PubMed

Front Immunol. 2025 Jan 22;16:1518181. doi: 10.3389/fimmu.2025.1518181. eCollection 2025.ABSTRACTBACKGROUND: Rheumatoid arthritis (RA) is a common chronic and systemic autoimmune disease. Numerous clinical studies have indicated a correlation between alterations in gut microbiota and the onset and progression of RA. This research aims to restore intestinal microbiota to a healthy state through the oral administration of Bifidobacterium in the early stages with the goal of delaying the onset and progression of RA.METHODS: Collagen-induced arthritis (CIA) rat model was constructed to assess the development of RA using arthritis clinical scores, paw thickness, pathological analysis of knee joint. The immune response was evaluated by determinating specific antibodies and cytokines in serum and synovial fluid. The expression of intestinal barrier protein was analyzed by qPCR to evaluate the intestinal barrier function. Alterations in gut microbiota and metabolites were assessed by 16S rDNA and non-targeted metabolomics.RESULTS: The findings reveal that administering Bifidobacterium animalis BD400 orally led to a significant reduction in arthritis clinical scores and paw swelling thickness in CIA rats. Additionally, there was a decrease in osteo-facial fusion and calcified cartilage thickening in the knee joint. Furthermore, the oral administration of B. animalis BD400 resulted in the down-regulation of inflammatory factors TNF-α and collagenase MMP-13 in the knee joint. Levels of specific antibodies (anti-CII IgG, anti-CII IgG1, and anti-CII IgG2a) and cytokine IL-17A in serum, as well as cytokines (TNF-α and IL-1β) in the synovial fluid of B. animalis BD400-treated CIA rats, were significantly reduced (p < 0.05). The gene expression levels of intestinal barrier proteins (occludin-1, MUC-2, and ZO-1) showed a significant increase (p < 0.05) in B. animalis BD400-treated CIA rats. The oral administration of B. animalis BD400 altered the composition of intestinal microorganisms in CIA rats at the phylum and genus levels, particularly affecting the genus HT002. B. animalis BD400 alleviates RA by down-regulating 1-methyl-L-histidine and urocanate in the histidine metabolism, laying a foundation for the RA prevention.CONCLUSION: By affecting genus HT002 and histidine metabolism in the gut microbiota of CIA rats, B. animalis BD400 restored intestinal permeability, inhibited systemic inflammatory response, and ultimately slowed down the development of RA.PMID:39911381 | PMC:PMC11794514 | DOI:10.3389/fimmu.2025.1518181

Front Microbiol. 2025 Jan 22;16:1510904. doi: 10.3389/fmicb.2025.1510904. eCollection 2025.ABSTRACTBACKGROUND: Intercropping Saccharum spp. (sugarcane) with the fungus Dictyophora indusiata together with bagasse amendment represents an innovative circular agriculture method that can enhance soil health, boost sugarcane yields, and increase farm profitability. Understanding the process by which D. indusiata degrades bagasse is key to optimizing this method.AIMS: This study aims to clarify the microbial and metabolic processes involved in bagasse degradation by D. indusiata in the sugarcane intercropping system.METHODS: Chemical composition analysis, metabarcoding sequencing, and metabolomic profiling were conducted on D. indusiata-degraded bagasse (DIBA) and naturally degraded bagasse (BA).RESULTS: Analysis of chemical composition revealed that only acid detergent fiber (ADF) and crude protein content differed significantly between the DIBA and BA treatments. Metabarcoding sequencing showed that DIBA significantly altered the bacterial and fungal communities, reducing microbial diversity. Metabolomic analysis indicated an enhancement of biological metabolism, particularly carbohydrate breakdown, in the DIBA treatment. Key metabolites, such as glucose, cellobiose, and D-mannose, were more abundant in DIBA samples. In addition, unique metabolites such as L-alanine, serine, and oxaloacetate were detected in the DIBA treatment, suggesting more efficient bagasse degradation compared with natural processes.CONCLUSION: The use of macrofungi such as D. indusiata can play a pivotal role in circular agriculture by transforming agricultural waste into valuable soil amendments. Future research should focus on the long-term impact of this system on soil quality and crop yield, as well as the underlying mechanisms, to further optimize intercropping systems and the use of fungi in agricultural waste management.PMID:39911253 | PMC:PMC11794506 | DOI:10.3389/fmicb.2025.1510904

