI3K-Akt signaling pathway, etc.). Among them, XDH was central to the regulatory network. Furthermore, Western blotting revealed higher expression of XDH in the ovaries of pre-broody geese than those of laying geese. Pearson correlation analysis indicated a significant correlation between XDH expression and oxidative stress markers in the ovaries of geese (r > 0.75). Overall, these results demonstrated that geese experience ovarian atrophy and remarkably increased oxidative stress during the broody period, suggesting that XDH may be a key driver of broodiness in geese.

Research into the cellular metabolic adaptations of Mucor circinelloides has gained significant interest due to its capability for lipid production, which has critical industrial applications. To address the regulatory mechanisms at the systems level, this study aimed to explore the global metabolic responses associated with lipid production in high and low lipid-producing strains of M. circinelloides, WJ11 and CBS277.49, respectively, through comparative transcriptome analysis and genome-scale model-driven analysis. The transcriptome analysis of expressed genes in M. circinelloides WJ11 (6398 genes), and CBS277.49 (6008 genes) were analyzed and compared. The results revealed 2811 significantly differentially expressed genes and highlighted strain-dependent differences in growth behavior and lipid production of M. circinelloides at the fast-growing stage, driven by transcriptional regulation across key metabolic pathways. Through genome-scale model-driven analysis, we identified 20 significant reporter metabolites that provide insights into the mechanisms employed by the WJ11 strain to optimize growth for lipid production in the subsequent lipid-accumulating stage. These interplay mechanisms are primarily involved in glycolysis, the TCA cycle, leucine metabolism, energy metabolism, and one-carbon metabolism towards lipid metabolism. These findings provide valuable insights into the regulatory mechanisms underlying lipid production in Mucor and highlight potential pathways for genetic and physiological optimization in high lipid-producing strains like WJ11. This research advances our understanding of how metabolic networks are interconnected and how they can be leveraged for more efficient lipid overproduction.

Equine melanocytic neoplasm (EMN) is a skin tumor commonly observed in grey horses. Limited research has yet to investigate proteomic profiles of EMN, particularly in the early stages and their expression patterns. This study, therefore, aimed to identify signature proteins from tissue biopsies to distinguish early EMN, severe EMN, and normal groups. Using proteomic analysis of 19 tissue samples (normal: n = 6, early EMN: n = 7, severe EMN: n = 6) through LC–MS/MS, 12,310 proteins were identified. Differentially expressed proteins (DEPs) and functional interaction analysis revealed significant overexpression of Wnt signature proteins, e.g., canonical (Wnt2B) and non-canonical (Wnt5B) Wnt signaling in early EMN stages. Immunohistochemical staining (IHC) towards immunolocalizing Wnt signature protein, particularly the Wnt2B functional signal, further verified its higher expression in early EMN compared to other groups. These findings suggest that the Wnt pathway and functional insight are key mediators in signal transduction during early EMN, offering potential markers for initial stage detection. This study enhances the understanding of EMN mechanisms and the role of Wnt proteins, with implications for developing future diagnostic and therapeutic strategies.

BACKGROUND:Atopic dermatitis (AD) and food allergy (FA) often originate early in life. Gut microbiota interactions with the host immune system influence allergy development, yet the distinct gut microbiome and functional profiles in individuals with AD, FA, or both AD+FA remain underexplored. OBJECTIVE:We investigated microbial colonization and proteomic profiles in infants with AD, FA, and AD+FA compared to age- and sex-matched controls from the Allergy Development in Early Life and Associated Factors in the Thai Birth Cohort (ALICE). METHODS:Gut microbiomes from stool samples were analyzed using 16S sequencing, and proteomic analysis was conducted by liquid chromatography-tandem mass spectrometry. RESULTS:The study included 16 AD, 5 FA, 5 AD+FA subjects, and 26 controls. AD+FA group exhibited the most severe dysbiosis. Enrichment of proteins involved in methionine biosynthesis in Bifidobacterium scardovii and high Erysipelotrichaceae colonization suggest a link to high-fat diets, known to reduce intestinal short-chain fatty acid and serotonin levels, contributing to allergies. Erysipelotrichaceae in AD+FA groups also expressed proteins related to histidine degradation. Low Bifidobacteriaceae levels were noted in FA and AD+FA, with more pathogenic strains colonized. Increased Bacteroidaceae in FA and AD+FA and Enterobacteriaceae in FA were detected. Pathways involving vitamin B1, a ligand for proliferator-activated receptor-γ (PPAR-γ) from Enterobacteriaceae could promote TH2 cells, type 2 innate lymphoid cells, and M2 macrophages, likely contribute to allergic inflammation. CONCLUSIONS:AD+FA phenotype exhibited the most distinctive gut microbiome alterations, highlighting unique dysbiosis patterns. Microbiome biosynthesis pathways involving metabolism of methionine, histidine, serotonin, and vitamin B1 point to new targets for modifying or treating AD and FA.

