PubMed

PLoS One. 2024 Nov 18;19(11):e0312517. doi: 10.1371/journal.pone.0312517. eCollection 2024.ABSTRACTCassava (Manihot esculentum Crantz) is a staple food source for many developing countries. Its edible roots are high in starch but lack micronutrients such as β-carotene. In the present study, analysis of pedigree breeding populations has led to the identification of cassava accessions with enhanced β-carotene contents up to 40 μg/g DW. This represents 0.2% of the Recommended Daily Allowance (RDA) for vitamin A. The β-branch of the carotenoid pathway predominates in cassava roots, with dominant levels of β-carotene followed by other minor epoxides of β-ring derived carotenoids. Metabolomic analysis revealed that steady state levels of intermediary metabolism were not altered by the formation of carotenoids, similar to starch and carbohydrate levels. Apocarotenoids appeared to be independent of their carotenoid precursors. Lipidomic analysis provided evidence of a significant positive correlation between carotenoid and lipid content, in particular plastid specific galactolipids. Proteomic analysis of isolated amyloplasts identified the majority of proteins associated with translation and carbohydrate/starch biosynthesis (e.g. glucose-1-phosphate adenylyltransferase). No carotenoid related proteins were detected even in the highest carotenoid containing lines. Carotenoids were associated with fractions typically annotated as plastoglobuli and plastid membranes (particularly the envelope). Proteomic analysis confirmed these structures apart from plastoglobuli, thus potentially amyloplast structures may not contain classical plastoglobuli structures.PMID:39556611 | DOI:10.1371/journal.pone.0312517

FASEB J. 2024 Nov 30;38(22):e70167. doi: 10.1096/fj.202401630R.ABSTRACTBile acids (BAs) are significantly altered in the liver and serum of patients with nonalcoholic steatohepatitis (NASH). However, the underlying mechanisms of these changes, particularly BA alternative pathways (BAP) responsible for non12-OH BAs, remain unclear. RNA-seq data were initially analyzed to reveal the changes of gene expression in NASH patients. Targeted metabolomics were conducted on plasma from NASH mice induced by high-fat or western diet with CCl4 for 10-24 weeks. Liver tissues were examined using proteomics, RT-qPCR, and western blotting. An integrated approach was then employed to analyze protein interactions and network correlations. Analysis of RNA-seq data revealed the inhibition of CYP7B1 in NASH patients, indicating the dysregulation of BAP. In NASH mouse models, dysregulation of BA circulation was observed by increased plasma total BA (TBA) levels and decreased liver TBA, with liver swelling and histopathological changes. Targeted metabolomics revealed suppressed levels of non12-OH BAs, which inversely correlated with increased liver injury markers. The reduced mRNA and protein expression of Fxr and upregulation of Lxr signaling in livers suggested the suppressed BAP was modulated by Fxr-Lxr signaling. Moreover, BAP interactions predominantly implicated multiple metabolism disruptions, involving 7 hub proteins (Hk1, Acadsb, Pklr, Insr, Ldlr, Cyp27a1, and Cyp7b1), offering promising therapeutic targets for NASH. We presented the metabolic and proteomic map of BAP and its regulatory network in NASH progression. Therapeutic targeting of BAP or its co-regulatory proteins holds promise for NASH treatment and metabolic syndrome management.PMID:39556333 | DOI:10.1096/fj.202401630R

Food Funct. 2024 Nov 18. doi: 10.1039/d4fo04667f. Online ahead of print.ABSTRACTHypobaric hypoxia causes oxidative stress and inflammatory responses and disrupts the gut microbiome and metabolome. In this study, we developed a synbiotic fermented whey beverage, combining kefir and Brassica rapa L. crude polysaccharides, to explore its protective effects against high-altitude induced injury in mice. The beverage, formulated with 0.8% (w/v) polysaccharides and kefir inoculation, demonstrated robust fermentation parameters and antioxidative capacity. When applied to a hypobaric hypoxia mouse model, the synbiotic fermented whey significantly reduced oxidation and protected the intestinal barrier by lowering inflammation, protecting the intestinal structure, increasing goblet cell counts, and reducing apoptosis. It also modulated the gut microbiota, enriching beneficial taxa as Intestinimonas and Butyricicoccaceae, while reducing harmful ones like Marvinbryantia and Proteus, and enhancing short-chain fatty acid (SCFA) production. Notably, the beverage increased berberine and nicotinic acid levels, activating the adenosine monophosphate-activated protein kinase (AMPK) signalling pathway and influencing nicotinate and nicotinamide metabolites linked to the suppression of Marvinbryantia, thereby alleviating intestinal inflammation and barrier damage. These effects contributed to the alleviation of hypoxia-induced intestinal damage in mice. This study highlights the potential of synbiotics and whey fermentation in novel nutritional interventions in high altitude environments.PMID:39555987 | DOI:10.1039/d4fo04667f