J Exp Biol. 2025 Feb 6:jeb.250076. doi: 10.1242/jeb.250076. Online ahead of print.ABSTRACTCold tolerance is a key determinant of poleward colonization in insects. However, the physiological basis underlying interspecific differences in cold tolerance is not fully understood. Here, we analyzed cold tolerance and metabolomic profiles in warm- and cold-acclimated phenotypes of 43 Drosophila species representing a latitudinal gradient from the tropics to the boreal zone. We found a strong positive correlation between cold tolerance and climatic variables associated with habitat seasonality and temperature. Including the effects of cold acclimation, we found most species to have similar 'safety margins', measured as the difference between the average environmental temperature and the lower lethal temperature. Searching for metabolomic signatures of cold tolerance, we found that the warm-acclimated flies of cold-hardy species had moderately but significantly higher constitutive signals of putative cryoprotectants such as trehalose, glucose, glycerol, and mannitol/sorbitol. Cold acclimation (and the transition to winter dormant phenotype) resulted in a strong accumulation of myo-inositol, which occurred only in species of the virilis group. Other temperate and boreal species either showed only moderate, idiosyncratic accumulations of sugars/polyols and free amino acids, or did not accumulate any 'classical' cryoprotectant at all. Thus, our results suggest that the colonization of boreal regions by Drosophila does not necessarily depend on the seasonal accumulation of classical cryoprotectants. In contrast, virtually all cold-acclimated species showed a significant increase in products of phospholipid catabolism, suggesting that remodeling of biological membranes is a clear and ubiquitous signature of cold acclimation in Drosophila.PMID:39911076 | DOI:10.1242/jeb.250076

J Sep Sci. 2025 Feb;48(2):e70089. doi: 10.1002/jssc.70089.ABSTRACTRecently, proteinogenic amino acids have become very interesting molecules, accompanied by a large variety of metabolic processes in humans and are associated with various diseases. In the era of system biology, including a broad spectrum of associated disciplines (e.g., metabolomics, lipidomics, proteomics, etc.), the possibility of identifying trustworthy biomarkers of diseases becomes much more likely. Changes in amino acid levels in plasma, serum, or cerebrospinal fluid reflect physiological or pathological conditions and, therefore, their regular monitoring can lead to early detection of the occurrence of a disease. Therefore, the exact determination of amino acids in biological fluids is of great importance. However, it is necessary to dispose with an effective, accurate, precise, selective, and robust analytical method. This protocol describes the complex procedure of amino acid analysis based on a combination of UHPLC with single quadrupole MS. The protocol presents a highly reproducible and robust methodology that has already been established in the quality control of biopharmaceuticals and determination of proteinogenic amino acids in urine in our laboratory. Here, the application potential is extended to the most frequently investigated biological fluid, that is, plasma and to the cerebrospinal fluid, which is investigated in many neurological conditions.PMID:39910690 | DOI:10.1002/jssc.70089

Genome Med. 2025 Feb 5;17(1):10. doi: 10.1186/s13073-025-01434-8.ABSTRACTBACKGROUND: Exercise rehabilitation therapy has garnered widespread recognition for its beneficial effects on the restoration of locomotor function in individuals with spinal cord injury (SCI). Notably, resistance exercise has demonstrated significant improvements in muscle strength, coordination, and overall functional recovery. However, to optimize clinical management and mimic exercise-like effects, it is imperative to obtain a comprehensive understanding of the molecular alterations that underlie these positive effects.METHODS: We conducted a randomized controlled clinical trial investigating the effects of resistance exercise therapy for incomplete SCI. We integrated the analysis of plasma proteomics and peripheral blood mononuclear cells (PBMC) transcriptomics to explore the molecular and cellular changes induced by resistance exercise. Subsequently, we established a weight-loaded ladder-climbing mouse model to mimic the physiological effects of resistance exercise, and we analyzed the plasma proteome and metabolome, as well as the transcriptomes of PBMC and muscle tissue. Lastly, to confirm the transmissibility of the neuroprotective effects induced by resistance exercise, we intravenously injected plasma obtained from exercised male mice into SCI female mice during the non-acute phase.RESULTS: Plasma proteomic and PBMC transcriptomic profiling underscored the notable involvement of the complement pathways and humoral immune response in the process of restoring locomotor function following SCI in the human trial. Moreover, it was emphasized that resistance exercise interventions could effectively modulate these pathways. Through employing plasma proteomic profiling and transcriptomic profiling of PBMC and muscle tissues in mice, our study revealed immunomodulatory responses that parallel those observed in human trials. In addition, our analysis of plasma metabolomics revealed an enhancement in lipid metabolism following resistance exercise. We observed that resistance exercise plasma exhibited significant effects in ameliorating locomotor disability after SCI via reducing demyelination and inhibiting neuronal apoptosis.CONCLUSIONS: Our investigation elucidates the molecular alterations associated with resistance exercise therapy promoting recovery of locomotor function following incomplete SCI. Moreover, we demonstrate the direct neuroprotective effects delivered via exercise plasma injection, which facilitates spinal cord repair. Mechanistically, the comprehensive multi-omics analysis involving both human and mice reveals that the principal constituents responsible for the observed neuroprotective effects within the plasma are predominantly immunoregulatory factors, warranting further experimental validation.TRIAL REGISTRATION: The study was retrospectively registered on 17 July, 2024, in Chinese Clinical Trial Registry (No.: ChiCTR2400087038) at https://www.chictr.org.cn/ .PMID:39910614 | DOI:10.1186/s13073-025-01434-8

