PubMed

Vet Sci. 2025 Feb 1;12(2):102. doi: 10.3390/vetsci12020102.ABSTRACTThis study aimed to investigate the changes in fecal short-chain fatty acids (SCFAs) content in UCP1 knock-in pigs (KI pigs) and their effect on adipogenesis. Fecal samples from five 6-month-old wild-type (WT) and KI pigs were collected for targeted metabolomics and 16s rRNA sequencing analyses to identify differences in SCFAs and gut microbiota that may contribute to regulating fat deposition in pigs. The metabolome of pig fecal samples targeted for an analysis of SCFAs identified seven SCFAs, with caproic acid (except isovaleric acid) being the significantly different one. The results of the fecal 16s rRNA analysis demonstrated a notable reduction in the abundance of Streptococcus spp. in the KI pigs in comparison to the WT pigs, with a statistically significant difference. Correlation analyses demonstrated a statistically significant positive correlation between the abundance of Streptococcus spp. and SCFAs, as well as pig body weight and fatness. It was postulated that the reduction in SCFAs in the intestinal tracts of KI pigs may be associated with a reduction in Streptococcus spp. abundance. Compared to WT pigs, the concentration of fecal SCFAs in KI pigs was significantly reduced, which may be related to the decreased abundance of Streptococcus. The in vitro experiments showed that caproic acid could significantly enhance the differentiation efficiency of porcine SVF cells into mature adipocytes by activating the FFAR4 gene.PMID:40005862 | DOI:10.3390/vetsci12020102

Vet Sci. 2025 Jan 22;12(2):79. doi: 10.3390/vetsci12020079.ABSTRACTIn lactating ewes, energy demand increases for milk production, reserve mobilizations, and body weight maintenance. For reconversion to energy, ruminants require ruminal propionate production because it is the most predominant substrate for gluconeogenesis and one of the most relevant pathways since it allows an adequate supply of glucose. Calcium propionate supplementation is an alternative to increase glucose production by an external additive. Thus, the objective was to evaluate the effect of calcium propionate (CaPr) on milk production and milk metabolomic profile on lactating ewes. Sixteen Rambouillet (65.3 ± 6.2 kg BW; three years old) were randomly assigned one of two experimental treatments: (a) basal diet without supplementation (CP/0S) and (b) basal diet + 30 g d-1 of CaPr (CP/30S). The experimental period was from parturition day until day 60 (baby lamb weaning). A completely randomized design was used and analyzed with a mixed model. Initial and final lactating weight and milk production differed statistically (p < 0.05) between treatments. CP/30S led to differential changes (p < 0.05) in the lactation curve, showing significant milk production over eight-week measurements. Lactation peak (mL), maximum production (mL), and lactational persistency (d) were superior (p < 0.05) for supplemented ewes. An 11.4% variability was shown in a principal component analysis between treatments. For CP/0S, 63 bioactive compounds were detected, and 55 for CP/30S treatment. The metabolites detected in CP/0S showed that only fatty acid biosynthesis, biosynthesis of unsaturated fatty acids, and fatty acid elongation pathways were affected (p < 0.05) in milk. However, for CP/30S, metabolic pathways related (p < 0.05) were fatty acid biosynthesis, biosynthesis of unsaturated fatty acids, fatty acid elongation, phenylalanine metabolism, and steroid metabolism in milk samples. Calcium propionate supplementation increases milk performance and lactation persistency-induced changes in specific metabolic milk production pathways.PMID:40005839 | DOI:10.3390/vetsci12020079