Microbiol Spectr. 2024 Nov 18:e0187824. doi: 10.1128/spectrum.01878-24. Online ahead of print.ABSTRACTChronic tinnitus is a central nervous system disorder. Currently, the effects of gut microbiota on tinnitus remain unexplored. To explore the connection between gut microbiota and tinnitus, we conducted 16S rRNA sequencing of fecal microbiota and serum metabolomic analysis in a cohort of 70 patients with tinnitus and 30 healthy volunteers. We used the weighted gene co-expression network method to analyze the relationship between the gut microbiota and the serum metabolites. The random forest technique was utilized to select metabolites and gut taxa to construct predictive models. A pronounced gut dysbiosis in the tinnitus group, characterized by reduced bacterial diversity, an increased Firmicutes/Bacteroidetes ratio, and some opportunistic bacteria including Aeromonas and Acinetobacter were enriched. In contrast, some beneficial gut probiotics decreased, including Lactobacillales and Lactobacillaceae. In serum metabolomic analysis, serum metabolic disturbances in tinnitus patients and these differential metabolites were enriched in pathways of neuroinflammation, neurotransmitter activity, and synaptic function. The predictive models exhibited great diagnostic performance, achieving 0.94 (95% CI: 0.85-0.98) and 0.96 (95% CI: 0.86-0.99) in the test set. Our study suggests that changes in gut microbiota could potentially influence the occurrence and chronicity of tinnitus, and exert regulatory effects through changes in serum metabolites. Overall, this research provides new perceptions into the potential role of gut microbiota and serum metabolite in the pathogenesis of tinnitus, and proposes the "gut-brain-ear" concept as a pathomechanism underlying tinnitus, with significant clinical diagnostic implications and therapeutic potential.IMPORTANCETinnitus affects millions of people worldwide. Severe cases may lead to sleep disorders, anxiety, and depression, subsequently impacting patients' lives and increasing societal healthcare expenditures. However, tinnitus mechanisms are poorly understood, and effective therapeutic interventions are currently lacking. We discovered the gut microbiota and serum metabolomics changes in patients with tinnitus, and provided the potential pathological mechanisms of dysregulated gut flora in chronic tinnitus. We proposed the innovative concept of the "gut-brain-ear axis," which underscores the exploration of gut microbiota impact on susceptibility to chronic tinnitus through serum metabolic profile modulation. We also reveal novel biomarkers associated with chronic tinnitus, offering a new conceptual framework for further investigations into the susceptibility of patients, potential treatment targets for tinnitus, and assessing patient prognosis. Subsequently, gut microbiota and serum metabolites can be used as molecular markers to assess the susceptibility and prognosis of tinnitus.Furthermore, fecal transplantation may be used to treat tinnitus.PMID:39555931 | DOI:10.1128/spectrum.01878-24

mBio. 2024 Nov 18:e0313324. doi: 10.1128/mbio.03133-24. Online ahead of print.ABSTRACTHeterotrimeric G protein signaling pathways control growth and development in eukaryotes. In the multicellular fungus Neurospora crassa, the guanine nucleotide exchange factor RIC8 regulates heterotrimeric Gα subunits. In this study, we used RNAseq and liquid chromatography-mass spectrometry (LC-MS) to profile the transcriptomes and metabolomes of N. crassa wild type, the Gα subunit mutants Δgna-1 and Δgna-3, and Δric8 strains. These strains exhibit defects in growth and asexual development (conidiation), with wild-type and Δgna-1 mutants producing hyphae in submerged cultures, while Δgna-3 and Δric8 mutants develop conidiophores, particularly in the Δric8 mutant. RNAseq analysis showed that the Δgna-1 mutant possesses 159 mis-regulated genes, while Δgna-3 and Δric8 strains have more than 1,000 each. Many of the mis-regulated genes are involved in energy homeostasis, conidiation, or metabolism. LC-MS revealed changes in levels of primary metabolites in the mutants, with several arginine metabolic intermediates impacted in Δric8 strains. The differences in metabolite levels could not be fully explained by the expression or activity of pathway enzymes. However, transcript levels for two predicted vacuolar arginine transporters were affected in Δric8 mutants. Analysis of arginine and ornithine levels in transporter mutants yielded support for altered compartmentation of arginine and ornithine between the cytosol and vacuole in Δric8 strains. Furthermore, we validated previous reports that arginine and ornithine levels are low in wild-type conidia. Our results suggest that RIC8 regulates asexual sporulation in N. crassa at least in part through altered expression of vacuolar transporter genes and the resultant mis-compartmentation of arginine and ornithine.IMPORTANCE: Resistance to inhibitors of cholinesterase-8 (RIC8) is an important regulator of heterotrimeric Gα proteins in eukaryotes. In the filamentous fungus Neurospora crassa, mutants lacking ric8 undergo inappropriate asexual development (macroconidiation) during submerged growth. Our work identifies a role for RIC8 in regulating expression of transporter genes that retain arginine and ornithine in the vacuole (equivalent of the animal lysosome) and relates this function to the developmental defect. Arginine is a critical cellular metabolite, both as an amino acid for protein synthesis and as a precursor for an array of compounds, including proline, ornithine, citrulline, polyamines, creatine phosphate, and nitric oxide. These results have broad relevance to human physiology and disease, as arginine modulates immune, vascular, hormonal, and other functions in humans.PMID:39555920 | DOI:10.1128/mbio.03133-24