Nat Cell Biol. 2025 Feb 5. doi: 10.1038/s41556-025-01609-w. Online ahead of print.NO ABSTRACTPMID:39910286 | DOI:10.1038/s41556-025-01609-w

Sci Rep. 2025 Feb 5;15(1):4314. doi: 10.1038/s41598-025-88494-3.ABSTRACTCopy number alterations (CNAs) play a fundamental role in cancer development and constitute a potential tool for tailored treatments. The CNAs recognition in formalin fixed paraffin embedded (FFPE) material for diagnostic purposes has relied for years mainly on fluorescence in situ hybridization. The introduction of other procedures, such as Next-Generation Sequencing has dramatically improved CNAs discovery at genome-wide level. The detection of CNAs by NGS in FFPE material is, nonetheless, a complex issue, which still requires validation studies. Herein, the CNAs detection by a widely used NGS assay (Oncomine Comprehensive Assay plus®, OCA+) were evaluated in 14 FFPE samples mirroring diagnostic daily practice and compared to a whole-genome assay. OCA+, a targeted DNA panel, showed lower CNAs detection sensitivity and equal specificity for gains and losses. According to proprietary software pipeline, OCA+ accurately identified gains characterized by CN ≥ 5,2. No significant threshold maximizing the difference between true and false positive losses was found. Orthogonal FISH tests validated seven CNAs characterized by CN gain ≥ 6 or complete loss. Considering the CNAs growing significance in precision medicine, our findings further prompt towards a robust validation of NGS detection in FFPE materials.PMID:39910096 | DOI:10.1038/s41598-025-88494-3

Gut Microbes. 2025 Dec;17(1):2455506. doi: 10.1080/19490976.2025.2455506. Epub 2025 Feb 5.ABSTRACTThe relationship between bacteria, cognitive function and obesity is well established, yet the role of archaeal species remains underexplored. We used shotgun metagenomics and neuropsychological tests to identify microbial species associated with cognition in a discovery cohort (IRONMET, n = 125). Interestingly, methanogen archaeas exhibited the strongest positive associations with cognition, particularly Methanobrevibacter smithii (M. smithii). Stratifying individuals by median-centered log ratios (CLR) of M. smithii (low and high M. smithii groups: LMs and HMs) revealed that HMs exhibited better cognition and distinct gut bacterial profiles (PERMANOVA p = 0.001), characterized by increased levels of Verrucomicrobia, Synergistetes and Lentisphaerae species and reduced levels of Bacteroidetes and Proteobacteria. Several of these species were linked to the cognitive test scores. These findings were replicated in a large-scale validation cohort (Aging Imageomics, n = 942). Functional analyses revealed an enrichment of energy, butyrate, and bile acid metabolism in HMs in both cohorts. Global plasma metabolomics by CIL LC-MS in IRONMET identified an enrichment of methylhistidine, phenylacetate, alpha-linolenic and linoleic acid, and secondary bile acid metabolism associated with increased levels of 3-methylhistidine, phenylacetylgluamine, adrenic acid, and isolithocholic acid in the HMs group. Phenylacetate and linoleic acid metabolism also emerged in the Aging Imageomics cohort performing untargeted HPLC-ESI-MS/MS metabolic profiling, while a targeted bile acid profiling identified again isolithocholic acid as one of the most significant bile acid increased in the HMs. 3-Methylhistidine levels were also associated with intense physical activity in a second validation cohort (IRONMET-CGM, n = 116). Finally, FMT from HMs donors improved cognitive flexibility, reduced weight, and altered SCFAs, histidine-, linoleic acid- and phenylalanine-related metabolites in the dorsal striatum of recipient mice. M. smithii seems to interact with the bacterial ecosystem affecting butyrate, histidine, phenylalanine, and linoleic acid metabolism with a positive impact on cognition, constituting a promising therapeutic target to enhance cognitive performance, especially in subjects with obesity.PMID:39910065 | DOI:10.1080/19490976.2025.2455506

