PubMed

mBio. 2025 Apr 11:e0047025. doi: 10.1128/mbio.00470-25. Online ahead of print.ABSTRACTGrowing evidence suggests that inadequate dietary fiber intake, termed the "fiber gap," is linked to disease states through disruption of the gut microbiota. Despite this, our understanding of how various fiber structures influence the microbiota and health is limited by the lack of diverse commercially available fibers. Studies have primarily focused on a limited range of fibers, rather than the diverse array of fibers representative of those commonly found in our diets. In this study, we aimed to investigate how naturally derived fibers impact the human microbiota and their metabolic products. We performed a comprehensive structural characterization and functional evaluation of a unique and highly diverse set of new, highly soluble fibers with varied monosaccharide compositions, glycosidic linkages, and polymer lengths. Using an ex vivo high-throughput human microbiota platform coupled with metabolomic profiling, we demonstrate that these diverse fibers drive distinct and consistent microbial and metabolic profiles across cohorts of donors in a structure-dependent manner. These metabolic effects were accompanied by both general and donor-specific changes in microbial taxa. Finally, we demonstrate that integrating detailed glycomic characterization with microbial and metabolomic data allowed for prediction of functional outcomes driven by a novel material, pineapple pulp fiber. This work highlights the potential for targeted dietary fiber interventions to modulate the microbiota and improve health outcomes, paving the way for the development of new fiber-rich products with specific health benefits.IMPORTANCEFiber deficiency is associated with numerous disease states, many of which are linked to disruption of the gut microbiota. This study encompasses the first systematic and comprehensive characterization of a diverse collection of naturally derived solubilized fibers and their impacts on the microbiota. The results expand our understanding of the beneficial effects of specific carbohydrate structures naturally found in the human diet, highlighting the potential for designing fiber-based health interventions. The high solubility of these fibers increases both the range of products they can be incorporated in as well as their assayability in experiments, enabling a widespread increase in fiber consumption and positive health impacts.PMID:40214223 | DOI:10.1128/mbio.00470-25

Arch Immunol Ther Exp (Warsz). 2025 Apr 11;73(1). doi: 10.2478/aite-2025-0011. eCollection 2025 Jan 1.ABSTRACTParkinson's disease (PD) affects millions of people globally. Accurate early diagnosis remains a challenge due to the lack of specific biomarkers. This systematic review explores the potential of 1H-NMR metabolomics in identifying diagnostic markers and therapeutic targets for PD. A comprehensive analysis was conducted across databases such as Scopus, Web of Science, PubMed, and Embase, focusing on studies that utilized 1H-NMR spectroscopy to profile metabolites associated with PD progression. The review identifies key metabolites-glutamate, taurine, myo-inositol, glutamine, and creatine-that play critical roles in the pathophysiology of PD. Glutamate, linked to excitotoxicity and neuronal degeneration, emerges as a prominent target for therapeutic intervention, while taurine is associated with oxidative stress. Myo-inositol, a key regulator of autophagy, underscores the biochemical dysregulation associated with PD, similar to glutamine and glutamate. Creatine's role in neuronal energy metabolism suggests potential avenues for treatment focused on energy supplementation. The reproducibility of metabolite findings varied, indicating the complexity of PD's metabolomic landscape. Despite challenges in consistency, these metabolites hold promise as biomarkers for diagnosing PD and tracking disease progression. The review underscores the need for further validation of these markers and their integration with other omics technologies to enhance PD management. By identifying key metabolic pathways, this study opens new directions for personalized medicine, offering potential therapeutic targets to slow disease progression and improve patient outcomes.PMID:40214076 | DOI:10.2478/aite-2025-0011

