Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

Impact of intragastric administration of donkey milk on mouse immunity utilizing gut microbiomics and plasma metabolomics

Thu, 27/03/2025 - 11:00
Front Vet Sci. 2025 Mar 12;12:1486406. doi: 10.3389/fvets.2025.1486406. eCollection 2025.ABSTRACTINTRODUCTION: Donkey milk demonstrates closer compositional resemblance to human milk compared to bovine milk, positioning it as an optimal nutritional substitute for infants with cow's milk allergy. Furthermore, its rich profile of bioactive compounds suggests potential immunomodulatory properties. This study systematically investigated the effects of donkey milk supplementation on murine immune function and gut microbiome dynamics, thereby providing mechanistic insights to support its clinical development in functional food applications.METHODS: Following daily intragastric administration of 10 mL/kg of body weight of donkey milk (DM) or distilled water (DW) to the mice for 28 consecutive days, liver tissues were harvested for immunological profiling, with concurrent collection of blood samples for plasma metabolomic analysis and fecal specimens for gut microbiome characterization. Subsequently, the modulatory effects of donkey milk supplementation on immune parameters, intestinal microbiota composition, and plasma metabolic profiles were systematically evaluated.RESULTS: Immunity analysis revealed that intragastric administration of DM raised the levels of IL-6 and TNF-α cytokines in mouse liver. In addition, DM modulated the composition of both the murine gut microbiome and plasma metabolites. One-hundred and forty-five differentially-produced metabolites were identified, most prominently nicotinamide, L-valine, and β-estradiol, that are primarily associated with valine, leucine, and isoleucine biosynthesis and degradation, nicotinate and nicotinamide metabolism, and unsaturated fatty acid biosynthesis. Alterations at phylum, genus, and species levels were evident in the fecal microbiota of mice after intragastric administration of DM. In particular, an increased abundance of the Lactobacillus bacterium was observed. Correlation analysis of differential metabolites and microbiomes indicated a correspondence between Falsiroseomonas and Salipiger species and the antioxidant coenzyme Q that has the potential to activate the immune system.CONCLUSION: The data collectively suggest that DM may adjust the murine gut microbiome and plasma metabolites thereby potentially improving immunity in mice.PMID:40144527 | PMC:PMC11938429 | DOI:10.3389/fvets.2025.1486406

Effects of high light exposure and heterologous expression of β-carotene ketolase on the metabolism of carotenoids in <em>Chlamydomonas reinhardtii</em>

Thu, 27/03/2025 - 11:00
Front Bioeng Biotechnol. 2025 Mar 10;13:1533661. doi: 10.3389/fbioe.2025.1533661. eCollection 2025.ABSTRACTINTRODUCTION: Stress from high light exposure and overexpression of β-carotene ketolase can have significant effects on the synthesis of carotenoids in Chlamydomonas reinhardtii. As a promising platform for carotenoid production, C. reinhardtii needs further research and technological innovation to address challenges, such as environmental interference, exogenous gene expression, and metabolic regulation, to achieve efficient and sustainable production of carotenoids.METHODS: Appropriate β-carotene ketolase were selected from different organisms and subjected for codon optimization based on the preferences of the nuclear genome of C. reinhardtii. After designation, including intron insertion and chloroplast transit peptide, expression vectors were constructed and used for nuclear transformation of C. reinhardtii CC849 by bead milling method. Subsequently, DNA-PCR and RT-PCR were used to identify positive transformants grown with antibiotic stress, LC-MS/MS and metabolic analysis were performed to evaluate the products of transformants.RESULTS: In this study, carotenoid metabolism regulation in C. reinhardtii was investigated in a time-dependent manner through high light exposure and heterologous expression of β-carotene ketolase. The results suggested that the stress from high light exposure (500 μmol/m2/s) negatively regulated the accumulation of β-carotene; positively induced the accumulation of zeaxanthin, echinenone, and canthaxanthin; and continuously promoted accumulation of zeaxanthin and canthaxanthin in C. reinhardtii. Metabolomics analysis suggested that high light exposure stress promoted biosynthesis of carotenoids, improved the intermediates associated with the astaxanthin synthesis pathway, and promoted conversion of β-carotene to downstream substances. Several strategies were implemented to improve canthaxanthin production in C. reinhardtii to achieve overexpression of β-carotene ketolase genes from different sources, including strong promoters, insertion introns, and chloroplast conduction peptides. It was found that β-carotene, echinenone, and canthaxanthin were all significantly increased in the transformed C. reinhardtii overexpressing β-carotene ketolase. Among these, the highest canthaxanthin content was found in pH124-CrtO, which was seven times that observed in the wild type. Moreover, the metabolomics analysis of carotenoids showed promotion of the abscisic acid and astaxanthin pathways in the transformed C. reinhardtii.DISCUSSION: The results of this study provide a new scheme for manipulating the metabolism of carotenoids and promoting the synthesis of high-value carotenoids in C. reinhardtii.PMID:40144396 | PMC:PMC11938120 | DOI:10.3389/fbioe.2025.1533661