Fitoterapia. 2025 Feb 3:106403. doi: 10.1016/j.fitote.2025.106403. Online ahead of print.ABSTRACTGouania lupuloides (L.) Urb. (Rhamnaceae), a medicinal plant commonly used in the Caribbean for dental health, is known as chew stick (chewstick) or bejuco de Indio. Few studies have assessed its chemistry and biological activity. The overall aim of this research is to understand the phytochemistry and antibacterial activity of Gouania lupuloides, as well as its continued cultural use. Authenticated Gouania lupuloides samples collected in the Jamaica were extracted, subjected to solvent-solvent partitioning, and evaluated for inhibitory activity against pathogenic oral bacteria. Commercial Caribbean samples of bejuco de Indio available in the United States were compared chemically to known Gouania lupuloides samples through targeted and untargeted UPLC-QTOF-MS analysis. Ethnobotanical fieldwork in rural and urban Jamaica demonstrated the ongoing cultural use of Gouania lupuloides as a natural toothbrush, and in the preservation of traditional fermented beverages. Antibacterial assays demonstrated that triterpenes from Gouania lupuloides, including isolated ceanothic acid, had activity against several of the tested oral pathogens, including Actinomyces viscosus, Prevotella intermedia, and Peptostreptococcus micros. Principal component analysis indicates that at least one of the chew stick samples sold as bejuco de Indio was chemically distinct from Gouania lupuloides type specimens. Presence of ceanothic acid was used to characterize a chemical fingerprint typical of Gouania lupuloides to aid in the chemotaxonomic identification of unknown chew sticks. Additionally, antibacterial ceanothic acid was present in similar relative abundance in all samples identified as Gouania lupuloides, further supporting its traditional use for oral health and hygiene.PMID:39909353 | DOI:10.1016/j.fitote.2025.106403

Int J Biol Macromol. 2025 Feb 3:140639. doi: 10.1016/j.ijbiomac.2025.140639. Online ahead of print.ABSTRACTSevere pneumonia, frequently accompanied by cytokine storms, stands as a perilous respiratory condition with alarmingly high mortality rates. Tetrastigma hemsleyanum polysaccharide (THP), a pivotal constituent derived from Tetrastigma hemsleyanum Diels et Gilg (TH), has demonstrated efficacy in treating lung inflammation. However, its precise efficacy and underlying mechanisms in the context of severe pneumonia remain elusive. Our research aims to elucidate THP's protective effects in a "two-hit" severe pneumonia model. Our observations indicate that THP administration markedly shields the lungs from injury, reduces pulmonary apoptosis, balances the formation of immune thrombus and alleviates oxidative stress in pneumonia-induced mice. Furthermore, THP significantly decreases the levels of pro-inflammatory cytokines, suggesting its robust anti-inflammatory capabilities. Notably, THP also plays a crucial role in normalizing gut microbiota imbalance, which is vital in the pathogenesis of severe pneumonia. Metabolomic analysis further validates THP's restorative effects on plasma metabolites, indicating its involvement in regulating energy metabolism and immune homeostasis. Mechanistically, THP targets the TLR4/NF-κB signaling pathway, a core mediator of inflammation, thereby dampening the inflammatory cascade. In summary, our findings underscore that THP, through its multifaceted actions targeting inflammation, oxidative stress, immune thrombus formation, gut microbiota regulation, and metabolic modulation, emerges as a promising therapeutic approach for severe pneumonia. This study provides invaluable insights into the potential applications of natural polysaccharides in treating severe pneumonia and highlights the significance of the TLR4/NF-κB pathway in the disease's progression.PMID:39909274 | DOI:10.1016/j.ijbiomac.2025.140639