Gut Microbes. 2025 Dec;17(1):2490207. doi: 10.1080/19490976.2025.2490207. Epub 2025 Apr 11.ABSTRACTInflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is considered significant global health concerns worldwide. Many studies have demonstrated that environmental and dietary factors influence the gut microbiota, which in turn orchestrates the host immune responses. These interactions are also involved in complex metabolic processes that contribute to the pathogenesis of IBD. Furthermore, recent studies in genomics and metabolomics have unveiled the intricate relationship between microbial influencers and host epigenetics. The dynamics of gut microbiota and its metabolites intricately align with DNA methylation, histone methylation, lactylation, glycosylation, and non-coding RNAs, which are key players in epigenetics. Here, we summarize and discuss the complex interplay among gut microbiota, epigenetics, and environmental and dietary factors, and their impact on the pathogenesis of IBD. Furthermore, we highlight the importance of multi-omics technologies in dissecting the host-microbe interactions in IBD, potentially offering a framework for developing effective treatment strategies.PMID:40213833 | DOI:10.1080/19490976.2025.2490207

Front Endocrinol (Lausanne). 2025 Mar 27;16:1433534. doi: 10.3389/fendo.2025.1433534. eCollection 2025.ABSTRACTINTRODUCTION: Pregnant women with subclinical hypothyroidism or clinical hypothyroidism often exhibit lipid metabolism disorders and are correlated with adverse pregnant outcomes. It was suggested that isolated positive thyroid peroxidase antibody (TPOAb) served as a risk factor for adverse outcomes. However, little was known about the lipid metabolism profile in pregnant women with isolated positive TPOAb. The purpose of this prospective observational study was to investigate the expression of lipid profiles among euthyroid pregnant women with positive TPOAb during there early pregnancy and to analyze their correlation with thyroid function.METHODS: Non-targeted liquid chromatography-mass spectrometry (LC-MS) technology was used to perform lipidomics analysis on serum samples collected during early pregnancy from pregnant women who with isolated positive TPOAb and those in the healthy control group. Partial least squares-discriminant analysis (PLS-DA), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis, and correlation analysis were conducted to explore differential lipid molecules and their associations with clinical parameters.RESULTS: A total of 90 pregnant women in the first trimester were enrolled in the analysis: 46 were TPOAb-positive euthyroid pregnant women, and 44 were healthy pregnant women. A total of 1238 lipid molecules were identified, and 202 differential lipid molecules were screened between the two groups. KEGG pathway enrichment analysis revealed that the differentially expressed lipids participate in several pathways. Correlation analysis showed LPC(20:4), LPC(18:0), LPC(22:4), LPC(22:5), LPC(18:1), PC(20:1/20:4) were both positively correlated with TPOAb titers and sCD40L. LPC(20:0) was positively correlated with the level of remnant cholesterol (RC) and PC(20:1/20:4) was negatively correlated with RC.DISCUSSION: The lipid profile of isolated TPOAb-positive euthyroid pregnant women was significantly different from that of healthy pregnant women and involved in several pathways. The pathophysiological role of altered lipid molecules should be further investigated since they might be potential biomarkers for adverse pregnancy outcome in pregnant women with isolated positive TPOAb.PMID:40213108 | PMC:PMC11982940 | DOI:10.3389/fendo.2025.1433534

J Sci Food Agric. 2025 Apr 11. doi: 10.1002/jsfa.14274. Online ahead of print.ABSTRACTBACKGROUND: Sojae semen praeparatum (SSP) is an edible fermented product and traditional Chinese medicinal, with demonstrated bioactivity. Fermentation is an important factor that influences the bioactivity of SSP. However, the changes in the bioactivity and bioactive compounds of SSP during the fermentation process remain largely unknown.RESULTS: The study revealed that fermentation significantly enhanced the bioactivity of SSP, particularly in terms of antioxidant capacity and acetylcholinesterase (AChE) inhibition. Antioxidant assays demonstrated that the antioxidant capacity of SSP increased significantly with prolonged fermentation time, indicating that fermentation duration is a critical factor in enhancing its functionality. Metabolic profiling revealed a substantial accumulation of organic acids and isoflavone compounds during fermentation, with flavonoid compounds such as casticin, naringenin, kaempferide, genistein, quercetin and daidzein exhibiting superior in vitro AChE inhibitory activity. Furthermore, the release of flavonoid compounds was significantly elevated during simulated digestion, further contributing to the enhanced functional properties of SSP.CONCLUSION: These findings suggest that flavonoid compounds are key bioactive components in SSP, and further research on these compounds is beneficial for improving the quality of SSP, as well as providing scientific insights into the comprehensive effects of the fermentation process on SSP and its bioactivity. © 2025 Society of Chemical Industry.PMID:40213821 | DOI:10.1002/jsfa.14274