Microorganisms. 2025 Feb 19;13(2):459. doi: 10.3390/microorganisms13020459.ABSTRACTGlobal climate change has accelerated the reduction of permafrost regions across different altitude gradients, shortening the duration of the freezing period to varying extents. However, the response of the soil microorganisms of frozen soils along altitude gradients remains unclear. In this study, we employed 16S rRNA sequencing and LC-MS metabolomics to investigate the response of soil microbial communities and soil metabolites to vertical stratification in the permafrost soils of the Qinghai Lake region. The results indicated that Proteobacteria, Firmicutes, and Actinobacteria were key soil bacterial phyla in the permafrost soils of Qinghai Lake during the freezing period, with Proteobacteria and Firmicutes showing significant sensitivity to vertical stratification (p < 0.05). The majority of the physicochemical factors exhibited a trend of initially increasing and then decreasing with increasing altitude, whereas pH showed the opposite trend. pH and moisture content were identified as the most important environmental factors influencing soil bacterial community structure. Deterministic processes dominated the assembly of bacterial communities of frozen soils in the Qinghai Lake basin. Co-occurrence network analysis showed that increasing altitude gradients led to a higher average degree of the bacterial network, while reducing network complexity and inter-species connectivity. Soil metabolomics analysis revealed that vertical stratification altered the metabolic profiles of 27 metabolites, with the significantly changed metabolites primarily associated with carbohydrate and amino acid metabolism. In conclusion, the characteristics of the Qinghai Lake permafrost were regulated by regional vertical stratification, which further influenced microbial community structure and soil metabolic characteristics, thereby altering carbon and nitrogen stocks. Specifically, higher altitudes were more favorable for the retention of the carbon and nitrogen stocks of frozen soils in the Qinghai Lake basin.PMID:40005823 | DOI:10.3390/microorganisms13020459

Microorganisms. 2025 Feb 8;13(2):372. doi: 10.3390/microorganisms13020372.ABSTRACTTo investigate the regulatory effect of a bacteriocin-producing strain of Enterococcus faecalis DH9003 on the gut microbiota of mice, 15 healthy C57 male mice were randomly administered an equal volume of sterile normal saline (HD, control group, n = 7) and E. faecalis DH9003 (YD, treatment group, n = 8) via gavage. Metagenomic and metabolomic analyses were performed to determine the composition and metabolic function of the intestinal microbiota in mice. The results showed that the relative abundance of Firmicutes continuously increased over time in YD compared to HD. The number of E. faecalis DH9003 increased slowly and remained steady from days 7 to 28, indicating that E. faecalis DH9003 could colonize a considerable number of mouse guts via intragastric administration. Supplementation with E. faecalis DH9003 demonstrated a regulatory effect on the intestinal microbiota composition of mice, causing a shift in the relative abundance of Bacteroidetes and Firmicutes at the phylum level. In addition, a total of 2426 different metabolites were found in mouse feces, including 1286 and 1140 metabolites in positive and negative modes, respectively. Vitamin B6 and succinate were the most regulated and downregulated metabolites in negative ion mode, and the most upregulated and downregulated metabolites in positive ion mode were N-methyl-glutamic acid and N-octanoyl sphingosine. In conclusion, E. faecalis DH9003 can colonize mice gut, affecting the gut microbiota and metabolic competence. This strain therefore offers considerable potential for application as a probiotic.PMID:40005739 | DOI:10.3390/microorganisms13020372

Microorganisms. 2025 Feb 5;13(2):338. doi: 10.3390/microorganisms13020338.ABSTRACTPhotosynthetic microorganisms, such as microalgae, are remarkable for their ability to harness sunlight, fix carbon dioxide, and produce a variety of bioactive compounds. These organisms are pivotal in climate mitigation strategies as they can absorb carbon dioxide while generating valuable biomolecules. Among the diverse cultivation approaches, mixotrophic growth combines light energy with both inorganic and organic carbon sources, offering a unique strategy to enhance biomass production and metabolic diversity in microalgae. Here, microalgal species such as Nannochloropsis granulata, Phaeodactylum tricornutum, and Chlorella sp. were investigated for their potential applications under different cultivation methods, including phototrophy and mixotrophy. Mixotrophic conditions significantly improved biomass production across all tested species. Among these, Phaeodactylum tricornutum, a marine diatom, emerged as a promising candidate for bioactive compound production, exhibiting higher antiproliferative activity against human melanoma cells and antibacterial effects against Staphylococcus aureus. Importantly, Chlorella sp. was also found to possess antibacterial activity against Staphylococcus aureus, broadening its potential applications. Additionally, metabolomics analysis was performed on Chlorella sp. and Phaeodactylum tricornutum to identify the compounds responsible for the observed bioactivity. This study highlights the value of mixotrophic cultivation in enhancing the productivity and bioactivity of microalgae, positioning them as versatile organisms for sustainable biotechnological applications.PMID:40005705 | DOI:10.3390/microorganisms13020338