J Pineal Res. 2024 Nov;76(8):e70005. doi: 10.1111/jpi.70005.ABSTRACTCadmium (Cd) is a widespread environmental contaminant with high toxicity to human health. Melatonin has been shown to improve Cd-induced liver damage. However, its mechanism has not yet been elucidated. In this study, we aimed to investigate the effects of melatonin on Cd-induced liver damage and fibrosis. A combination of 16S rRNA gene sequencing and mass spectrometry-based metabolomics was adopted to investigate changes in the gut microbiome and its metabolites on the regulation of melatonin in Cd-induced liver injury and fibrosis of mice. Further, nonabsorbable antibiotics, a fecal microbiota transplantation (FMT) program and intestine-specific farnesoid X receptor (FXR) knockout mice were employed to explore the mechanism of melatonin (MT) on liver injury and fibrosis in Cd treated mice. MT significantly improved hepatic inflammation, bile duct hyperplasia, liver damage, and liver fibrosis, with a notable decrease in liver bile acid levels in Cd-exposed mice. MT treatment remodeled the gut microbiota, improved gut barrier function, and reduced the production of gut-derived lipopolysaccharide (LPS). MT significantly decreased the intestinal tauro-β-muricholic acid levels, which are known as FXR antagonists. Notably, MT prominently activated the intestinal FXR signaling, subsequently inhibiting liver bile acid synthesis and decreasing hepatic inflammation in Cd-exposed mice. However, MT could not ameliorate Cd-induced liver damage and fibrosis in Abx-treated mice. Conversely, MT still exerted a protective effect on Cd-induced liver damage and fibrosis in FMT mice. Interestingly, MT failed to reverse liver damage and fibrosis in Cd-exposed intestinal epithelial cell-specific FXR gene knockout mice, indicating that intestinal FXR signaling mediated the protective effect of MT treatment. MT improves Cd-induced liver damage and fibrosis through reshaping the intestinal flora, activating the intestinal FXR-mediated suppression of liver bile acid synthesis and reducing LPS leakage in mice.PMID:39555739 | DOI:10.1111/jpi.70005

New Phytol. 2024 Nov 18. doi: 10.1111/nph.20282. Online ahead of print.ABSTRACTLocalized clathrin mediated endocytosis is vital for secretion and wall deposition in apical growing plant cells. Adaptor and signalling proteins, along with phosphoinositides, are known to play a regulatory, yet poorly defined role in this process. Here we investigated the function of Arabidopsis ECA4 and EPSIN3, putative mediators of the process, in pollen tubes and root hairs. Homozygous eca4 and epsin3 plants exhibited altered pollen tube morphology (in vitro) and self-pollination led to fewer seeds and shorter siliques. These effects were augmented in eca4/epsin3 double mutant and quantitative polymerase chain reaction data revealed changes in phosphoinositide metabolism and flowering genes suggestive of a synergistic action. No visible changes were observed in root morphology, but atomic force microscopy in mutant root hairs showed altered structural stiffness. Imaging and FRET-FLIM analysis of ECA4 and EPSIN3 X-FP constructs revealed that both proteins interact at the plasma membrane but exhibit slightly different intracellular localization. FT-ICR-MS metabolomic analysis of mutant cells showed changes in lipids, amino acids and carbohydrate composition consistent with a role in secretion and growth. Characterization of double mutants of eca4 and epsin3 with phospholipase C genes (plc5, plc7) indicates that phosphoinositides (e.g. PtdIns(4,5)P2) are fundamental for a combined and complementary role of ECA4-EPSIN3 in cell secretion.PMID:39555685 | DOI:10.1111/nph.20282