Bile acid signaling in skeletal muscle homeostasis: from molecular mechanisms to clinical applications

Thu, 27/03/2025 - 11:00
Front Endocrinol (Lausanne). 2025 Mar 12;16:1551100. doi: 10.3389/fendo.2025.1551100. eCollection 2025.ABSTRACTThe intricate relationship between bile acid metabolism and skeletal muscle function has emerged as a crucial area of research in metabolic health. This review synthesizes current evidence highlighting the fundamental role of bile acids as key signaling molecules in muscle homeostasis and their therapeutic potential in muscle-related disorders. Recent advances in molecular biology and metabolomics have revealed that bile acids, beyond their classical role in lipid absorption, function as essential regulators of muscle mass and function through multiple signaling pathways, particularly via the nuclear receptor FXR and membrane receptor TGR5. Clinical studies have demonstrated significant associations between altered bile acid profiles and muscle wasting conditions, while experimental evidence has elucidated the underlying mechanisms linking bile acid signaling to muscle protein synthesis, energy metabolism, and regeneration capacity. We critically examine the emerging therapeutic strategies targeting bile acid pathways, including receptor-specific agonists, microbiome modulators, and personalized interventions based on individual bile acid profiles. Additionally, we discuss novel diagnostic approaches utilizing bile acid-based biomarkers and their potential in early detection and monitoring of muscle disorders. This review also addresses current challenges in standardization and clinical translation while highlighting promising future directions in this rapidly evolving field. Understanding the bile acid-muscle axis may provide new opportunities for developing targeted therapies for age-related muscle loss and metabolic diseases.PMID:40144297 | PMC:PMC11936799 | DOI:10.3389/fendo.2025.1551100

Soil microbiome transplantation to enhance the drought response of <em>Salvia officinalis</em> L

Thu, 27/03/2025 - 11:00
Front Microbiol. 2025 Mar 12;16:1553922. doi: 10.3389/fmicb.2025.1553922. eCollection 2025.ABSTRACTINTRODUCTION: Soil microbiome transplantation is a promising technique for enhancing plant holobiont response to abiotic and biotic stresses. However, the rapid assessment of microbiome-plant functional integration in short-term experiments remains a challenge.METHODS: This study investigates the potential of three evergreen sclerophyll species, Pistacia lentiscus (PL), Rosmarinus officinalis (RO), and Juniperus phoenicea (JP), to serve as a reservoir for microbial communities able to confer enhanced tolerance to drought in Salvia officinalis cultivated under water shortage, by analyzing biomass production, plant phenotype, plant ecophysiological responses, and leaf metabolome.RESULTS: Our results showed that the inoculation with the three rhizomicrobiomes did not enhance total plant biomass, while it significantly influenced plant architecture, ecophysiology, and metabolic responses. The inoculation with the JP rhizomicrobiome led to a significant increase in root biomass, resulting in smaller leaves and a higher leaf number. These morphological changes suggest improved water acquisition and thermoregulation strategies. Furthermore, distinct stomatal conductance patterns were observed in plants inoculated with microbiomes from PJ and PL, indicating altered responses to drought stress. The metabolome analysis demonstrated that rhizomicrobiome transplantation significantly influenced the leaf metabolome of S. officinalis. All three rhizomicrobiomes promoted the accumulation of phenolic compounds, terpenoids, and alkaloids, known to play crucial roles in plant defense and stress response. Five molecules (genkwanin, beta-ionone, sumatrol, beta-peltatin-A-methyl ester, and cinnamoyl-beta-D-glucoside) were commonly accumulated in leaves of inoculated sage, independently of the microbiome. Furthermore, unique metabolic alterations were observed depending on the specific inoculated rhizomicrobiome, highlighting the specialized nature of plant-microbe interactions and the possible use of these specific molecules as biomarkers to monitor the recruitment of beneficial microorganisms.DISCUSSION: This study provides compelling evidence that microbiome transplantation can induce phenotypic and metabolic changes in recipient plants, potentially enhancing their resilience to water scarcity. Our findings emphasize the importance of considering multiple factors, including biomass, physiology, and metabolomics, when evaluating the effectiveness of microbiome engineering for improving plant stress tolerance.PMID:40143859 | PMC:PMC11937098 | DOI:10.3389/fmicb.2025.1553922

Comprehensive analysis on the regulatory mechanism of active ingredient accumulation during fermentation process of Massa Medicata Fermentata: microbe and metabolic profiles