Microorganisms. 2025 Jan 26;13(2):279. doi: 10.3390/microorganisms13020279.ABSTRACTVarious bacterial strains with nitrate-reducing capacity (NRC), such as Haemophilus, Actinomyces, and Neisseria, are known to promote NH3 production, control pH in the oral cavity, and inhibit the growth of aciduric bacteria. However, experimental evidence on various estimated bacterial networks within the salivary microbiome is insufficient. This study aims to explore potential bacterial compositional competition observed within saliva samples from dental caries patients through a co-culture assay of mitis Streptococci, which is a primary colonizer in the salivary microbiome, and nitrate-reducing bacteria Haemophilus parainfluenzae. We investigated bacterial growth efficiency change by co-culture time using the qRT-PCR method. In addition, we applied LC/Q-TOF-based metabolites screening to confirm metabolic interactions between oral bacterial species and their association with dental caries from a metabolomics perspective. As a result, we first found that the nitrate reduction ability of H. parainfluenzae is maintained even in a co-culture environment with the mitis Streptococci group through a nitrate reduction test. However, nitrate reduction efficiency was hindered when compared with monoculture-based nitrate reduction test results. Next, we designed species-specific primers, and we confirmed by qRT-PCR that there is an obvious competitive relationship in growth efficiency between H. parainfluenzae and two mitis Streptococci (S. australis and S. sanguinis). Furthermore, although direct effects of nitrate reduction on competition have not been identified, we have potentially confirmed through LC/Q-TOF-based metabolite screening analysis that the interaction of various metabolic compounds synthesized from mitis Streptococci is driving inter-strain competition. In particular, we constructed a basic reference core-metabolites list to understand the metabolic network between each target bacterial species (H. parainfluenzae and mitis Streptococci) within the salivary microbiome, which still lacks accumulated research data. Ultimately, we suggest that our data have potential value to be referenced in further metagenomics and metabolomics-based studies related to oral health care.PMID:40005646 | DOI:10.3390/microorganisms13020279

Microorganisms. 2025 Jan 22;13(2):234. doi: 10.3390/microorganisms13020234.ABSTRACTBiofilms are one of the ways microorganisms exist in natural environments. In recent years, research has gradually shifted its focus to exploring the complexity and interactions of multi-species biofilms. A study showed that nine gut bacteria can form a multi-species biofilm on wheat fibers (M9 biofilm). However, the previous study did not clarify the reasons why M9 exhibited a better biofilm formation ability than the mono-species biofilms. In this study, the gene expression levels and metabolic accumulation of the M9 multi-species biofilm and biofilms of each individual bacterium were analyzed using transcriptomes and metabolomes. The differentially expressed genes (DEGs) showed that there were 740 common DEGs that existed in all of the nine groups, and they could regulate five pathways related to bacterial motility, cellular communication, and signal transduction. The metabolome results revealed that many peptides/amino acids and derivatives were produced in the M9 biofilm. Furthermore, purine metabolism was significantly enhanced in the M9 biofilm. L-arginine, l-serine, guanosine, and hypoxanthine were the common differentially accumulated metabolites (DAMs). The combined analysis of the transcriptomes and metabolomes showed that there were 26 common DEGs highly correlated with the four common DAMs, and they were involved in five metabolic pathways related to amino acids and purines. These results indicate that M9 can regulate multi-species biofilm formation by modulating genes related to bacterial motility, cellular communication, signal transduction, and the metabolism of amino acids and purines. This study provides insights into the interactions of microbial biofilms.PMID:40005603 | DOI:10.3390/microorganisms13020234