Theranostics. 2025 Mar 1;15(9):3713. doi: 10.7150/thno.104739. eCollection 2025.ABSTRACT[This corrects the article DOI: 10.7150/thno.18788.].PMID:40213655 | PMC:PMC11980663 | DOI:10.7150/thno.104739

Front Immunol. 2025 Mar 27;16:1537398. doi: 10.3389/fimmu.2025.1537398. eCollection 2025.ABSTRACTINTRODUCTION: Following the approval of Chimeric Antigen Receptor T-cell Immunotherapy(CAR-T) in multiple countries, the Food and Drug Administration (FDA) approved tumor-infiltrating lymphocytes (TILs) and T-cell receptor-engineered T cells (TCR-T) treatments this year. The utilization of adoptive immunotherapy in tumor treatment has become increasingly prominent. Optimizing the cytotoxic effects of immune cells under in vitro culture conditions represents a current hot research topic in this domain.METHODS: In the current experiment, we conducted in vitro heat treatment on Jurkat-derived T cells at 39°C. On this basis, we utilized nine distinct injectable solutions and over 70 monomer components of Traditional Chinese Medicine (TCM). Subsequently, we co-cultured these treated Jurkat cells with K562-eGFP cells, and the co-culture process was monitored in real-time using the IncuCyte live-cell analysis system. Equally important, we combined HiMAP high-throughput transcriptome sequencing, proteomics, and metabolomics for in-depth examination. We screened for compounds possessing anti-tumor properties and thoroughly investigated their mechanisms of action.RESULTS AND DISCUSSION: The findings indicated that heating treatment augmented the cytotoxic effect of Jurkat cells against malignant tumors, and the optimal effect was achieved when T cells were exposed to 39°C for a duration of 24 hours(48% increase in cell proliferation rate compared to 37°C treatment). By triggering the generation of heat shock proteins and facilitating mitochondrial energy supply, the 39°C treatment amplified the anti-tumor functions of T cells. By analyzing the data, we identified 3 injectable solutions and more than 20 effective monomers capable of further enhancing the tumor-killing ability of T cells. High-throughput transcriptomics studies disclosed that the combination of thermotherapy and TCM promoted Jurkat cell proliferation, activation, and cytotoxic functions of Jurkat cells, thereby activating the Regulation of mitotic cell cycle to exert anti-tumor effects. The integration of transcriptomic and proteomic data demonstrated that Shengmai Injection significantly enhances the tumor-killing effect of Jurkat cells by down-regulating the Regulation of Apoptosis and Regulation of mitotic cell cycle signaling pathways.PMID:40213558 | PMC:PMC11983556 | DOI:10.3389/fimmu.2025.1537398