Thu, 27/03/2025 - 11:00
Front Microbiol. 2025 Mar 12;16:1548427. doi: 10.3389/fmicb.2025.1548427. eCollection 2025.ABSTRACTBACKGROUND: Massa Medicata Fermentata (MMF) is a traditional medicinal/edible fermented product; however, comprehensive research on the fermentation process from a microscopic perspective remains limited. In this study, we aimed to investigate the dynamic changes and correlations of physicochemical properties, microbial communities, and metabolite profiles in different fermentation stages (0, 48, 72, and 96 h) of MMF.METHODS: Standard analytical tests, microbiome sequencing, broad-target metabolism, mixed standard-based mass spectrometry, and fine structure analysis were integrated to elucidate fluctuations in physicochemical, microbial, and metabolic levels during MMF fermentation.RESULTS: During the fermentation process, bacterial diversity generally shows an increasing trend, whereas fungal diversity generally shows a decreasing trend. Revealing that the differentially abundant metabolites were primarily categorized into lipids, amino acids and derivatives, phenolic acids, organic acids, flavonoids, lignans and coumarins, nucleotides and derivatives, and alkaloids. Structural equation modeling and correlation analysis indicated that two species of bacteria (Bacillus velezensis, Bacillus safensis) and four species of fungi (Apiotrichum montevideense, Geotrichum bryndzae, f_Dipodascaceae, Saccharomycopsis fibuligera) showed significant positive correlations with five types of differential metabolites, including lipids, flavonoids, phenolic acids, lignans and coumarins, and organic acids. These differential metabolites are essential components responsible for the therapeutic effects of MMF, particularly those that reach peak concentrations at 72 h of fermentation.CONCLUSION: These findings are expected to provide a reference for developing strategies to strengthen the quality of MMF and promote its modern application.PMID:40143856 | PMC:PMC11936943 | DOI:10.3389/fmicb.2025.1548427

Metabolic transition from childhood to adulthood based on two decades of biochemical time series in three longitudinal cohorts

Thu, 27/03/2025 - 11:00
Int J Epidemiol. 2025 Feb 16;54(2):dyaf026. doi: 10.1093/ije/dyaf026.ABSTRACTBACKGROUND: This is the first large-scale longitudinal study of children that describes the temporal trajectories of an extensive collection of metabolic measures that are relevant for lifelong cardiometabolic risk. We also provide a comprehensive picture on how metabolism develops into mature adult sex-specific phenotypes.METHODS: Children born in 1962-92 were recruited by three European studies (n = 20 377 eligible). Biochemical data for ages 0-26 years were available for n = 14 958 participants (n = 8385 with metabolomics). Age associations for 168 metabolic measures (6 physiological traits, 6 clinical biomarkers, and 156 serum metabolomics measures) were determined by using curvilinear regression. Puberty effects were calculated by using logistic regression of biological sex for pre- and post-pubertal age strata.RESULTS: Age-specific concentrations were reported for all measures. Nonlinear age associations were typical, including insulin (R2 = 20.7% ±0.6% variance explained ±SE), glycerol (13.3% ±1.3%), glycoprotein acetyls (40.3% ±1.5%), and branched-chain amino acids (19.5% ±1.6%). Apolipoprotein B was not associated with age (0.7% ±0.4%). Multivariate modeling indicated that boys diverged from girls metabolically during ages 13-17 years. Puberty effects were observed for large high-density lipoprotein cholesterol (P = 8.5 × 10-288), leucine (P < 2.3 × 10-308), glutamine (P < 2.3 × 10-308), albumin (P = 1.7 × 10-161), docosahexaenoic acid (P = 5.2 × 10-50), and sphingomyelin (P = 4.4 × 10-90).CONCLUSION: Novel associations between emerging cardiometabolic risk factors, such as amino acids and glycoprotein acetyls, and growth and puberty were observed. Conversely, apolipoprotein B was stable, which favors its utility for early assessments of lifetime cardiovascular risk.PMID:40143821 | DOI:10.1093/ije/dyaf026

Lycopene improves cisplatin induced hepatointestinal injury in rats by modulating the microbe-gut-liver axis

Thu, 27/03/2025 - 11:00
Food Funct. 2025 Mar 27. doi: 10.1039/d4fo06059h. Online ahead of print.ABSTRACTCisplatin (CIS) is a commonly used antitumor drug in clinics, but its application is limited due to hepatotoxicity, nephrotoxicity and gastrointestinal toxicity. In recent years, a large number of studies have shown that the imbalance of intestinal flora is one of the important factors in the malignant development of diseases. Therefore, improving organ function by regulating intestinal flora may be an important strategy to prevent the side effects of chemotherapy drugs. Lycopene (LYC) is found in a wide range of red foods and has antioxidant, anti-inflammatory and immune-enhancing effects. So the purpose of this study was to explore its effect on hepatointestinal injury caused by chemotherapy drugs. The results of this study showed that CIS could significantly restore body weight, diet, water intake, and AST, ALT and other physiological and biochemical indexes of rats. HE staining, projective electron microscopy and TUNEL results showed that LYC alleviated morphological and ultrastructural damage of the liver and intestine. Then, ELISA results showed that LYC can reduce cell apoptosis by increasing the antioxidant capacity and reducing inflammatory response. Secondly, 16sRNA and metabolome results showed that LYC enriched beneficial bacteria (Firmicutes and Proteobacteria), reduced harmful bacteria (E. coli, etc.), enhanced metabolic pathway changes such as taurine and hypotaurine metabolism, and alleviated organ damage caused by CIS. Finally, network pharmacology, molecular docking and immunohistochemistry showed that LYC could reduce CIS induced hepatocyte inflammation and apoptosis by activating the PI3K/AKT pathway. In summary, LYC alleviates the toxic side effects of chemotherapy drugs by regulating the PI3K/AKT pathway and the intestinal microbiota-metabolite-liver axis.PMID:40143795 | DOI:10.1039/d4fo06059h