Pathogens. 2025 Jan 22;14(2):106. doi: 10.3390/pathogens14020106.ABSTRACTChagas disease, caused by Trypanosoma cruzi, is a parasitic zoonosis with significant health impacts, particularly in Latin America. While traditionally associated with vector-borne transmission, increased migration has expanded its reach into urban and non-endemic regions. Congenital transmission has become a critical route of infection, involving intricate maternal-fetal immune interactions that challenge diagnosis and treatment. This review synthesizes findings from three RNA-seq studies that explore the molecular underpinnings of congenital Chagas disease, emphasizing differentially expressed genes (DEGs) implicated in host-pathogen interactions. The DAVID tool analysis highlighted the overexpression of genes associated with the innate immune response, including pro-inflammatory cytokines that drive chemotaxis and neutrophil activation. Additionally, calcium-dependent pathways critical for parasite invasion were modulated. T. cruzi exploits the maternal-fetal immune axis to establish a tolerogenic environment conducive to congenital transmission. Alterations in placental angiogenesis, cellular regeneration, and metabolic processes further demonstrate the parasite's ability to manipulate host responses for its survival and persistence. These findings underscore the complex interplay between the host and pathogen that facilitates disease progression. Future research integrating transcriptomic, proteomic, and metabolomic approaches is essential to unravel the molecular mechanisms underlying congenital Chagas disease, with a particular focus on the contributions of genetic diversity and non-coding RNAs in immune evasion and disease pathogenesis.PMID:40005483 | DOI:10.3390/pathogens14020106

Medicina (Kaunas). 2025 Feb 4;61(2):262. doi: 10.3390/medicina61020262.ABSTRACTKidney transplantation stands as the preferred treatment for end-stage kidney disease, significantly improving both the quality and longevity of life compared to dialysis. In recent years, the survival rates for patients and grafts have markedly increased thanks to innovative strategies in desensitization protocols for incompatible transplants and advancements in immunosuppressive therapies. For kidney transplant recipients, preventing allograft rejection is of paramount importance, necessitating the use of immunosuppressive medications. Regular follow-up appointments are essential, as monitoring the function of the kidney allograft is critical. Currently, established biomarkers such as serum creatinine, estimated Glomerular Filtration Rate (eGFR), proteinuria, and albuminuria are commonly employed to assess allograft function. However, these biomarkers have limitations, as elevated levels often indicate significant allograft damage only after it has occurred, thereby constraining treatment options and the potential for restoring graft function. Additionally, kidney biopsies, while considered the gold standard for diagnosing rejection, are invasive and carry associated risks. Consequently, the identification and development of new, sensitive, and specific biomarkers like dd-cfDNA, microRNAs (e.g., miR-21, miR-155), and sCD30 for allograft rejection are crucial. To tackle this challenge, intensive ongoing research employing cutting-edge technologies, including "omics" approaches, like genomic techniques, proteomics, or metabolomics, is uncovering a variety of promising new biomarkers.PMID:40005378 | DOI:10.3390/medicina61020262

Molecules. 2025 Feb 19;30(4):957. doi: 10.3390/molecules30040957.ABSTRACTThe secondary metabolome of Nemania diffusa, isolated as an ash endophytic fungus, was analyzed in detail. From its cultures, a previously undescribed cytochalasin 1 was isolated using preparative HPLC, together with six known congeners: 18-dehydroxy-cytochalasin E (2), cytochalasins Z7 (3), Z8 (4), and E (5), 18-dehydroxy-17-didehydro-cytochalasin E (6), and K Steyn (7). The structures of these compounds were determined using data from high-resolution mass spectrometry (HR-MS), in combination with 1D and 2D nuclear magnetic resonance (NMR) spectroscopy. Metabolites 1-4 share a characteristic 12-membered lactone moiety, placing them within a rarely examined cytochalasin subclass. Thus, the compounds were incorporated into our ongoing screening campaign to study the structure-activity relationship of this metabolite family. We initially determined their cytotoxicity in eukaryotic mouse fibroblast L929 cells using an MTT-based colorimetric assay, and further investigated their effect on the cellular actin dynamics of the human osteosarcoma cell line U-2OS in detail. Unexpectedly, we discovered a high number of irreversible compounds (1, 2, and 4). Additionally, we highlighted specific structural features within the 12-membered cytochalasin subclass that may play a role in directing the reversibility of these compounds.PMID:40005267 | DOI:10.3390/molecules30040957