Int J Biol Macromol. 2025 Feb 3:140661. doi: 10.1016/j.ijbiomac.2025.140661. Online ahead of print.ABSTRACTResistant starch (RS) is one of the bioactive polysaccharides to produce Short-chain fatty acids (SCFAs) in the colon and contributes to allergic diseases including atopic dermatitis (AD). However, the bioactive mechanism of RS relieving AD needs to be elucidated. In this study, RS was prepared using chickpeas. Its microstructure and crystal structure were thoroughly characterized. Chickpea RS significantly improved the clinical symptoms and restored Th1/Th2 immune balance in mice with AD induced by calcipotriol. These benefits were eliminated by antibiotic cocktail treatment, suggesting that gut microbiota mediated the alleviation effects of chickpea RS on AD. Based on metagenomic sequencing and untargeted metabolomic analysis, chickpea RS treatment significantly increased the proportions of Butyricimonas virosa, Bifidobacterium pseudolongum, and Faecalibaculum rodentium, and a total of 206 differential metabolites were altered, especially the increase in propionate and butyrate production. Furthermore, we found that acylated butyrate, but not propionate, improved the pathological characteristics by activating GPR109A, which inhibit the phosphorylation levels of IκB-α, p50, p65, JNK, and p-JNK. Collectively, chickpea RS exhibited the bioactive function for regulating the communication of the gut-skin axis via regulating butyrate production to activate GPR109A.PMID:39909254 | DOI:10.1016/j.ijbiomac.2025.140661

J Ethnopharmacol. 2025 Feb 3:119435. doi: 10.1016/j.jep.2025.119435. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Ischemic stroke (IS) is a leading cause of long-term disability and mortality worldwide. The Chinese Pharmacopeia 2020 lists Naoxintong Capsule (NXT), a traditional Chinese medicine prescription, as having demonstrated substantial therapeutic efficacy for IS.AIM OF THE STUDY: Our study aimed to evaluate the mechanism by which NXT treats IS by integrating the microbiome, transcriptome, and metabolomics.MATERIALS AND METHODS: In a middle cerebral artery occlusion (MCAO) mouse model, the infarction rate, neurological scores, lipopolysaccharide (LPS) levels, inflammatory factor levels (IL-1β, IL-17A, and IL-6), and intestinal permeability proteins (ZO-1, MUC2, and MUC4) were measured to confirm the effect of NXT on the brain and colon. 16S rRNA sequencing, transcriptomics analysis, and targeted amino acid (AA) metabolism were employed to evaluate the mechanism by which NXT treats IS. Furthermore, the neuroprotective effects of specific AAs, identified through targeted AA metabolism, were assessed in PC12 cells following oxygen-glucose deprivation (OGD) injury. In addition, the TLR4/NF-κB pathway was evaluated by western blot (WB).RESULTS: NXT administration substantially alleviated brain damage and colon injury by decreasing the infarction rate, neurological scores, LPS levels, and inflammatory factors, and increasing the expression of intestinal permeability protein. Transcriptomic analysis revealed that NXT regulated "inflammatory response," "Toll-like receptor signaling pathway,", and "NF-κB signaling pathway." Furthermore, WB confirmed that NXT inhibited the brain TLR4/NF-κB pathway. 16S rRNA sequencing indicated that NXT adjusted the intestinal microbiota composition and decreased the abundance of pathogenic bacteria, including Parasutterella_massiliensis and Ihubacter_excrementihominis. Targeted AA metabolism analysis demonstrated that NXT regulated the serum levels of serine, lysine, and proline in MCAO mice. Furthermore, serine, lysine, and proline inhibited the TLR4/NF-κB pathway to protect against OGD injury in PC12 cells.CONCLUSION: Our study indicates that NXT reduces the abundance of Parasutterella_massiliensis and Ihubacter_excrementihominis, while increasing the levels of serine, lysine, and proline. These changes are significantly associated with neuroinflammation. Furthermore, NXT alleviates IS-induced neuroinflammation by inhibiting the TLR4/NF-κB pathway. Importantly, our study provides novel insights into the mechanisms underlying NXT's therapeutic effects on IS.PMID:39909118 | DOI:10.1016/j.jep.2025.119435