Accuracy of Metabolomics in Peri-Implant Crevicular Fluid for Diagnosis and Prognosis of Peri-Implantitis

Thu, 27/03/2025 - 11:00
J Periodontal Res. 2025 Mar 26. doi: 10.1111/jre.13400. Online ahead of print.ABSTRACTAIMS: Poor accuracy of diagnostic and prognostic tools prevents the prediction of peri-implant disease stability or progression. We analyzed metabolites from peri-implant crevicular fluid (PICF) samples from healthy and diseased implants to identify those diagnostic of health and peri-implant disease and predictive of peri-implant bone loss over time.METHODS: Clinical, radiographic examinations and PICF samples were collected from 59 healthy implants, 33 implants with peri-implantitis, and 38 implants with peri-implant mucositis in 71 subjects. A subset of implants was evaluated at 6, 12, 18, and 24 months. Over time, all initially healthy implants remained stable (Group B, N = 28), whereas 6 initially diseased implants continued to lose bone and 8 did not (Group C). PICF metabolites were measured using proton-nuclear magnetic resonance (1H-NMR) 2-dimensional Total Correlation Spectroscopy. PCA and PLS-DA tested the cross-sectional clustering and importance of each metabolite, while the AUC summarized the accuracy of predicting radiographic bone changes ≥ 1 mm at 6-month intervals.RESULTS: At baseline, the Cadaverine/Lysine and Putrescine/Lysine signatures diagnosed peri-implantitis (AUC = 0.76 and 0.70; p < 0.000) with good accuracy, while alpha-ketoglutarate diagnosed implant health (AUC = 0.706; p = 0.002). Combining metabolites increased diagnostic accuracy (AUCCadaverine/Lysine+Methionine = 0.81; p < 0.01). Proline and 1-3-diaminopropane predicted future bone loss (AUCProline = 0.917 and AUC1-3-diaminopropane = 0.854). ANOVA post hoc analysis established that biotin and propionate levels were higher in Group C compared to Groups A and B (p < 0.001; AUCbiotin = 0.889; AUCpropionate = 0.87). Valine levels were higher in Groups A and C compared to Group B (p = 0.002; AUC = 0.841).CONCLUSIONS: 1H-NMR 2-dimensional spectroscopy identified PICF metabolites diagnostic of peri-implantitis with high accuracy. Despite the small number of affected implants, metabolite signatures that predict future bone loss in peri-implantitis appear to be different from those diagnostic of peri-implantitis.PMID:40143571 | DOI:10.1111/jre.13400

Integration of Metabolomics and 16S Ribosomal RNA Sequencing to Elucidate the Pathogenesis of Ankylosing Spondylitis

Thu, 27/03/2025 - 11:00
Immun Inflamm Dis. 2025 Mar;13(3):e70183. doi: 10.1002/iid3.70183.ABSTRACTOBJECTIVE: Despite growing interest in the gut microbiota and blood metabolome in patients with ankylosing spondylitis (AS), its role remains poorly understood. Here, we investigate how microbial and metabolic alterations contribute to AS.METHODS: Fecal microbiome data from 40 AS patients were compared with those from 40 healthy controls (HCs) using 16S ribosomal RNA (rRNA) gene sequencing. The plasma metabolic profiles were analyzed and integrated with the microbiota data to identify biological characteristics specific to AS.RESULTS: AS patients showed significant enrichment of specific genera, including Megamonas, Elusimicrobium, Dysgonomonas, Ruminococcus_gauvreauii_group, and unclassified_Prevotellaceae. Pathways with the most differentially expressed metabolites included bile secretion; neomycin, kanamycin, and gentamicin biosynthesis; and arachidonic acid metabolism. Positive correlations between Megamonas and Elusimicrobium and metabolites such as piribedil, l-cystathionine, and crocetin dialdehyde suggested microbial enrichment in AS patients.CONCLUSIONS: A disrupted gut microbiota and altered metabolites are present in AS patients. Integrating microbiome and metabolomic data reveals significant disruptions in AS patients, improving our understanding of its pathogenesis.PMID:40143557 | DOI:10.1002/iid3.70183