Noncoding RNA Res. 2025 Feb 28;12:141-151. doi: 10.1016/j.ncrna.2025.01.003. eCollection 2025 Jun.ABSTRACTOBJECTIVE: Recent evidence underscores the pivotal role of long noncoding RNAs (lncRNAs) in orchestrating bone remodeling and skeletal homeostasis by harmonizing osteoblast and osteoclast development. Notably, the oncogenic lncRNA, Hottip, implicated in osteogenesis regulation, remains insufficiently elucidated. This study aims to delineate Hottip's role in bone remodeling and skeletal homeostasis.METHODS: Hottip knockout mice were generated to discern its impact on bone metabolism. In vitro experiments probed cellular mechanisms influenced by Hottip, while molecular interactions were explored to understand its basis. The therapeutic potential of Hottip overexpression was investigated through in vivo experiments.RESULTS: Hottip knockout mice displayed disrupted bone metabolism, aberrant tissue, and compromised quality, leading to delayed fracture healing. In vitro, Hottip knockdown impeded osteoblast differentiation, while promoting osteoclast differentiation, with converse effects upon Hottip overexpression. Mechanistically, Hottip physically interacted with EZH2, inducing its degradation and enhancing osteogenic gene transcription by suppressing H3K9me3 and H3K27me3. In vivo experiments validated Hottip overexpression's potential to promote bone regeneration and hasten fracture healing.CONCLUSION: In summary, this study identifies Hottip as a critical regulator in osteoblast and osteoclast differentiation, crucial for maintaining skeletal homeostasis. Hottip emerges as a promising therapeutic target for enhancing bone regeneration. These findings contribute valuable insights into lncRNA-mediated mechanisms governing skeletal dynamics.PMID:40213386 | PMC:PMC11985131 | DOI:10.1016/j.ncrna.2025.01.003

Food Chem X. 2025 Mar 24;27:102410. doi: 10.1016/j.fochx.2025.102410. eCollection 2025 Apr.ABSTRACTTea quality in greenhouse was certain gap with open air. Metabolites and foliar microorganisms were investigated under seaweed fertiliser (CF) and gibberellin (CH) treatments using sensory evaluation, HPLC, untargeted metabolomics, 16S rDNA, and Internal Transcribed Spacer. CF tea was mellow, less astringent, and of better quality compared to CH. Catechin, -(-)Epicatechin, and Epigallocatechin were notably lower in CF. Differentially accumulated metabolites (DAMs) were notably enriched in Flavonoid and Phenylpropanoid biosynthesis, both involved in Catechin synthesis. DAMs in these pathways appeared down-regulated in CF. The CF improved quality by down-regulating metabolites in Phenylpropanoid biosynthesis in conjunction with microbial community metabolism enriched in amino acid and secondary metabolite biosynthesis. Metabolite- microbial correlation analysis indicated that the highest correlation with phenylpropane pathway metabolites was in bacteria Variovorax and Pseudomonas, and in fungi Filobasidium. The study provides theoretical basis for regulating flavour quality of greenhouse tea.PMID:40213339 | PMC:PMC11985128 | DOI:10.1016/j.fochx.2025.102410

Food Chem X. 2025 Mar 21;27:102407. doi: 10.1016/j.fochx.2025.102407. eCollection 2025 Apr.ABSTRACTKoumiss is a fermented mare's milk beverage with a long history. However, due to the current lack of specialized starters, the product quality is unstable. Therefore, we used dual-omics combined with pure culture technology to screen out strains with excellent fermentation performance for koumiss. The results showed that: (1) The dominant species in koumiss were mainly Lactobacillus and Lactococcus, and metabolites such as arachidonic acid and ascorbic acid were significantly enriched in koumiss. (2) There was a significant correlation between specific microbial species and metabolites. (3) Through preliminary screening using experiments such as milk-based curdling experiments and acid resistance tests, and then rescreening through fermentation tests, five strains with excellent fermentation characteristics were screened out. They are Lacticaseibacillus paracasei SXM-5, Lactobacillus kefianofaciens MGE42-8, Lactobacillus helveticus CFS12-11-1, Saccharomyces cerevisiae PFD-2, and Kluyveromyces marxianus PYM-1. The screened strains supply microbial resources for koumiss products and boost the development of milk beverages.PMID:40213331 | PMC:PMC11984606 | DOI:10.1016/j.fochx.2025.102407