ABSTRACT Exploring dietary methods to alter microbial communities and metabolic functions is becoming an increasingly fascinating strategy for improving health. Copra meal hydrolysate (CMH) is alternatively used as a gut health supplement. However, the functional diversity and metabolic activities in gut microbiome in relation to CMH treatment remain largely unknown. Therefore, this study aimed to identify key predominant groups of bacterial species toward diversified metabolic functions, activities, and routes using metaproteomics. As a result, the integrative analysis of metaproteomic data revealed that seven key families across 11 dominant gut bacterial species were concerted. Consistently, across 76,206 proteins assigned to the metabolism of the 255,964 annotated proteins, short-chain fatty acid (SCFA) biosynthesis, lipopolysaccharide (LPS) biosynthesis, and bile acid (BA) metabolism were positively associated with CMH. Further identification of cooperative metabolic routes promisingly highlighted the importance of glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle, inositol phosphate metabolism, steroid hormone biosynthesis, O-antigen repeat unit biosynthesis, and chloroalkane and chloroalkene degradation. This work presents an initial study of metaproteomics associated with prebiotic diet in a Thai population-based cohort in a developing Southeast Asian country.IMPORTANCEStudies primarily focused on the impact of CMH on gastrointestinal symptoms and gut microbial compositions. However, as the field moves toward understanding the relationship between microbiome and diet in relation to gut health, it is critical to evaluate how changes in metabolic activities relate to cooperative metabolic routes in the gut microbiome for promoting human health. Through the use of metaproteomics, our findings highlighted the key predominant groups of bacterial species, potential proteins, and their metabolic routes involved in gut metabolism. This study provides comprehensive insights into the fundamental relationship between microbiome and dietary supplements and suggests that metaproteomics is a powerful method for monitoring metabolic functions, activities, and routes in the gut microbiome.

Background/Objectives:Limosilactobacillus fermentum KUB-D18, a heterofermentative lactic acid bacterium with promising probiotic properties, is known for promoting gut health and nutrient absorption. Originally isolated from chicken intestines, this strain demonstrates versatile metabolic capabilities in diverse gastrointestinal environments. However, the metabolic functions and sugar transport-related genes remain largely unexplored. This study thus aimed to dissect metabolic functions and sugar transports of L. fermentum KUB-D18. Methods: Next-generation and third-generation sequencing techniques using integrative genomic platform towards transportome analysis were performed. Results: The complete genome, sized at 2.12 Mbps with a GC content of 51.36%, revealed 2079 protein-encoding genes, of which 1876 protein functions were annotated and identified in top categories involved in amino acids, nucleotide, energy, and carbohydrate transports and metabolisms. Comparative genes analysis identified 50 core and 12 strain-specific genes linked to probiotic properties, e.g., acid resistances and bile tolerances, antioxidant functions, or anti-inflammatory properties. Further, sugar transportome analysis uncovered 57 transporter genes, demonstrating diverse carbon utilization and phosphotransferase (PTS) systems, corroborated by API 50 CHL test results for carbohydrate metabolism profile. Conclusions: These findings enhance the comprehensive metabolic understanding of L. fermentum KUB-D18, supporting its industrial potential and applications in engineered probiotics.

Morchella esculenta, a nutritious and medicinal edible mushroom, has gained an increasing attention due to the bioactive properties of its polysaccharides. This study employed in vitro simulated human digestion and fecal fermentation models to evaluate the effects of M. esculenta polysaccharide on gut microbiota composition and short-chain fatty acids (SCFAs) production. Additionally, a relationship between M. esculenta polysaccharide composition, gut microbiota, and functional role was constructed to elucidate their interactions. The results revealed that 44.87 % of M. esculenta polysaccharide was digested, leading to a reduction in molecular weight and alterations in monosaccharide composition, including decreased glucose and increased galactose and mannose. Fermentation of M. esculenta polysaccharide significantly enhanced SCFAs production and promoted the growth of beneficial gut bacteria, such as Bacteroides, Collinsella, and Bifidobacterium, while notably reducing Ruminococcus torques. Carbohydrate metabolism was enriched in Collinsella and Bifidobacterium which positively correlated with SCFAs biosynthesis e.g., propanoate and butanoate biosynthesis. These findings provide valuable insights into M. esculenta polysaccharide as prebiotic potential, highlighting its functional role in modulating gut microbiota and promoting gut health.