Puerarin Targets HIF-1α to Modulate Hypoxia-Related Sphingolipid Metabolism in Diabetic Hepatopathy via the SPTLC2/Ceramide Pathway

Thu, 27/03/2025 - 11:00
Pharmaceuticals (Basel). 2025 Mar 12;18(3):398. doi: 10.3390/ph18030398.ABSTRACTBackground and Objectives: Diabetic hepatopathy, characterized by hepatic hypoxia and metabolic dysregulation, has a rising global incidence and prevalence, with limited effective treatments. Hepatic hypoxia activates hypoxia-inducible factor-1 alpha (HIF-1α), regulating sphingolipid metabolism and elevating ceramide, a key factor in insulin resistance. Puerarin (Pue), a flavonoid derived from Pueraria lobata, exhibits therapeutic effects in diabetes, but its effects on hypoxia-related hepatic metabolism are unclear. This study investigates Pue's mechanisms in modulating hepatic metabolism, focusing on HIF-1α and sphingolipid metabolism. Methods: Using bioinformatics and molecular docking, HIF-1α was identified as a key target in diabetic liver disease, confirmed via drug affinity responsive target stability. In vitro experiments utilized insulin-resistant HepG2 cells to assess glucose intake and HIF-1α expression. In vivo, type 2 diabetes mellitus (T2DM) was induced in mice using a high-fat diet and streptozotocin injections. Pue administration was evaluated for its effects on fasting blood glucose, oral glucose tolerance, and hepatoprotective effects. Liver metabolomics and qPCR/Western blot analyses were conducted to assess metabolic pathways. Results: Pue increased glucose uptake in HepG2 cells and bound HIF-1α. Pue reduced HIF-1α expression in HepG2 cells, an effect attenuated by the HIF-1α stabilizer DMOG. Pue improved fasting blood glucose, oral glucose tolerance, and hepatoprotective effects in T2DM mice, which DMOG reversed. Metabolomics revealed that Pue modulates sphingolipid metabolism, decreasing ceramide content. qPCR and Western blot results confirmed that Pue dramatically decreases HIF-1α and SPTLC2 expression. Conclusions: Pue improves diabetic hepatopathy by reducing ceramide expression through the HIF-1α/SPTLC2 pathway, offering a novel therapeutic strategy for diabetes management.PMID:40143173 | DOI:10.3390/ph18030398

Supercritical Extraction and Identification of Bioactive Compounds in <em>Dryopteris fragrans</em> (L.) Schott

Thu, 27/03/2025 - 11:00
Pharmaceuticals (Basel). 2025 Feb 21;18(3):299. doi: 10.3390/ph18030299.ABSTRACTBackground: This is a comparative metabolomic study of the medicinal plant Dryopteris fragrans (L.) Schott from the family Dryopteridaceae Herter (or Aspidiaceae Mett. ex Frank) growing under cold pole conditions in the Oymyakon region of the Republic of Sakha (Yakutia). Methods: The aerial parts of D. fragrans were subjected to extraction using supercritical CO2 extraction and maceration methods. Several experimental conditions were investigated, including a pressure range of 50-300 bar and a temperature range of 31-60 °C. A 1% volume of ethanol was used as a co-solvent in the liquid phase of the extraction. Results: The most effective D. fragrans extraction conditions were 200 Bar pressure and a temperature of 55 °C. Tandem mass spectrometry was used to detect the target analytes. A total of 141 bioactive compounds (86 compounds from the polyphenol group and 55 compounds from other chemical groups) were tentatively identified in extracts of aerial parts of D. fragrans. Among these, thirty chemical constituents from the polyphenol group were identified for the first time. Other compound classes that were newly identified in D. fragrans include naphthoquinones (5,8-dihydroxy-6-methyl-2,3-dihydro-1,4-naphthoquinone, 1,8-dihydroxy-anthraquinone, 1,4,8-trihydroxyanthraquinone, chrysophanol, etc.), diterpenoids (tanshinone IIa, cryptotanshinone, isocryptotanshinone II, tanshinone IIb, etc.), polysaccharides, triterpenoids, and sesquiterpenes. Conclusions: These results highlight that D. fragrans is rich in bioactive compounds and put forward several newly detected compounds for further investigation.PMID:40143079 | DOI:10.3390/ph18030299

Operationalizing Team Science at the Academic Cancer Center Network to Unveil the Structure and Function of the Gut Microbiome