J Ethnopharmacol. 2025 Feb 3:119438. doi: 10.1016/j.jep.2025.119438. Online ahead of print.ABSTRACTETHNOPHARMACOLOGICAL RELEVANCE: Huafengdan (HFD), a traditional Chinese medicine from Guizhou, is known for its efficacy in treating ischemic stroke (IS). Yaomu, a principal component of HFD, undergoes fermentation, yet the role of this process in enhancing HFD's therapeutic effects remains unclear. Investigating the synergistic mechanism of fermented Yaomu in HFD's treatment of IS provides a theoretical basis for its clinical application.PURPOSE: This study aimed to explore how Yaomu fermentation enhances HFD's effectiveness and elucidates the underlying mechanisms.METHODS: Differential components of HFD, with and without fermented Yaomu, were identified using UPLC-Q-TOF-MS/MS. Newly added and upregulated components underwent network pharmacological analysis. An IS rat model was established, and neurobehavioral scores, cerebral infarction volumes, and levels of superoxide dismutase (SOD), malondialdehyde (MDA), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) were measured to assess efficacy. Multivariate statistics and pathway analyses were conducted using UPLC-Q-TOF-MS/MS data. A "metabolite-enzyme-reaction-gene" network, integrating pharmacological and metabolomic data, identified key synergistic pathways, which were validated through protein analysis.RESULTS: The UPLC-Q-TOF-MS/MS analysis identified 54 novel components in HFD after Yaomu fermentation and detected 51 differential components between fermented and unfermented HFD, with 15 components downregulated and 36 upregulated. Network pharmacology revealed 53 active synergistic components and 642 component-disease intersection targets. Enrichment analysis of these intersecting targets indicated that Yaomu fermentation might enhance HFD's efficacy by influencing the cAMP signaling pathway and neuroactive ligand-receptor interactions. Pharmacodynamic studies demonstrated that both HFD and HFD containing unfermented Yaomu significantly reduced neurobehavioral scores and infarct volumes in IS models, elevated SOD levels, and decreased MDA, TNF-α, and IL-6 levels. However, the efficacy of HFD was significantly higher than that of HFD containing unfermented Yaomu. Metabolic analysis identified five critical pathways involved in HFD's therapeutic effects on IS, while three pathways were associated with the synergistic impact of Yaomu fermentation on HFD. By integrating network pharmacology and metabolomics, the "metabolite-enzyme-reaction-gene" network was constructed, revealing tryptophan metabolism as the primary synergistic pathway.CONCLUSION: Yaomu fermentation enhances the therapeutic efficacy of HFD in IS treatment, primarily through the tryptophan metabolism pathway.PMID:39909116 | DOI:10.1016/j.jep.2025.119438

Cell Metab. 2025 Jan 28:S1550-4131(24)00495-9. doi: 10.1016/j.cmet.2024.12.013. Online ahead of print.ABSTRACTImmune checkpoint blockade (ICB) therapy has revolutionized cancer treatment but remains effective in only a subset of patients. Emerging evidence suggests that the gut microbiome and its metabolites critically influence ICB efficacy. In this study, we performed a multi-omics analysis of fecal microbiomes and metabolomes from 165 patients undergoing anti-programmed cell death protein 1 (PD-1)/programmed death ligand 1 (PD-L1) therapy, identifying microbial and metabolic entities associated with treatment response. Integration of data from four public metagenomic datasets (n = 568) uncovered cross-cohort microbial and metabolic signatures, validated in an independent cohort (n = 138). An integrated predictive model incorporating these features demonstrated robust performance. Notably, we characterized five response-associated enterotypes, each linked to specific bacterial taxa and metabolites. Among these, the metabolite phenylacetylglutamine (PAGln) was negatively correlated with response and shown to attenuate anti-PD-1 efficacy in vivo. This study sheds light on the interplay among the gut microbiome, the gut metabolome, and immunotherapy response, identifying potential biomarkers to improve treatment outcomes.PMID:39909032 | DOI:10.1016/j.cmet.2024.12.013