Aquac Nutr. 2024 Aug 12;2024:4253969. doi: 10.1155/2024/4253969. eCollection 2024.ABSTRACTIn the present study, we investigated the effect of dietary supplementation with the probiotic Bacillus amyloliquefaciens AV5 (OR647358) on the growth, serum and mucus immune responses, metabolomics, and lipid metabolism of Oreochromis niloticus. Fishes (27.2 ± 1.7 g and 9.0 ± 1.2 cm) were fed three distinct meals: a commercial diet (control-GC) and two treatment diets supplemented with probiotics at 106 (G1) and 108 cfu/g (G2), respectively, for 30 days. In the G2 group, the final weight, specific growth rate, weight gain rate, survival rate, and feed conversion ratio of the fish were significantly improved (p < 0.05). Lysozyme, myeloperoxidase, and alkaline phosphatase activities in the mucus of fish were significantly higher (p < 0.05) in the G1 and G2 groups. The serum total protein, superoxide dismutase, glutathione peroxidase, reactive oxygen species, and reactive nitrogen species levels were noticeably higher (p < 0.05) in fish fed G1 and G2. In addition, in the G1 and G2 groups, higher levels of enzymes involved in lipid metabolism, such as pyruvate kinase, 2-hydroxyethyl-ThPP, and dihydrolipoamide dehydrogenase, were increased. Distal gastrointestinal metabolites, such as glycerophospholipids and histidine, were observed. These findings strongly indicate that incorporating B. amyloliquefaciens AV5 at 108 cfu/g into commercial feeds positively influences fish growth, immunity, and lipid metabolism.PMID:39555520 | PMC:PMC11333138 | DOI:10.1155/2024/4253969

Aquac Nutr. 2024 May 13;2024:5539701. doi: 10.1155/2024/5539701. eCollection 2024.ABSTRACTTannin (TA), as a natural phenolic compound with strong antioxidant activity, has been used as a feed additive for various animals. In this study, we fed a diet containing 800 mg/kg of tannin on Litopenaeus vannamei for 56 days and then subjected to acute ammonia stress for 48 hr to investigate the effect of dietary tannin on the ammonia stress response of L. vannamei through transcriptomic and metabolomic analysis. The transcriptome analysis indicated that ammonia stress-induced differential expression of 4,185 genes, while tannin-fed shrimp only had 964 differentially expressed genes. Compared with the TA_0 group, 59 pathways were significantly altered, and the pathways of "starch and sucrose metabolism," "retinol metabolism," "arachidonic acid metabolism," "lysosome," and "amino sugar and nucleotide sugar metabolism" were highly enriched in the TS_0 group. Compared with the TS_0 group, six pathways were significantly altered, and the pathways of "dilated cardiomyopathy," "complement and coagulation cascades," "cardiac muscle contraction," "fructose and mannose metabolism," "cGMP-PKG signaling pathway," and "beta-alanine metabolism" were significantly enriched in the TS_800 group. Metabolomic analysis showed that a total of 107 differential metabolites (DMs) were identified in the TS_0 vs. TA_0 group, while 75 DMs were identified in the TS_800 vs. TS_0 group. Based on KEGG annotation, it was found that a large amount of DM was significantly enriched in amino acid metabolism pathways in the TS_0 group, including "arginine and proline metabolism," "alanine, aspartic acid, and glutamic acid metabolism," "β-Alanine metabolism and tyrosine metabolism" indicated that tannins affect the metabolism of amino acids. The integration of DEGs and DMs indicates that dietary tannins highly alter the digestion and absorption functions of proteins, as well as the biosynthesis and metabolism of amino acids. This study provides new insights into the adaptation of Pacific white shrimp to ammonia stress and the addition of tannins to feed to enhance immune function.PMID:39555517 | PMC:PMC11105962 | DOI:10.1155/2024/5539701