Food Chem X. 2025 Mar 14;27:102368. doi: 10.1016/j.fochx.2025.102368. eCollection 2025 Apr.ABSTRACTObesity has emerged as a critical global health challenge in recent decades, driving increased scientific interest in honey as a sugar alternative. Despite its perceived nutritional benefits, the inherent high fructose-glucose ratio in honey continues to raise concerns regarding metabolic implications for overweight individuals. In this study, Amur linden honey (LH) was evaluated as a low-glycemic-index (GI) dietary intervention, demonstrating significant anti-obesity effects through murine model. Subsequently, nine principal polyphenols (PC) were identified by metabolomics and proven anti-obesity activity in cellular assays, suggesting their potential role in mediating the biological effects of LH. Notably, the anti-obesity effects of LH were more pronounced as compared to the equivalent amount of glucose and fructose, and this effect was further facilitated by addition of the PC. Furthermore, LH and HP (LH with the addition of PC) attenuate obesity by modulating gut microbiota, promoting production of SCFA especially acetate and propionate etc., and activating the AMPK/PI3K/AKT pathways. The present study revealed that LH, enriched with diverse bioactive compounds, presents the potential to be a healthy and safe sugar substitutes due to its positive effects on the obesity.PMID:40213330 | PMC:PMC11985147 | DOI:10.1016/j.fochx.2025.102368

Food Chem X. 2025 Mar 21;27:102405. doi: 10.1016/j.fochx.2025.102405. eCollection 2025 Apr.ABSTRACTThe national tea standard sample is an important reference for the evaluation of tea grades. Clarifying the taste characteristics of different grades of Rougui tea (RGT) and its characteristic metabolites is of great significance for the standardization and scientificization of national standard samples. In this study, metabolites of different grades of RGT were analyzed by sensory evaluation and metabolomics, and symbolic metabolites were obtained and verified. The results showed that the higher the RGT grade, the stronger the mellowness and fresh and brisk taste, and the weaker the bitterness and astringency. Cyclo-glycyl-L-phenylalanine and calyxanthone can be used as the main symbolic metabolites to evaluate the quality of RGT, and their contents in 15 different grades of RGT verified the conclusion. This study lays an important foundation for the production of national tea standards and the measurement of commercial tea quality.PMID:40213328 | PMC:PMC11984596 | DOI:10.1016/j.fochx.2025.102405

Mater Today Bio. 2025 Mar 19;32:101685. doi: 10.1016/j.mtbio.2025.101685. eCollection 2025 Jun.ABSTRACTRecently, the nanozyme Pd@Pt has garnered attention due to its notable specific surface area and superior enzyme-like catalytic activity, leading to extensive examination and application in previous studies. However, the comprehensive impact of Pd@Pt nanozyme on treating metabolic disorders, such as diabetes and its associated conditions, remains largely unexplored. This research aimed to clarify how Pd@Pt influences metabolic balance at both the transcriptome and microbiome levels and to explore the interactions between microbiota and genes. We conducted an examination of mice subjected to a high-fat diet (HFD) following treatment with Pd@Pt. Transcriptome analysis was performed to identify differentially expressed genes (DEGs), and microbiome analysis was conducted to identify significant bacterial correlations associated with Pd@Pt exposure. The results indicated enhancements in glucose metabolism dysfunctions in the treated mice. Transcriptome analysis revealed that DEGs after Pd@Pt administration were enriched in the PI3K-Akt, NF-κB, and MAPK signaling pathways in the liver. Microbiome analysis identified four significant bacteria that exhibited a strong negative correlation with Pd@Pt exposure, while ten bacteria showed a positive correlation. Furthermore, a correlation network established among the gut microbiota, metabolites, and DEGs demonstrated a robust association. This research enhances our understanding of the mechanisms by which Pd@Pt affects the regulation of metabolic diseases in HFD-exposed environments and proposes a novel strategy for utilizing nanozymes in human health management.PMID:40213158 | PMC:PMC11984605 | DOI:10.1016/j.mtbio.2025.101685