J Chromatogr A. 2025 Feb 1;1745:465747. doi: 10.1016/j.chroma.2025.465747. Online ahead of print.ABSTRACTCitrus-derived raw medicinal materials are frequently used for health care, flavoring, and therapeutic purposes. However, Due to similarities in origin or appearance, citrus herbs are often misused in the market, necessitating effective differentiation methods. For the first time, this study constructed automated discrimination models for 16 citrus species (239 batches) while previous studies focused on a limited number of species. Seven machine learning models -Tree, Discriminant, Support Vector Machine, K-Nearest Neighbor, Ensemble, Neural Network, and Partial least squares discriminant analysis-were compared, with the Ensemble model achieving 100% accuracy in the test set. 16 Orthogonal partial least squares discriminant analysis models were constructed to screen and identify 53 differential markers. These markers were successfully utilized to determine the absence or presence of specified components in the 20 citrus products. This study provides a comprehensive solution for the quality control of citrus herbs, enabling the differentiation of raw herbs and processed slices, as well as the identification of complex systems such as Chinese patent medicines.PMID:39908954 | DOI:10.1016/j.chroma.2025.465747

Microbiol Res. 2025 Jan 30;293:128085. doi: 10.1016/j.micres.2025.128085. Online ahead of print.ABSTRACTGrapevine trunk diseases (GTDs), particularly Esca, represent a major challenge for viticulture worldwide, leading to substantial economic losses. With no effective control treatments available, developing new methods such as biocontrol is crucial for managing GTDs. Our aim was to select biocontrol bacteria effective against the white-rot fungal pathogen Fomitiporia mediterranea (Fmed) and to investigate their mechanisms of action. A stepwise screening of 58 bacterial strains was conducted in vitro to assess their ability to inhibit Fmed growth through volatile and diffusible metabolites production. The screening was also done on wood sawdust from seven different grapevine cultivars. Out of 58 tested strains, 49 inhibited Fmed growth by over 50 % through their volatile organic compounds, only eight achieving this through their agar-diffusible metabolites. Pseudomonas lactis SV9, Pseudomonas paracarnis S45, and Paenibacillus polymyxa SV13 exhibited a strong efficacy in inhibiting Fmed on wood sawdust in a cultivar-dependent manner. We selected these strains for whole genome analysis and metabolomic profiling via LC-MS/MS for diffusible compounds and SPME GC-MS for volatile compounds. P. polymyxa SV13 inhibited Fmed primarily through diffusible metabolites, producing mainly fusaricidin-type compounds. Conversely, Pseudomonas strains acted mainly via their volatile metabolites, producing mainly the antifungal compound dimethyl disulfide. Genome analysis of the three bacterial strains revealed gene clusters responsible for regulating both direct and indirect mechanisms in biocontrol agents (BCAs). Our findings highlight the importance of comprehensive studies that combine in vitro experiments mimicking field conditions, with detailed investigations into modes of action to improve BCAs efficacy.PMID:39908943 | DOI:10.1016/j.micres.2025.128085

Food Chem. 2025 Jan 29;473:143137. doi: 10.1016/j.foodchem.2025.143137. Online ahead of print.ABSTRACTThis study analyzed raw milk's microbial community and chemical profile during the natural creaming process of Parmigiano Reggiano production by comparing milk from farms following two different organic certifications. Specifically, the natural creaming process underlined the positive accumulation of potentially pro-dairy bacteria, particularly those of the genera Lactococcus and Streptococcus, and a significant reduction of negative bacterial genera, such as Acinetobacter and Rothia, in the final mix milk. Meanwhile, untargeted metabolomic analysis confirmed the representativeness of lipids and lipid-derivatives as chemical markers involved in the overnight creaming process, with fatty acid esters and long fatty acids enriched in the evening samples. Finally, by using a multi-omics approach, we integrated microbial and metabolomic datasets and identified correlations between specific microbial populations and metabolite changes. This integrative analysis revealed microbial-metabolite interactions that may be a starting point to better understand the pivotal role exerted by milk creaming on the final cheese quality.PMID:39908777 | DOI:10.1016/j.foodchem.2025.143137