iScience. 2024 Oct 10;27(11):111135. doi: 10.1016/j.isci.2024.111135. eCollection 2024 Nov 15.ABSTRACTDi (2-ethylhexyl) phthalate (DEHP) is an environmental endocrine disruptor and commonly used as a plasticizer. Exposure to DEHP and its active metabolite mono-2-ethylhexyl phthalate (MEHP) can lead to adverse health consequences; however, the toxic mechanism is remains unclear. In this research, male and female rats were exposed to DEHP and MEHP by oral gavage for 60 consecutive days. Pathological analysis revealed that DEHP and MEHP exposure could affect liver, heart, kidney, and testis tissues, as well as alter biochemical indicators. Metagenomics (16S rRNA gene sequencing) analysis indicated that DEHP and MEHP could reduce the diversity and alter the composition of the gut microbiota. Toxic exposure also affected the levels of short chain fatty acids (SCFAs), with noticeable variations between genders. Metabolomic analysis revealed that DEHP and MEHP could influence bile acids, amino acids, hormones, and lipids. These results demonstrate that exposure to DEHP and MEHP can induce toxicity in rats via the gut-liver axis.PMID:39555414 | PMC:PMC11565036 | DOI:10.1016/j.isci.2024.111135

Mass Spectrom (Tokyo). 2024;13(1):A0155. doi: 10.5702/massspectrometry.A0155. Epub 2024 Nov 12.ABSTRACTSeveral database search methods have been employed in untargeted metabolomics utilizing high-resolution mass spectrometry to comprehensively annotate acquired product ion spectra. Recent technical advancements in in silico analyses have facilitated the sorting of the degree of coincidence between a query product ion spectrum, and the molecular structures in the database. However, certain search results may be false positives, necessitating a method for controlling the false discovery rate (FDR). This study proposes 4 simple methods for controlling the FDR in compound search results. Instead of preparing a decoy compound database, a decoy spectral dataset was created from the measured product-ion spectral dataset (target). Target and decoy product ion spectra were searched against an identical compound database to obtain target and decoy hits. FDR was estimated based on the number of target and decoy hits. In this study, 3 decoy generation methods, polarity switching, mirroring, and spectral sampling, were compared. Additionally, the second-rank method was examined using second-ranked hits in the target search results as decoy hits. The performances of these 4 methods were evaluated by annotating product ion spectra from the MassBank database using the SIRIUS 5 CSI:FingerID scoring method. The results indicate that the FDRs estimated using the second-rank method were the closest to the true FDR of 0.05. Using this method, a compound search was performed on 4 human metabolomic data-dependent acquisition datasets with an FDR of 0.05. The FDR-controlled compound search successfully identified several compounds not present in the Human Metabolome Database.PMID:39555379 | PMC:PMC11565486 | DOI:10.5702/massspectrometry.A0155

Front Cell Infect Microbiol. 2024 Nov 1;14:1482919. doi: 10.3389/fcimb.2024.1482919. eCollection 2024.ABSTRACTAerobic respiration is the key driver of Vibrio cholerae proliferation and infection. Our previous transcriptome results suggested that degS knockout downregulates a few genes involved in NADH and ATP synthesis in the aerobic respiratory pathway. In this study, non-targeted metabolomics results showed that the differential metabolites affected by degS knockout were associated with aerobic respiration. Further results suggested that the key products of aerobic respiration, NADH and ATP, were reduced upon degS deletion and were not dependent on the classical σE pathway. The two-component system response factor aerobic respiration control A (ArcA) is involved in regulating NADH and ATP levels. qRT-PCR demonstrated that DegS negatively regulates the transcription of the arcA gene, which negatively regulates the expression of isocitrate dehydrogenase (ICDH), a key rate-limiting enzyme of the tricarboxylic acid cycle. NADH and ATP levels were partially restored with the knockout of the arcA gene in the ΔdegS strain, while levels were partially restored with overexpression of ICDH in the ΔdegS strain. In a growth experiment, compared to the ΔdegS strain, the growth rates of ΔdegSΔarcA and ΔdegS-overexpressed icdh strains (ΔdegS+icdh) were partially restored during the logarithmic growth period. Colonization of the intestines of suckling mice showed a significant reduction in the colonizing ability of the ΔdegS strain, similar colonizing ability of the ΔdegS::degS strain and the wild-type strain, and a partial recovery of the colonizing ability of the ΔdegS+icdh strain. Overall, these findings suggest that the DegS protease regulates the expression of ICDH through ArcA, thereby affecting the NADH and ATP levels of V. cholerae and its growth and intestinal colonization ability.PMID:39554810 | PMC:PMC11564185 | DOI:10.3389/fcimb.2024.1482919