Data Brief. 2025 Mar 22;60:111474. doi: 10.1016/j.dib.2025.111474. eCollection 2025 Jun.ABSTRACTThe marine biome is a rich source of bioactive compounds. The discovery of anti-cancer compounds in Cryptotheca crypta in 1950 initiated a wave of bioprospecting efforts focused on marine sponges. Jaspis sp., a marine sponge, has been reported to exhibit anti-cancer activity against human colorectal cancer. A sample of Jaspis sp., collected from the waters off Pulau Banggi, Sabah, Malaysia, was analyzed through a non-polar metabolite survey. The non-polar crude extract was profiled using UHPLC-QTOF in both positive and negative modes. The detected metabolic features were clustered, and representative features were tentatively identified through a combination of spectral database searches (using various MS2 spectral databases) and in silico compound identification. This dataset provides a valuable foundation for future bioprospecting endeavors involving Jaspis sp.PMID:40213043 | PMC:PMC11985046 | DOI:10.1016/j.dib.2025.111474

Nanotheranostics. 2025 Mar 24;9(2):110-120. doi: 10.7150/ntno.108320. eCollection 2025.ABSTRACTWith the apparent rise in lifestyle-related changes, there has been a significant decline in renal health. Metabolomics plays a crucial role in the prognosis, diagnosis, and treatment of various renal conditions, including chronic kidney disease, acute kidney injury, diabetic kidney disease, kidney cancer, and post-transplant complications. Metabolomics has identified novel biomarkers, providing insights into altered pathways and potential therapeutic targets for kidney diseases. Kidney diseases and metabolomics keywords were searched in correspondence with the assigned keywords, including chronic kidney diseases, acute kidney injury, kidney carcinoma, kidney transplant, and diabetic kidney diseases on literature search engines. The applicable studies from this search were extracted and included in the study. This review is focused on the biomarkers identified in different kidney diseases such as chronic kidney diseases, acute kidney injury, diabetic kidney disease, kidney carcinoma and kidney transplant.PMID:40212952 | PMC:PMC11980039 | DOI:10.7150/ntno.108320

Ecol Evol. 2025 Apr 9;15(4):e71221. doi: 10.1002/ece3.71221. eCollection 2025 Apr.ABSTRACTReintroduction plays a significant role in the self-maintenance and reconstruction of wild animal populations, serving as a communication bridge between captive and wild animals. The Chinese alligator (Alligator sinensis) is a distinct and endangered reptile species found in China. The mechanisms by which artificially bred Chinese alligators adapt following their release into the wild remain poorly understood. This study aims to elucidate the alterations in gut microbiomes and metabolic phenotypes of Chinese alligators during their reintroduction. During the Chinese alligator's reintroduction, Fusobacterium and Cetobacterium became more abundant, while typical pathogens declined significantly. The gut type of the Chinese alligator changed from Acinetobacter to Cetobacterium. The construction of the gut microbial community was dominated by neutral (random) processes and shifted towards deterministic processes with the progression of reintroduction. In terms of species function, reintroduction significantly upregulated the expression of host immune-related genes and significantly decreased the expression of gut bacterial pathogenic genes and antibiotic resistance genes. Metagenomic and metabolomic KEGG enrichment analyses indicate that glucoside hydrolase families 13 and 23-alongside glycolysis and gluconeogenesis pathways-may play pivotal roles in energy metabolism, host-pathogen interactions, and homeostasis maintenance for Chinese alligators. Differential metabolite analysis identified significant upregulation of metabolites related to neuroendocrine immune modulation and significant down-regulation of anti-inflammatory metabolites during Chinese alligator reintroduction. Association analysis showed that there were significant co-metabolic effects between microorganisms and metabolites, which coordinated host adaptive interaction. This study provides insights into the synergistic mechanisms of host adaptation and wild environment adaptation for Chinese alligators.PMID:40212922 | PMC:PMC11981878 | DOI:10.1002/ece3.71221