Cordycepin, a bioactive adenosine analog, holds promise in pharmaceutical and health product development. However, large-scale production remains constrained by the limitations of natural producers, Cordyceps spp. Herein, we report the reconstruction of the first genome-scale metabolic model (GSMM) for a cordycepin-producing strain of recombinant Aspergillus oryzae. The model, iNR1684, incorporated 1684 genes and 1947 reactions with 93% gene-protein-reaction coverage, which was validated by the experimental biomass composition and growth rate. In silico analyses identified key gene amplification targets in the pentose phosphate and one-carbon metabolism pathways, indicating that folate metabolism is crucial for enhancing cordycepin production. Nutrient optimization simulations revealed that chitosan, D-glucosamine, and L-aspartate preferentially supported cordycepin biosynthesis. Additionally, a carbon-to-nitrogen ratio of 11.6:1 was identified and experimentally validated to maximize production, higher than that reported for Cordyceps militaris. These findings correspond to a faster growth rate, enhanced carbon assimilation, and broader substrate utilization by A. oryzae. This study demonstrates the significant role of GSMM in uncovering rational engineering strategies and provides a quantitative framework for precision fermentation, offering scalable and sustainable solutions for industrial cordycepin production.

Bifidobacterium fermentation has been shown to provide significant health benefits and safety advantages. This study investigated the impact of Bifidobacterium fermentation on the physicochemical characteristics, metabolic profiles, and sensory properties of Hylocereus megalanthus juice (HMJ). Bifidobacterium fermentation enhanced the physicochemical profile of HMJ by improving bioactive components and increasing the antioxidant activity. Notably, the increased soluble dietary fiber (SDF) and sodium cholate adsorption capacity (SCAC) of fermented HMJ possessed potential hypolipidemic effects. A total of 638 differential metabolites were identified by non-targeted metabolomics, mainly enriched in amino acid and carbohydrate metabolism. Targeted analysis of sugar metabolism further highlighted the transformation of mono-, di-, and tri-saccharides, particularly within the pentose phosphate pathway. Additionally, electronic tongue analysis and sensory evaluation demonstrated an improvement in the flavor profile of HMJ. These findings highlight the application of Bifidobacterium fermentation in enhancing the nutritional and sensory properties of HMJ, making it a more functional beverage.

Fermentation with lactic acid bacteria (LAB) enhances the nutritional value and flavor of food matrices. This study investigated the impact of Pediococcus acidilactici HNU168, Bifidobacterium animalis subsp. lactis HNU329, and their combined fermentation on Millennium cherry tomato juice (MFJ). Fermentation boosted organic acids, total flavonoid content (TFC), xanthine oxidase (XOD) inhibitory activity, and antioxidant activities. Mixed-strain fermentation significantly increased antioxidant activity and lycopene content beyond single-strain fermentation. Non-targeted metabolomics identified 745 differential metabolites, mainly enriched in purine metabolism and phenylpropanoid biosynthetic pathways, facilitating key metabolite biotransformation. Notably, lycoperodine l, 3-(4-hydroxyphenyl) lactate, indole-3-lactic acid, and dihydrocoumarin contents increased significantly. Molecular docking and XOD inhibitory activity confirmed strong interactions between key metabolites and XOD. Also, electronic tongue analysis showed that LAB-fermented MFJ had increased richness and reduced bitterness and astringency. These results illustrate that LAB fermentation improves MFJ's nutrition, bioactivities, and sensory properties, offering potential applications in functional or anti-hyperuricemia foods.