Molecules. 2025 Feb 18;30(4):945. doi: 10.3390/molecules30040945.ABSTRACTAquilaria spp. are a highly valuable plant species found in the Chinese herbal medicine and agarwood fragrance supplement industries for fumigation, combustion and perfume. The phytochemical composition of agarwood oils (extracts) was derived from Aquilaria sinensis and its subspecies 'Qi-Nan' using supercritical CO2 extraction technology. Gas chromatography connected with a mass spectrometry apparatus was employed for qualitative and quantitative analyses. Comparing the agarwood oils from six planting areas, 12 common components were obtained, among which sesquiterpenes and chromones had the highest relative content. Genetic and environmental factors had the greatest impact on the three chromones, especially on 2-phenyl-4H-chromen-4-one. According to the PCA and PLS-DA models, the 'Qi-Nan' was derived from a variety selected from the native A. sinensis, and the difference in the volatile components was able to indirectly prove that it was genetically heterogeneous with the native A. sinensis. Using the 73 components obtained from GC-MS analysis, the VIP values and S-plots were generated using the OPLS-DA model. Seven components with VIP values > 1.0 were selected from two groups of agarwood oils of the native A. sinensis and 'Qi-Nan' subspecies. In addition, by analyzing 12 common components, the differential components with VIP values > 1 were 2-phenyl-4H-chromen-4-one and 2-(4-methoxyphenethyl)-4H-chromen-4-one. Chromones were the main component of agarwood oils extracted by supercritical CO2, and 2-phenyl-4H-chromen-4-one could be used as a volatile marker, especially in the 'Qi-Nan' subspecies, where this marker exhibited more prominent characteristics.PMID:40005255 | DOI:10.3390/molecules30040945

Molecules. 2025 Feb 17;30(4):924. doi: 10.3390/molecules30040924.ABSTRACTPulsed electric field (PEF) has previously been recognized as a method of gentle food processing, and its use has been shown to be helpful in reducing the levels of toxigenic Fusarium micromycetes developed during malting. The aim of this study was to describe the effects of PEF on gene expression and metabolite production at the pre-finishing stage of barley malting by using a novel multi-omics data-driven approach. The study helps to uncover the processes occurring in the germinated grain and discusses the up-/downregulation of genes and metabolites in relation to fungal infection and/or PEF-induced abiotic stress. Among the factors upregulated by PEF and previously described as supportive against Fusarium diseases, we identified the increased expression of genes encoding vegetative gp1-like protein, which positively correlated with flavonoids, (methylsulfanyl)prop-2-enoates, triterpenoid glycosides, and indole alkaloids. On the other hand, some genes associated with barley resistance to fungal infection were also overexpressed in the untreated control (in particular, genes encoding ethylene response factor 3-like, putrescine hydroxycinnamoyltransferase 3-like, and dirigent protein 21-like). This study provides the first 'data-driven' basic research results that contribute to the understanding of the role of PEF as an effective fungal decontamination strategy and allows the formulation of new hypotheses related to Fusarium pathogen crosstalk.PMID:40005235 | DOI:10.3390/molecules30040924