Thu, 27/03/2025 - 11:00
J Clin Med. 2025 Mar 17;14(6):2040. doi: 10.3390/jcm14062040.ABSTRACTOncologists increasingly recognize the microbiome as an important facilitator of health as well as a contributor to disease, including, specifically, cancer. Our knowledge of the etiologies, mechanisms, and modulation of microbiome states that ameliorate or promote cancer continues to evolve. The progressive refinement and adoption of "omic" technologies (genomics, transcriptomics, proteomics, and metabolomics) and utilization of advanced computational methods accelerate this evolution. The academic cancer center network, with its immediate access to extensive, multidisciplinary expertise and scientific resources, has the potential to catalyze microbiome research. Here, we review our current understanding of the role of the gut microbiome in cancer prevention, predisposition, and response to therapy. We underscore the promise of operationalizing the academic cancer center network to uncover the structure and function of the gut microbiome; we highlight the unique microbiome-related expert resources available at the City of Hope of Comprehensive Cancer Center as an example of the potential of team science to achieve novel scientific and clinical discovery.PMID:40142848 | DOI:10.3390/jcm14062040

Effects of Feeding Fermented Cassava Leaves on Intestinal Morphology, Cecal Microbiota, and Metabolome in Hybrid Geese

Thu, 27/03/2025 - 11:00
Microorganisms. 2025 Mar 14;13(3):660. doi: 10.3390/microorganisms13030660.ABSTRACTIn this study, we characterized the effects of a diet supplemented with fermented cassava leaves (FCLs) on growth performance, intestinal morphology, the cecal microbiota, and cecal metabolites in hybrid geese. We found that the FCL diet was beneficial to goose growth performance and also promoted a healthy intestinal morphology, as reflected by better morphology properties of the duodenum, jejunum, ileum, and cecum. Moreover, the FCL diet significantly altered cecal microbial diversity and composition, increasing the diversity and abundance of the beneficial Bacteroides. Further, the FCL diet increased the complexity and stability of cecal microbial co-occurrence network interactions as a result of altered topological distributions in the network, such as edges, density, degree, and betweenness. The FCL diet had clear impacts on the composition and abundance of cecal metabolites, with increases in metabolites involved in amino acid biosynthesis, digestion, and absorption, as well as an upregulation of associated metabolic pathways. Based on these benefits to growth performance, intestinal development, and cecal microbe-mediated metabolism in geese, FCLs can be utilized as a reliable feed resource for geese in tropical and subtropical regions.PMID:40142552 | DOI:10.3390/microorganisms13030660

Metabolomics Provides New Insights into the Mechanisms of Wolbachia-Induced Plant Defense in Cotton Mites

Thu, 27/03/2025 - 11:00
Microorganisms. 2025 Mar 6;13(3):608. doi: 10.3390/microorganisms13030608.ABSTRACTEndosymbiotic bacteria play a significant role in the co-evolution of insects and plants. However, whether they induce or inhibit host plant defense responses remains unclear. In this study, non-targeted metabolomic sequencing was performed on cotton leaves fed with Wolbachia-infected and uninfected spider mites using parthenogenetic backcrossing and antibiotic treatment methods. A total of 55 differential metabolites were identified, which involved lipids, phenylpropanoids, and polyketides. KEGG pathway enrichment analysis revealed seven significantly enriched metabolic pathways. Among them, flavonoid and flavonol biosynthesis, glycerophospholipid metabolism, and ether lipid metabolism showed extremely significant differences. In Wolbachia-infected cotton leaves, the flavonoid biosynthesis pathway was significantly up-regulated, including quercetin and myricetin, suggesting that the plant produces more secondary metabolites to enhance its defense capability. Glycerophosphocholine (GPC) and sn-glycerol-3-phosphoethanolamine (PE) were significantly down-regulated, suggesting that Wolbachia may impair the integrity and function of plant cell membranes. The downregulation of lysine and the upregulation of L-malic acid indicated that Wolbachia infection may shorten the lifespan of spider mites. At various developmental stages of the spider mites, Wolbachia infection increased the expression of detoxification metabolism-related genes, including gene families such as cytochrome P450, glutathione S-transferase, carboxylesterase, and ABC transporters, thereby enhancing the detoxification capability of the host spider mites. This study provides a theoretical basis for further elucidating the mechanisms by which endosymbiotic bacteria induce plant defense responses and expands the theoretical framework of insect-plant co-evolution.PMID:40142501 | DOI:10.3390/microorganisms13030608

Impact of Fecal Microbiota Transplant Formulations, Storage Conditions, and Duration on Bacterial Viability, Functionality, and Clinical Outcomes in Patients with Recurrent <em>Clostridioides difficile</em> Infection