J Environ Manage. 2025 Feb 4;375:124221. doi: 10.1016/j.jenvman.2025.124221. Online ahead of print.ABSTRACTThe co-culture system of Chlorella sorokiniana and Aspergillus oryzae has demonstrated exceptional tolerance and efficiency in the removal of pollutants from swine manure. This study evaluates the ability of the co-culture system to remove Zn(II) and estrone, while assessing the impact of these pollutants on the system's overall functionality. Results indicated that co-cultivation achieved higher biomass accumulation, peaking at 0.88 g/L after 96 h. Increasing estrone exposure concentration reduced photosynthetic activity and chlorophyll content, whereas Zn(II) exposure initially enhanced and later inhibited chlorophyll synthesis. Co-cultivation secreted extracellular polymeric substances, including protein-like and humus-like substances, to alleviate environmental stress and form algal-fungal community. After 96 h of cultivation, the removal efficiencies reached 86.44% for 1.5 mg/L Zn(II) and 84.55% for 20 mg/L estrone. The Quantitative Structure Activity Relationship model revealed a reduction in the ecotoxicity of estrone intermediate products to varying degrees. Metabolomics analysis showed that exposure to estrone and Zn(II) significantly boosted the production of Gibberellic acid, Indole-3-acetic acid, and Zeatin riboside in Chlorella sorokiniana, while reducing Abscisic Acid levels. Furthermore, the exposure led to an increase in various metabolites in the Tricarboxylic acid cycle of the co-cultivation system, influencing the synthesis and metabolism of key biochemical components like carbohydrates, lipids, and proteins. These findings elucidate the biochemical responses of Chlorella sorokiniana-Aspergillus oryzae co-culture system to pollutants and provide insights into its potential application in the treatment of wastewater containing endocrine disrupting chemicals and heavy metals.PMID:39908605 | DOI:10.1016/j.jenvman.2025.124221

Anal Chem. 2025 Feb 5. doi: 10.1021/acs.analchem.4c06133. Online ahead of print.ABSTRACTComplex diseases involve extensive metabolic interactions within intricate biological networks. Consequently, it is advantageous to analyze metabolic phenotype data through metabolite interactions rather than focus on individual metabolites in isolation. In this article, we propose a novel analysis strategy called SynNet, which constructs multiscale synergy networks associated with specific metabolic phenotypes, offering new perspectives on the metabolic response mechanisms of diseases, including the mechanisms underlying disease comorbidity. The SynNet strategy begins with the construction of a metabolite-level synergy network (m-SynNet). This network is based on the definition and identification of significant metabolite pair interactions that distinguish disease phenotypes. Subsequently, a pathway synergy effect is defined by mapping these synergistic metabolite pairs onto the predefined metabolic pathways and performing a hypergeometric test to assess the probability of these pairs affecting a given pathway pair. The resulting significant pathway pairs identified form a pathway-level synergy network (p-SynNet). Both m-SynNet and p-SynNet offer complementary insights into disease mechanisms that go beyond conventional metabolomics analysis. For example, nodes with high connectivity in m-/p-SynNet suggest a strong correlation with the phenotype, while shared pathways across different phenotypes offer clues about the mechanisms of disease comorbidity. We applied the SynNet strategy to two real-world metabolomic data sets of disease comorbidity and identified key pathways associated with disease comorbidity from the p-SynNet. The candidate pathways are supported by the existing literature. Thus, the SynNet strategy may represent an alternative approach for metabolomic data analysis, providing novel insights into disease mechanisms and comorbidity.PMID:39908457 | DOI:10.1021/acs.analchem.4c06133

Environ Toxicol Chem. 2025 Feb 5:vgaf040. doi: 10.1093/etojnl/vgaf040. Online ahead of print.ABSTRACTArthropods, abundant in farmland, have unique biological traits that make them valuable for studying the ecotoxicological impacts of pollutants. Recent advancements in multi-omics technologies have enhanced their use in assessing pollution risks and understanding toxicity mechanisms. This paper reviews recent developments in applying omics technologies-genomics, transcriptomics, proteomics, metabolomics and meta-omics to ecotoxicological research on farmland arthropods. Agricultural arthropods manage genes and proteins like metallothioneins (MTs), antioxidant enzyme systems, heat shock proteins, cytochrome P450 (CYP450), carboxylesterases (CarEs), and glutathione S-transferases (GSTs), for detoxification and antioxidant purposes. They adjust amino acid, sugar, and lipid metabolism to counteract pollutant-induced energy drain and modify gut microbiota to aid in detoxification. This study advocates for enhanced analysis of compound pollution and emerging pollutants using multi-omics, especially meta-omics, to clarify the toxicological mechanisms underlying arthropod responses to these pollutants. Furthermore, it underscores the urgent need for subsequent gene function mining and validation to support biological control strategies and promote sustainable agricultural practices. The findings of this research provide significant insights into the toxicological impacts and mechanisms of pollutants within farmland ecosystems, thereby contributing to the preservation of arthropod diversity.PMID:39908451 | DOI:10.1093/etojnl/vgaf040