Front Cell Infect Microbiol. 2025 Mar 27;15:1524987. doi: 10.3389/fcimb.2025.1524987. eCollection 2025.ABSTRACTBACKGROUND: The interaction between the host and microbiota is influenced by host circadian rhythm. However, it is unknown what the changes of gut microbiota and metabolites.METHODS: We conducted a cross-sectional study (n=72) in which participants' fecal DNA was detected by macrogenomic sequencing analysis. The feces, urine and blood were analyzed by widely targeted metabolomics analysis.RESULTS: Pearson correlation analysis showed that most of the clinical symptoms of people with circadian rhythm disorders were moderately positively correlated with gastrointestinal symptoms. By distilling the results of multinomic analysis, we reported a variety of different species (19 species in the gut) and metabolites. In our results, the correlation of multiomics is mostly concentrated in Lachnospiraceae bacterium and Streptococcus mitis oralis pneumoniae. Bile acid-related metabolites are the most significant metabolites associated with these species.DISCUSSION: Our study demonstrates the severity of clinical manifestations caused by circadian rhythm disorder is closely related to microbiota and metabolism. In the future, personalized interventions targeting specific microbial species or metabolites may help alleviate the physical and psychological discomfort induced by circadian rhythm disturbances.PMID:40212846 | PMC:PMC11983646 | DOI:10.3389/fcimb.2025.1524987

Small Sci. 2022 Feb 9;2(5):2100118. doi: 10.1002/smsc.202100118. eCollection 2022 May.ABSTRACTExosomes are regarded as the emerging potential targets for liquid biopsy and bioprocess study owing to their abundant inclusive cargos that carry significant disease information. In addition, metabolites have been promising biomarkers for diagnosis. However, little metabolic research on exosomes is carried out by now. Herein, the mix-crystal titania-assisted laser desorption/ionization mass spectrometry (LDI-MS) method is established, which features fast speed, high throughput, and efficiency, to directly extract urinary exosome metabolic patterns of healthy controls (HC) and membrane nephropathy (MN) patients. Besides, this method is also adopted to acquire the primitive urinary metabolic patterns from the same samples for comparison. By taking advantage of principal component analysis, unpaired parametric t-test, and orthogonal partial least squares discriminant analysis on the exosome metabolic patterns, 27 significant m/z signals are filtrated, which possess more prominent differentiation capacity toward HC and MN patients (AUC = 0.942), and hold greater potential in MN diagnosis, compared to primitive urine (AUC = 0.801). The work reveals the important clinical value of exosome metabolic analysis, and paves a way to exosome-based diagnosis at metabolomic level toward large-scale clinical use.PMID:40212598 | PMC:PMC11935978 | DOI:10.1002/smsc.202100118

Biomater Res. 2025 Apr 10;29:0181. doi: 10.34133/bmr.0181. eCollection 2025.ABSTRACTRenal microcirculatory disturbances and tissue hypoxia play a pivotal role in acute kidney injury (AKI) initiation and progression, and addressing renal hypoxia during the acute phase presents a promising therapeutic strategy for preventing AKI or protecting kidney function. In this study, we explored the renal protective potential of perfluorocarbon nanoparticles (PFPs), engineered for superior oxygen-carrying and delivery capacities, in an AKI mouse. Specifically, PFP-treated mice exhibited significant reductions in tubular dilation, necrosis, and brush border loss in renal tubules. Additionally, PFP pretreatment reduced tissue inflammation and fibrosis, as indicated by decreased nuclear factor-kappa B, α-smooth muscle actin, fibronectin, and collagen I expression. Serum creatinine and blood urea nitrogen levels improved, decreasing by 26.9% and 41.7%, respectively. Flow cytometry further showed controlled levels of f4/80+ macrophages and CD45+ inflammatory markers, with f4/80+ macrophages reduced by approximately 31.2% and CD45+ inflammatory factors reduced by 40.5%. Metabolomic analyses highlighted PFP's modulation of key metabolic pathways linked to renal recovery, notably up-regulating slc22a19 by 48.3%, a gene encoding a short-chain fatty acid transporter, and down-regulating hyaluronic acid synthesis in renal tissue. These findings are the first to demonstrate that PFPs, as an oxygen carrier, can enhance renal resilience against IR (ischemia-reperfusion)-induced AKI, offering compelling evidence of PFP's clinical potential in AKI management.PMID:40212394 | PMC:PMC11982615 | DOI:10.34133/bmr.0181