Synbiotic interventions have gained increasing attention for modulating gut microbiota and metabolic functions in obesity-related disorders. This study evaluated the effects of Limosilactobacillus reuteri KUB-AC5 (10⁸ CFU) and Wolffia globosa powder (6 g/day) using an in vitro continuous human gastrointestinal model. Fecal samples from obese donors were used to simulate the ascending and descending colon, with microbial viability, diversity, and metabolite production assessed over 14 days via culture-dependent and culture-independent methods. Synbiotic supplementation increased anaerobic bacterial counts by 2.6 log CFU/mL in the ascending colon and 2.2 log CFU/mL in the descending colon, with notable increases in lactic acid bacteria and reductions in Enterobacteriaceae. Metagenomic analysis revealed an increasing trend in microbial diversity and evenness after 7 days of treatment, though the changes were not statistically significant. PERMANOVA analysis confirmed significant shift in microbial community composition between stabilization, treatment, and washout periods (p < 0.05). Additionally, butyrate levels significantly increased (p < 0.05), while p-cresol, a deleterious metabolite, significantly decreased (p < 0.05). Bile acid composition was modulated, with increased tertiary bile acid 3-oxo-LCA and enhanced bile acid deconjugation, suggesting improved lipid metabolism and potential weight management benefits. These findings highlight the potential of synbiotic supplementation to enhance beneficial bacterial populations, improve microbial diversity, and support metabolic health in obesity management.

Programmed cell death (PCD) is the collective term for the intrinsically regulated death of cells. Various types of cell death are triggered by their own programmed regulation during the growth and development of organisms, as well as in response to environmental and disease stresses. PCD encompasses apoptosis, pyroptosis, necroptosis, autophagy, and other forms. PCD plays a crucial role not only in the growth and development of organisms but also in serving as a component of the host innate immune defense and as a bacterial virulence strategy employed by pathogens during invasion. The zoonotic pathogen Salmonella has the ability to modulate multiple forms of PCD, including apoptosis, pyroptosis, necroptosis, and autophagy, within the host organism. This modulation subsequently impacts the bacterial infection process. This review aims to consolidate recent findings regarding the mechanisms by which Salmonella initiates and controls cell death signaling, the ways in which various forms of cell death can impede or restrict bacterial proliferation, and the interplay between cell death and innate immune pathways that can counteract Salmonella-induced suppression of host cell death. Ultimately, these insights may contribute novel perspectives for the diagnosis and treatment of clinical Salmonella-related diseases.

The genome-scale metabolic model (GSMM) of Cordyceps militaris provides a comprehensive basis of carbon assimilation for cell growth and metabolite production. However, the model with a simple mass balance concept shows limited capability to probe the metabolic responses of C. militaris under light exposure. This study, therefore, employed the transcriptome-integrated GSMM approach to extend the investigation of C. militaris's metabolism under light conditions. Through the gene inactivity moderated by metabolism and expression (GIMME) framework, the iPS1474-tiGSMM model was furnished with the transcriptome data, thus providing a simulation that described reasonably well the metabolic responses underlying the phenotypic observation of C. militaris under the particular light conditions. The iPS1474-tiGSMM obviously showed an improved prediction of metabolic fluxes in correlation with the expressed genes involved in the cordycepin and carotenoid biosynthetic pathways under the sucrose culturing conditions. Further analysis of reporter metabolites suggested that the central carbon, purine, and fatty acid metabolisms towards carotenoid biosynthesis were the predominant metabolic processes responsible in light conditions. This finding highlights the key responsive processes enabling the acclimatization of C. militaris metabolism in varying light conditions. This study provides a valuable perspective on manipulating metabolic genes and fluxes towards the target metabolite production of C. militaris.

The association between the gut mycobiome and its potential influence on host metabolism in the Thai Cohort was assessed. Two distinct predominant enterotypes, Saccharomyces (Sa) and Aspergillus / Penicillium (Ap/Pe) showed differences in gut mycobiota diversity and composition. Notably, the Sa enterotype exhibited lower evenness and richness, likely due to the prevalence of Saccharomyces , while both enterotypes displayed unique metabolic behaviors related to nutrient metabolism and body composition. Fiber consumption was positively correlated with adverse body composition and fasting glucose levels in individuals with the Sa enterotype, whereas in the Ap/Pe enterotype it was positively correlated with fat and protein intake. The metabolic functional analysis revealed the Sa enterotype associated with carbohydrate metabolism, while the Ap/Pe enterotype involved in lipid metabolism. Very interestingly, the genes involved in the pentose and glucuronate interconversion pathway, such as polygalacturonase and l -arabinose-isomerase, were enriched in the Sa enterotype signifying a metabolic capacity for complex carbohydrate degradation and utilization of less common sugars as energy sources. These findings highlight the interplay between gut mycobiome composition, dietary habits, and metabolic outcomes within the Thai cohort studies.