Drug Des Devel Ther. 2024 Nov 12;18:5087-5108. doi: 10.2147/DDDT.S476494. eCollection 2024.ABSTRACTPURPOSE: Inflammatory bowel disease (IBD) is a serious disease that affects the metabolism and inflammatory responses of human beings. From the perspective of traditional Chinese medicine, damp-heat syndrome is one of the main syndromes of IBD. Rhizoma Paridis, also known as the root of Paris polyphylla, a well-known herbal medicine used in China, is used to treat IBD with damp-heat syndrome (IBD-DH). However, uncertainty still exists regarding the underlying mechanisms and the impact of Rhizoma Paridis on IBD-DH.METHODS: The rats in the model (DAT) and medication administration (Rhizoma Paridis total saponins (RPTS) and Pennogenin (PN)) groups were given a high temperature and high humidity environment, high fat and high sugar diet combined with 2,4,6-trinitrobenzene sulfonic acid (TNBS) to establish the model of experimental colitis of damp-heat type, and the normal control group (RNC) rats were given a normal diet at normal temperature and humidity. Damp-heat control group (DNC) was set with the same condition as DAT without TNBS. Hematoxylin-Eosin (HE) staining was used to observe the histopathological morphology of the rat colorectum. The expression of the metabolism-related genes (Phospholipase A2 (sPLA2, cPLA2), and phosphatidylethanolamine N-methyltransferase (PEMT)) was assessed by using real-time quantitative PCR analysis (RT-qPCR). And the levels of the metabolism-related proteins (sPLA2, cPLA2), S100A8/9, Arg-1, and cytokines were detected by enzyme-linked immunosorbent assay (ELISA) kit. To investigate lipids and amino acids which closely associated with the IBD and IBD-DH, lipid pseudotargeted metabolomics with UHPLC-TQ/MS analysis method, as well as targeted quantitative amino acid analysis were performed.RESULTS: Our data showed that RPTS (50 mg/kg) and PN (20 mg/kg) significantly ameliorated the severity of TNBS-induced colitis and downregulated the levels of circulating proinflammatory cytokines. Compared with RNC group, lipid pseudotargeted metabolomics demonstrated that glycerophospholipids, sphingolipids, carnitine, and glycerolipids were the four most perturbed lipid classes, and amino acids targeted metabolomics demonstrated that serine, N-acetylneuraminic acid, histidine, proline, taurine, and kynurenine changed significantly in DAT group . Correlation analyses showed tight associations between most of differential metabolites and proinflammatory cytokines. RPTS and PN both regulated glycerophospholipid metabolism and sphingolipid metabolism. However, both of them did not have a significant effect on amino acid modulation. RPTS and PN potentially regulated sPLA2, cPLA2, and PEMT.CONCLUSION: These results showed that RPTS (50 mg/kg) and PN (20 mg/kg) effectively alleviated rats' colitis of damp-heat type, affected cytokines, and altered lipid metabolism without significant modulation on amino acid metabolism.PMID:39554759 | PMC:PMC11568858 | DOI:10.2147/DDDT.S476494

Front Plant Sci. 2024 Nov 1;15:1461357. doi: 10.3389/fpls.2024.1461357. eCollection 2024.ABSTRACTBACKGROUND: Gongju is recognized as one of the four traditional Chinese medicinal herbs, and its main constituents are chlorogenic acid (CGA) and its derivative material. CGA content in autooctoploid Gongju are considerably elevated compared with those in parental tetraploid Gongju at different flowering stages. However, the underlying molecular mechanisms governing the regulation CGA content remain poorly understood.METHODS: Therefore, we conducted integrated transcriptome and metabolome analyses of different flowering stages in autooctoploid and tetraploid Gongju to elucidate the underlying molecular mechanisms governing CGA biosynthesis.RESULTS: Transcriptome analysis showed that the number of differentially expressed genes in the budding stage (BS), early flowering stage (EF), and full flowering stage (FF) of tetraploid and octoploid Gongju were 3859, 11,211, and 6837, respectively. A total of 563, 466, and 394 differential accumulated metabolites were respectively identified between the bud stages of tetraploid and octoploid Gongju (4BS vs. 8BS), between the early flowering stages of tetraploid and octoploid Gongju (4EF vs. 8EF), and the full flowering stages of tetraploid and octoploid Gongju (4FF vs. 8FF) groups. The integrated analysis of transcriptomics and metabolomics revealed that the expression of pma6460 and mws0178, which are key enzymes involved in the CGA synthesis pathway, increased during the flowering stages of octoploid Gongju relative to that of tetraploid Gongju. The expression levels of CmHQT and CmC3H genes associated with CGA synthesis were higher in octoploid plants than in tetraploid plants at various flowering stages. To investigate the potential regulation of transcription factors involved in CGA synthesis, we analyzed the coexpression of CmC3H and CmHQT with CmMYBs and CmbHLHs. Results indicated that transcription factors, such as CmMYB12 (Cluster-30519.0), CmMYB26 (Cluster-75874.0), CmMYB5 (Cluster-94106.0), CmMYB1 (Cluster-71968.7), CmbHLH62 (Cluster-32024.1), CmbHLH75 (Cluster-62341.0), CmbHLH62 (Cluster-32024.8), CmbHLH75 (Cluster-60210.0), and CmbHLH16 (Cluster-90665.1) play a pivotal role in CGA synthesis regulation. The present study provides novel insights into the molecular mechanisms underlying CGA accumulation in autopolyploid Gongju.PMID:39554524 | PMC:PMC11563975 | DOI:10.3389/fpls.2024.1461357