PeerJ. 2025 Apr 7;13:e19206. doi: 10.7717/peerj.19206. eCollection 2025.ABSTRACTBACKGROUND: Yupingfeng san is a traditional Chinese medicine formula composed of siler, atractylodes, and astragalus. The herbal medicine fermentation process relies on the role of probiotics. Bacillus coagulans is a probiotic commonly used to ferment food and drugs. It produces a variety of beneficial metabolites during fermentation. However, the study on the interaction between B. coagulans and yupingfeng san is still blank.METHODS: During solid-state fermentation of yupingfeng san, we used metabolomics technology and 16S rDNA sequencing to analyze the differential metabolites and microbial flora of B. coagulans at 0, 3, 7, 11, and 15 d, which corresponded to groups A0, B3, B7, B11, and B15, respectively. This research explored the correlation between microorganisms and metabolites in fermented compound Chinese medicine.RESULTS: The results revealed a significant difference in species β diversity between group A0 and the B groups (P < 0.01). At the phylum level, in fermentation groups B3, B7, B11, and B15, the Cyanobacteria relative abundance decreased by 6.69%, 9.09%, 5.74%, and 2.24%, respectively (P < 0.05). The Firmicutes relative abundance increased by 39.73%, 35.65%, 49.09%, and 68.66% (P < 0.05), respectively. The Proteobacteria relative abundance decreased by 39.86% and 26.70%, respectively, in groups B11 and B15 (P < 0.05). The relative abundance of Actinobacteria increased initially with extended fermentation time, and then gradually decreased after reaching its peak in group B7. At the genus level, compared with group A0, the relative abundance of Actinobacteria increased to its highest level of 21.12% in fermentation group B3 and decreased to 9.51% after a fermentation time of 15 d. The abundance of Leuconostoc in fermentation groups B3, B7, and B11 was significantly higher than in group A0 (20.93%, 20.73%, and 21.00%, respectively, P < 0.05). Pediococcus in fermentation groups B3, B7, B11, and B15 was also significantly higher than in group A0 (4.20%, 2.35%, 18.84%, and 52.01%, P < 0.05). Both Pediococcus and Leuconostoc, which belong to lactic acid bacteria, increased fivefold, accounting for a total abundance of 62%. After yupingfeng san fermentation, using nontargeted metabolomics, we identified 315 differential metabolites. This results showed a decrease in the content of alkene and an increase in the contents of acids, lipids, ketones, and amino acids. In addition, in group B3, the contents of quercetin, paeoniflorin-3-O-glucoside, netin, iristin, anthocyanin, caffeic acid, rosmarinic acid, liquiritin, and isoliquiritin were significantly upregulated.CONCLUSION: In this study, the composition and metabolic profile of yupingfeng san after the fermentation of B. coagulans were studied, and it was found that the fermentation group showed rich species diversity, in which the abundance of Leuconostoc and Weisseria increased significantly, while the opportunistic pathogens such as Pseudomonas aeruginosa and Enterobacter decreased significantly. The analysis of metabolic products showed that the contents of acids, lipids and ketones were significantly increased, rich in a variety of beneficial microorganisms and small molecular compounds with antibacterial effects, and these changes worked together to inhibit the growth of pathogens and maintain intestinal health. The study not only helps to elucidate the assembly mechanism and functional expression of microorganisms after Chinese traditional medicine fermentation, but also provides a solid scientific basis for the development of efficient and safe micro-ecological feed additives.PMID:40212372 | PMC:PMC11984470 | DOI:10.7717/peerj.19206