Thu, 27/03/2025 - 11:00
Microorganisms. 2025 Mar 4;13(3):587. doi: 10.3390/microorganisms13030587.ABSTRACTFecal microbiota transplantation (FMT) is the most effective therapy for preventing recurrent Clostridioides difficile infection (rCDI). However, the impact of FMT formulations and storage conditions on bacterial viability, community structure, functionality, and clinical efficacy remains under-investigated. We studied the effect of different storage conditions on the bacterial viability (live/dead staining and cell sorting), community structure (16S rDNA analysis), and metabolic functionality (fermentation) of frozen and lyophilized FMT formulations. The clinical success rates of rCDI patients were correlated retrospectively with FMT formulations, storage durations, and host factors using the Edmonton FMT program database. Bacterial viability remained at 10-20% across various storage conditions and formulations and was comparable to that of fresh FMT. Live and dead bacterial fractions in both frozen and lyophilized FMT preparations exhibited distinct community structures. Storage durations, but not temperatures, negatively affected bacterial diversity. More short-chain fatty acids were found in the metabolomic profiling of in vitro fermentation products using lyophilized than frozen FMT. Clinical success rates in 537 rCDI patients receiving a single dose of FMT were not significantly different among the three formulations. However, longer storage durations and advanced recipient age negatively impacted clinical efficacy. Together, our findings suggest that FMT formulations and storage durations should be considered when establishing guidelines for product shelf life for optimal treatment outcomes.PMID:40142480 | DOI:10.3390/microorganisms13030587

Metabolic Reprogramming in Response to Freund's Adjuvants: Insights from Serum Metabolomics

Thu, 27/03/2025 - 11:00
Microorganisms. 2025 Feb 22;13(3):492. doi: 10.3390/microorganisms13030492.ABSTRACTFreund's adjuvants have been used in vaccine and autoimmune settings, and their effects can be overlapping or unique to each. While both incomplete Freund's adjuvants (IFA) and complete Freund's adjuvants (CFA) influence antibody and T cell responses, the robust T helper 1 cytokines induced by the mycobacterial components make CFA the powerful immunostimulating adjuvant. In these studies, the adjuvant effects are investigated in a select population of cells, and the changes, if any, with the metabolic alterations in the systemic compartment are unclear. We investigated whether the effects of IFA and CFA can be influenced by the metabolic shifts in mice immunized with saline, IFA, or CFA using Mycobacterium tuberculosis var. bovis Bacillus Calmette-Guérin (BCG) as a positive control. After seven days of immunization, we analyzed the serum metabolite profiles using liquid chromatography coupled with high-resolution mass spectrometry and multivariate statistical analysis to identify metabolic features between the groups. The data revealed that, in the scores space, the CFA and BCG groups were more closely aligned compared to the saline group, while the IFA group displayed an intermediate profile. Furthermore, comparisons between the CFA and BCG groups showed more significant perturbations in lipid and amino acid metabolism, particularly involving glycerophospholipids, cysteine, and aromatic amino acids. In contrast, comparisons between the BCG and IFA groups indicated a more pronounced disruption in central energy metabolism pathways, such as the citric acid cycle and pyruvate metabolism. Together, the data suggest that the serum metabolite profiles in response to IFA and CFA might play a role in modulating the immune responses.PMID:40142385 | DOI:10.3390/microorganisms13030492

Untargeted Lipidomic Biomarkers for Liver Cancer Diagnosis: A Tree-Based Machine Learning Model Enhanced by Explainable Artificial Intelligence

Thu, 27/03/2025 - 11:00
Medicina (Kaunas). 2025 Feb 26;61(3):405. doi: 10.3390/medicina61030405.ABSTRACTBackground and Objectives: Liver cancer ranks among the leading causes of cancer-related mortality, necessitating the development of novel diagnostic methods. Deregulated lipid metabolism, a hallmark of hepatocarcinogenesis, offers compelling prospects for biomarker identification. This study aims to employ explainable artificial intelligence (XAI) to identify lipidomic biomarkers for liver cancer and to develop a robust predictive model for early diagnosis. Materials and Methods: This study included 219 patients diagnosed with liver cancer and 219 healthy controls. Serum samples underwent untargeted lipidomic analysis with LC-QTOF-MS. Lipidomic data underwent univariate and multivariate analyses, including fold change (FC), t-tests, PLS-DA, and Elastic Network feature selection, to identify significant biomarker candidate lipids. Machine learning models (AdaBoost, Random Forest, Gradient Boosting) were developed and evaluated utilizing these biomarkers to differentiate liver cancer. The AUC metric was employed to identify the optimal predictive model, whereas SHAP was utilized to achieve interpretability of the model's predictive decisions. Results: Notable alterations in lipid profiles were observed: decreased sphingomyelins (SM d39:2, SM d41:2) and increased fatty acids (FA 14:1, FA 22:2) and phosphatidylcholines (PC 34:1, PC 32:1). AdaBoost exhibited a superior classification performance, achieving an AUC of 0.875. SHAP identified PC 40:4 as the most efficacious lipid for model predictions. The SM d41:2 and SM d36:3 lipids were specifically associated with an increased risk of low-onset cancer and elevated levels of the PC 40:4 lipid. Conclusions: This study demonstrates that untargeted lipidomics, in conjunction with explainable artificial intelligence (XAI) and machine learning, may effectively identify biomarkers for the early detection of liver cancer. The results suggest that alterations in lipid metabolism are crucial to the progression of liver cancer and provide valuable insights for incorporating lipidomics into precision oncology.PMID:40142216 | DOI:10.3390/medicina61030405