Molecules. 2025 Feb 17;30(4):923. doi: 10.3390/molecules30040923.ABSTRACTAstragali Radix (AR), a traditional food and medicinal herb used for thousands of years, is widely recognized for its role in enhancing immunity, particularly when combined with adjuvant chemotherapy. The two primary types of AR available in the market are imitation wild AR (grown for seven years) and cultivated AR (grown for two years). However, whether differences exist in their immune-enhancing effects and chemical constituents remains unclear. In this study, a comparative analysis was performed to evaluate the immune activity and chemical composition of cultivated and imitation wild AR. Immune activity was assessed through in vivo animal studies, while metabolomic analysis was used to characterize their chemical profiles. The results demonstrate that AR possesses significant antitumor and immune-enhancing activities, with imitation wild AR showing superior efficacy compared with cultivated AR. Following 16 days of daily AR treatment, both the thymus and spleen coefficients were significantly increased, effectively reversing the immune dysfunction induced by cyclophosphamide (CTX). Moreover, the administration of AR showed no significant toxicity, as evidenced by the stable liver and kidney function indicators, including ALT, UREA, and CRE levels. To investigate chemical differences, a customized chemotaxonomic-based in-house library containing 215 compounds was developed and integrated with the Progenesis QI informatics platform for metabolite annotation. Using multivariate analysis, 48 constituents were identified in total: 46 unique to the imitation wild AR and 45 specific to the cultivated AR. The correlation between chemical constituents and the pharmacological effects of AR was evaluated. Based on orthogonal partial least-squares discriminant analysis (OPLS-DA) and S-plot analysis, five potential biomarkers were identified, including Calycosin-7-glucoside, Rhamnocitrin-3-O-β-D-glucopyranoside, Ononin, 3,5-Dicaffeoylquinic acid, and Acetylastragaloside I. These biomarkers likely account for the differences in immune-enhancing effects between the two AR types. This study provides a scientific foundation for the rational use of Astragali Radix.PMID:40005233 | DOI:10.3390/molecules30040923

Molecules. 2025 Feb 12;30(4):850. doi: 10.3390/molecules30040850.ABSTRACTNowadays, the diagnosis of Parkinson's disease (PD) remains essentially clinical, based on the subjective observations of clinicians. In addition, misdiagnosis with other neuro disorders, such as Alzheimer's (AD), can occur. Herein, an untargeted lipidomic analysis of 75 plasma samples was performed to identify lipid species capable of discriminating between these two neuro groups. Therefore, PLS-DA and OPLS-DA analysis revealed significant differences in patient profiles in the sphingolipid and glycerophospholipid categories. As a result, a putative lipid biomarker panel was developed, which included HexCer (40:1; O2) and PC (O-32:0), with an area under the receiver operating characteristic curve (AUC) > 80, respectively. This panel was effective in discriminating between diseased and healthy subjects, but most importantly, it could discriminate between two neurodegenerative disorders that can present similar symptoms, namely PD and AD. Together, these findings suggest that the dysregulated metabolism of lipids plays a critical role in AD and PD pathology and may represent a valuable clinical tool for their diagnosis. Thus, further targeted studies are encouraged to better understand the underlying mechanisms of PD and confirm the diagnostic potency of the identified lipid metabolites.PMID:40005161 | DOI:10.3390/molecules30040850

Molecules. 2025 Feb 10;30(4):821. doi: 10.3390/molecules30040821.ABSTRACTNatural matrices have historically been a cornerstone in drug discovery, offering a rich source of structurally diverse and biologically active compounds. However, research on natural products often faces significant challenges due to the complexity of natural matrices, such as urine, and the limitations of bioactivity assessment assays. To ensure reliable insights, it is crucial to optimize experimental conditions to reveal the bioactive potential of samples, thereby improving the validity of statistical analyses. Approaches in metabolomics further strengthen this process by identifying and focusing on the most promising compounds within natural matrices, enhancing the precision of bioactive metabolite prioritization. In this study, we assessed the bioactivity of 17 dromedary urine samples on human renal cells under serum-reduced conditions (1%FBS) in order to minimize possible FBS-derived interfering factors. Using viability assays and Annexin V/PI staining, we found that the tumor renal cell lines Caki-1 and RCC-Shaw were more sensitive to the cytotoxic effects of the small molecules present in dromedary urine compared to non-tumor HK-2 cells. Employing NMR metabolomics analysis combined with detected in vitro activity, our statistical model highlights the presence of bioactive compounds in dromedary urine, such as azelaic acid and phenylacetyl glycine, underscoring its potential as a sustainable source of bioactive molecules within the framework of green chemistry and circular economy initiatives.PMID:40005133 | DOI:10.3390/molecules30040821