Food Sci Nutr. 2024 Jun 14;12(9):6284-6297. doi: 10.1002/fsn3.4266. eCollection 2024 Sep.ABSTRACTSweet pepper, a globally commercialized horticultural crop, has been demonstrated to impede fat accumulation, but its mechanism remains incompletely understood. This study was designed to explore the potential mechanism of sweet pepper in reducing fat accumulation in Caenorhabditis elegans through RNA-seq and metabolome analysis. A total of 22 metabolites were identified from sweet pepper by UHPLC-ESI-TOF-MS analysis. In vivo, sweet pepper significantly inhibited α-glucosidase activity and reduced the levels of glucose, triglycerides (TG), total cholesterol (TC), and the area stained with oil red O. Additionally, it increased body length and the number of head swings in C. elegans compared to the control group. The KEGG enrichment analysis revealed significant enrichment of the biosynthesis of unsaturated fatty acids signaling pathway among the differentially expressed genes and metabolites. Furthermore, the mRNA levels of sterol regulatory element-binding proteins (SREBPs) ortholog SBP-1, as well as the stearyl CoA desaturase-1 (SCD1), including fat-5, fat-6, and fat-7, were significantly decreased after treatment with sweet pepper. Collectively, sweet pepper effectively reduces fat accumulation, which is probably related to downregulating the SREBP-SCD axis, offering new insights for future functional food development.PMID:39554335 | PMC:PMC11561784 | DOI:10.1002/fsn3.4266

Food Sci Nutr. 2024 Jun 26;12(9):6648-6659. doi: 10.1002/fsn3.4264. eCollection 2024 Sep.ABSTRACTThe pomegranate fruit is valued for its nutritional and medicinal properties, and the composition and content of primary and secondary metabolites are the main factors impacting its nutritional and medicinal properties. However, a deep understanding of metabolites in different parts of fruit is still lacking. Here, the peel, aril, and seed of mature pomegranate fruits were analyzed separately to compare metabolic component differences using UPLC/MS-MS. A total of 858 metabolites belonging to 11 classes were identified, of which flavonoids, such as delphinidin-3-O-glucoside and cyanidin-3-O-glucoside; tannins, such as ellagic acid and punicalin; and terpenoids, such as corosolic acid and madasiatic acid, were upregulated in the peel. Lipids, such as punicic acid, methyl linolenate, and linoleic acid; alkaloids, such as indole and choline; nucleotides and derivatives mainly including 2-deoxyribose-1-phosphate and 9-(arabinosyl)-hypoxanthine, were upregulated in seeds. Phenolic acids, such as 1-O-galloyl-4,6-(S)-HHDP-β-D-glucose and 1,7-di-O-galloyl-D-sedoheptulose, and flavonoids, such as cyanidin-3-O-glucoside, cyanidin-3-O-(2″-O-xylosyl) galactoside, and delphinidin-3-O-glucoside, were upregulated in aril. The flavone and flavonol biosynthesis (ko00944) pathways were significantly enriched between the peel and seed, as were the anthocyanin biosynthesis (ko00944) pathways between the aril and seed and the flavonoid biosynthesis (ko00941) pathways between the peel and aril. Additionally, functional antioxidants, such as 10,16-dihydroxypalmitic acid, 3-O-methylellagic acid, and 3,3'-O-dimethylellagic acid, were first identified in pomegranate fruits. Our results revealed the composition and abundance of primary and secondary metabolites in pomegranate fruit, which can lay the foundation for further elucidation of its nutritional and medicinal properties.PMID:39554325 | PMC:PMC11561811 | DOI:10.1002/fsn3.4264