New Insights into the Metabolic Profile and Cytotoxic Activity of <em>Kigelia africana</em> Stem Bark

Thu, 27/03/2025 - 11:00
Molecules. 2025 Mar 20;30(6):1388. doi: 10.3390/molecules30061388.ABSTRACTUltra-high-performance liquid chromatography coupled to Orbitrap high-resolution mass spectrometry (UHPLC-HRMS) was recently employed in many fields to obtain a rapid characterization of plant extracts. Kigelia africana (family Bignoniaceae) is a quintessential African herbal medicinal plant with immense indigenous medicinal and non-medicinal applications. The aim of the present research was to obtain an in-depth metabolite profiling of the K. africana stem bark extract using UHPLC-HRMS and to conduct a preliminary screening of its anticancer activity against a panel of malignant human cell lines of different origin. The UHPLC-HRMS analysis revealed 63 secondary metabolites including phenolic acids, gallo- and ellagitannins, iridoids, naphthoquinones, and anthraquinones. A total of 34 of all annotated compounds are reported for the first time in K. africana stem bark. The studied profile was dominated by trimethylellagic acid, dimethylellagic acid isomers, and ellagic acid. In all tumor models, we established a pronounced inhibition of cell growth in a mostly dose-dependent manner, with IC50 values ranging near and well below (4-30 µg/mL) the lowest treatment concentration of 25 µg/mL. The established cytotoxicity profile of the K. africana extract, highly biased toward malignantly transformed but not normal cells, suggests specific modulation of defined molecular tumor targets. This study revealed K. africana stem bark as a new source of gallo- and ellagitannins, and highlighted the studied herbal drug as an antiproliferative agent with potential pharmaceutical application.PMID:40142163 | DOI:10.3390/molecules30061388

Direct 3D Mass Spectrometry Imaging Analysis of Environmental Microorganisms

Thu, 27/03/2025 - 11:00
Molecules. 2025 Mar 14;30(6):1317. doi: 10.3390/molecules30061317.ABSTRACTAssessing the spatial distribution of microorganisms' metabolites in growth medium remains a challenge. Here, we present the first use of the newly developed LARAPPI/CI-MSI 3D (laser ablation remote atmospheric pressure photoionization/chemical ionization mass spectrometry imaging) method for direct three-dimensional (3D) mass spectrometry imaging of bacterial and fungal metabolites in solid culture media. Two-dimensional (2D) MSI was also performed, and it indicated the presence of metabolites belonging to, and including, amino acids and their derivatives, dipeptides, organic acids, fatty acids, sugars and sugar derivatives, benzene derivatives, and indoles. Distribution at a selected depth within the culture medium with the estimation of concentration across all dimensions of 16 metabolites was visualized using LARAPPI/CI-MSI 3D. The imaging results were correlated with the results of ultra-high-performance liquid chromatography-ultra-high-resolution mass spectrometry (UHPLC-UHRMS). A total of 351-393 chemical compounds, depending on the tested microorganism, were identified, while 242-262 were recognized in the HMDB database in MetaboAnalyst (v 6.0). The LARAPPI/CI-MSI 3D method enables the rapid screening of the biotechnological potential of environmental strains, facilitating the discovery of industrially valuable biomolecules.PMID:40142092 | DOI:10.3390/molecules30061317

New Horizon in Selective Tocols Extraction from Deodorizer Distillates Under Mild Conditions by Using Deep Eutectic Solvents

Thu, 27/03/2025 - 11:00
Molecules. 2025 Mar 8;30(6):1217. doi: 10.3390/molecules30061217.ABSTRACTTocols are commonly known as vitamin E, which comprise tocopherols and tocotrienols. Although vegetable oils are natural sources of tocols, deodorizer distillates (DDs) are attractive feedstock due to their potential abundance from oil refining processes and economic price. Deep eutectic solvents (DESs) are a family of neoteric solvents that show promising performance for tocols extraction. Besides their characters occupying the green chemistry concept, this review presents the current research on the potential performances of DESs in extracting tocols selectively and efficiently from DDs. The application of DESs in tocols extraction is presented considering three different ways: mono-phasic, in situ DESs formation, and bi-phasic systems. The basic principles of intermolecular interactions (H-bond, van der Walls bond, and misfit interaction) between DESs or their components with tocols are discussed to understand the mechanism by which DESs selectively extract tocols from the mixture. This is mainly observed to be a function of the intrinsic properties of DESs and/or tocols, which could be beneficial for tuning the appropriate DESs for extracting tocols selectively and effectively under mild operation conditions. This review is expected to provide insight in the potential application of DESs in the extracting of natural compounds with a phenolic structure and also briefly discusses the toxicity of DESs.PMID:40141994 | DOI:10.3390/molecules30061217

Pages