Molecules. 2025 Feb 8;30(4):782. doi: 10.3390/molecules30040782.ABSTRACTAccurate quantification of indoxyl sulfate (IndS) and p-cresyl sulfate (pCS) is essential for understanding their role in chronic kidney disease (CKD) progression and for developing strategies to mitigate their harmful effects, including cardiovascular morbidity and renal fibrosis. Advances in liquid chromatography-high-resolution mass spectrometry (LC-HRMS) enable the integration of powerful diagnostic tools into clinical laboratories. Along with accurate quantification, precise mass measurements allow for untargeted compound identification.METHODS: An LC-HRMS was validated for quantifying IndS and pCS in human serum, following EMA guidelines. The method involved protein precipitation with methanol, micro-LC for chromatographic separation, and detection based on accurate mass, with simultaneous high-resolution full-scan acquisition. Clinical samples from patients with varying degrees of renal insufficiency and samples obtained before and after hemodiafiltration were analyzed.RESULTS: The method demonstrated acceptable linearity, precision, and accuracy. The measurement range for both analytes was from 100 to 40,000 ng/mL. Serum levels of IndS and pCS correlated with decreased renal function. After hemodiafiltration, there was a significant reduction of IndS (50%) and pCS (43%). Simultaneous untargeted analysis allowed to identify metabolites significantly underexpressed after hemodiafiltration.CONCLUSIONS: An accurate LC-HRMS method was validated for the quantification of IndS and pCS serum levels in patients with CKD, providing insights into toxin dynamics and enabling untargeted metabolic evaluation.PMID:40005095 | DOI:10.3390/molecules30040782

Molecules. 2025 Feb 7;30(4):779. doi: 10.3390/molecules30040779.ABSTRACTThe rapid and accurate annotation of the complex compounds and metabolites in natural products remains a significant challenge. In this study, we developed an integrated strategy to efficiently and accurately profile both the prototypes and metabolites of natural products in vivo. And this was achieved by establishing a gypenosides constituent database and utilizing R programming language to combine sample selection, virtual metabolite database construction, polygon mass defect filtering, and Kendrick mass defect filtering. In addition, the annotation strategy was successfully applied to identify the prototypes and metabolites of gypenosides in mice serum. As a case study, gypenoside LXXV was used to validate the feasibility of this approach. The results demonstrated 36 prototypes and 108 metabolites were annotated from the serum by the established annotation strategy. The prototype and eight metabolites of gypenoside LXXV were further confirmed, indicating that the proposed strategy is available. This study provides a novel approach for the rapid and accurate identification of prototypes and metabolites of natural products and offers new insights into the metabolic processes of gypenosides in vivo.PMID:40005091 | DOI:10.3390/molecules30040779

Molecules. 2025 Feb 7;30(4):772. doi: 10.3390/molecules30040772.ABSTRACTPeperomia campylotropa (Piperaceae) is a species with a traditional Mexican gastroprotective use that has never-before been studied using metabolomics. This study explores the ethnobotanical use of the species, aiming to define the gastroprotective effect of the aqueous extract and characterize its secondary metabolites by UHPLC-MS analysis. To validate its use, we botanically identified the species re-collected in the Municipality of Buenavista de Cuéllar, Guerrero, Mexico. We conducted interviews to provide evidence of the traditional details of its consumption and knowledge. Subsequently, qualitative phytochemical tests were performed to elucidate the possible secondary metabolites, which were also characterized under UHPLC-MS analysis and analyzed according to their primary type and retention times. Indomethacin (IND)- and ethanol (EtOH)-induced gastric damage models in Wistar rats were used for pharmacological evaluation, considering the ulceration index and gastroprotection percentage. Along with the participation in the mechanism of action of nitric oxide (NO), sulfhydryl (-SH) groups and prostaglandins (PG) were elucidated by Wistar rats pretreated with N(ω)-nitro-L-arginine methyl ester (L-NAME), N-Ethylmaleimide (NEM), and IND, respectively. Acute intragastric toxicity was also estimated in NIH female mice. Ninety people were interviewed, revealing the traditional knowledge of P. campylotropa as food and medicine for stomach diseases, including irritation and indigestion. The presence of phenolic compounds (48%), N-containing compounds (22%), glycosides (21%), terpenoids (7%), and lactones (4%) were verified by preliminary phytochemical analysis and by UHPLC-MS in which 162 secondary metabolites were characterized. Besides that, the aqueous extract at 62.5, 125, and 250 mg/kg of body weight (b.w.) decreased the ulcerative index, showing gastroprotection percentages between 60 and 80%, similar to that of omeprazole. Furthermore, -SH group participation in its activity was established. All this evidence supports the gastroprotective activity of P. campylotropa for the first time and contributes to understanding its secondary metabolite content.PMID:40005084 | DOI:10.3390/molecules30040772

Molecules. 2025 Feb 7;30(4):770. doi: 10.3390/molecules30040770.ABSTRACTBACKGROUND/OBJECTIVES: This study explores the metabolic adaptations and quality differences between wild and farmed gilthead seabream (Sparus aurata), with a particular focus on lipid composition and metabolite profiles. These differences are examined in the context of varying environmental conditions, feeding regimes, and post-harvest processes. High-resolution magic-angle-spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy was employed to perform the metabolomic analysis.RESULTS: Farmed seabream exhibited higher lipid content and PUFA levels (e.g., DHA and EPA) due to aquaculture diets, while wild seabream showed lower lipid concentrations and elevated levels of polar metabolites. Metabolic trade-offs in wild seabream reflected greater physical activity and environmental adaptation. The K-value indicated faster spoilage in farmed seabream, particularly from Greece, linked to handling conditions. HR-MAS provided precise, reproducible results, allowing direct quantification of key metabolites without altering sample integrity.METHODS: HR-MAS NMR was employed to analyze muscle tissue from wild and farmed seabream (produced in Spain and imported from Greece), providing high-resolution spectra without requiring sample extraction. Metabolite quantification included polyunsaturated fatty acids (PUFAs), creatine, taurine, lactate, and trimethylamine N-oxide (TMAO). Freshness was monitored using the K-value index, calculated from ATP derivative levels in samples stored at 4 °C.CONCLUSIONS: The study highlights the influence of diet and environment on the metabolic profiles of seabream. HR-MAS NMR emerges as a robust method for metabolomic studies and freshness assessment. Findings emphasize the potential for dietary adjustments to optimize aquaculture practices and fish quality while underscoring the importance of sustainable production strategies. Further research into lipid metabolism genes and environmental factors is recommended to deepen understanding of these adaptations.PMID:40005081 | DOI:10.3390/molecules30040770

Nutrients. 2025 Feb 18;17(4):724. doi: 10.3390/nu17040724.ABSTRACTBackground/Objectives: Long-term spaceflight in a microgravity environment frequently results in gastrointestinal dysfunction, presenting substantial challenges to astronauts' health. Hericium erinaceus, a plant recognized for its dual use as food and medicine, contains a key functional component called Hericium erinaceus polysaccharide (HEP), which is purported to promote gastrointestinal health. This study aims to investigate the protective effects of HEP against gastrointestinal disturbances induced by simulated weightlessness and to elucidate its regulatory mechanisms. Methods: Sprague Dawley rats subjected to a tail suspension model were administered either a standard diet or a diet supplemented with 0.125% HEP over a period of 4 weeks (the intake of HEP is approximately 157.5 mg/kg bw/d, n = 8), metagenomics and targeted metabolomics to investigate the effects of HEP on gastrointestinal hormone secretion disorders, gut microbiota dysbiosis, and intestinal barrier damage induced by simulated weightlessness. Results: Dietary supplementation with HEP was observed to significantly alleviate weightlessness-induced gastrointestinal hormone disruptions, enhancing motility and intestinal barrier function while reducing inflammation. In addition, HEP improved gut microbiota by boosting beneficial bacteria as Oscillibacter sp.1-3, Firmicutes bacterium ASF500, and Lactobacillus reuteri, while reducing harmful bacteria like Escherichia coli and Mucispirillum schaedleri at the species level. Furthermore, HEP altered the serum metabolic profile of the rats, reducing inflammation by upregulating the tryptophan metabolism pathway and enhancing the production of short-chain fatty acids. Conclusions: HEP effectively protects against gastrointestinal dysfunction induced by simulated weightlessness by regulating hormone secretion and maintaining intestinal homeostasis.PMID:40005052 | DOI:10.3390/nu17040724