Food Sci Nutr. 2024 Jun 18;12(9):6442-6460. doi: 10.1002/fsn3.4279. eCollection 2024 Sep.ABSTRACTNonalcoholic fatty liver disease (NAFLD) is a common chronic liver disease, but there is currently no effective treatment method. Probiotics have been used as an adjunct therapy for NAFLD, but the mechanism is not clear. This study used Bifidobacterium longum BL19 (BL-19) to treat the NAFLD mice induced by a high-fat diet, and explored the treatment mechanism through gut microbiota and serum metabolomics techniques. We found that BL-19 effectively prevented rapid weight gain in NAFLD mice and reduced their overall food and energy intake, decreased liver inflammatory factors expressions, and increased the bile acid synthetase enzyme CYP7A1 and superoxide dismutase. After BL-19 treatment, the abundances of butyric acid bacteria (Oscillospira and Coprococcus) in the feces of mice increased significantly, and the concentration of butyric acid also increased significantly. We believe that BL-19 promotes the production of butyrate in the intestines, which in turn regulates the activity of CYP7A1 in the liver and bile acid synthesis, ultimately treating liver inflammation and lipid accumulation in NAFLD mice. Serum metabolomics results indicated that BL-19 affected multiple pathways related to inflammation and lipid metabolism in NAFLD mice. These findings suggest that BL-19 shows promise as an adjunct therapy for NAFLD, as it can significantly improve oxidative stress, reduce inflammation in the liver, and decrease lipid accumulation.PMID:39554323 | PMC:PMC11561819 | DOI:10.1002/fsn3.4279

bioRxiv [Preprint]. 2024 Nov 2:2024.10.29.620864. doi: 10.1101/2024.10.29.620864.ABSTRACTBACKGROUND: Breast cancer, the most common cancer type among women, was recently found to contain a specific tumor microbiome, but its impact on host biology remains unclear. CD8 + tumor-infiltrating lymphocytes (TILs) are pivotal effectors of anti-tumor immunity that influence cancer prognosis and response to therapy. This study aims to elucidate interactions between CD8 + TILs and the breast tumor microbiome and metabolites, as well as how the breast tumor microbiome may affect the tumor metabolome.METHODS: We investigated the interplay among CD8 + TILs, the tumor microbiome, and the metabolome in a cohort of 46 breast cancer patients with mixed subtypes (Cohort A). We characterized the tumor metabolome by mass spectrometry and CD8 + TILs by immunohistochemistry. Microbiome composition and T cell gene transcript levels were obtained from data from our previous study, which utilized 16S rRNA gene sequencing and a targeted mRNA expression panel. To examine interactions between intratumoral Staphylococcus and specific breast cancer subtypes, we analyzed RNA sequencing data from an independent cohort of 370 breast cancer patients (Cohort B). We explored the functions of the tumor microbiome using mouse models of triple-negative breast cancer (TNBC).RESULTS: In tumors from Cohort A, the relative abundance of Staphylococcus positively correlated with the expression of T cell activation genes. The abundances of multiple metabolites exhibited significant correlations with CD8 + TILs, of which NADH, γ-glutamyltryptophan, and γ-glutamylglutamate displayed differential abundance in Staphylococcus -positive versus Staphylococcus -negative breast tumors. In a larger breast cancer cohort (Cohort B), we observed positive correlations between tumoral Staphylococcus and CD8 + TIL activity exclusively in TNBC. Preclinical experiments demonstrated that intratumoral administration of S. aureus , the predominant species of Staphylococcus in human breast tumors, resulted in a depletion of total NAD metabolites, and reduced the growth of TNBC tumors by activating CD8 + TILs.CONCLUSIONS: We identified specific metabolites and microbial taxa associated with CD8 + TILs, delineated interactions between the breast tumor microbiome and metabolome, and demonstrated that intratumoral Staphylococcus influences anti-tumor immunity and TIL-associated metabolites. These findings highlight the role of low-biomass microbes in tumor tissues and provide potential biomarkers and therapeutic agents for breast cancer immunotherapy that merit further investigation.PMID:39554133 | PMC:PMC11565759 | DOI:10.1101/2024.10.29.620864

bioRxiv [Preprint]. 2024 Nov 2:2024.10.31.621412. doi: 10.1101/2024.10.31.621412.ABSTRACTN -acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N -acyl lipids with untargeted mass spectrometry-based metabolomics, we created a reference spectral library retrieving N -acyl lipid patterns from 2,700 public datasets, identifying 851 N -acyl lipids that were detected 356,542 times. 777 are not documented in lipid structural databases, with 18% of these derived from short-chain fatty acids and found in the digestive tract and other organs. Their levels varied with diet, microbial colonization, and in people living with diabetes. We used the library to link microbial N -acyl lipids, including histamine and polyamine conjugates, to HIV status and cognitive impairment. This resource will enhance the annotation of these compounds in future studies to further the understanding of their roles in health and disease and highlight the value of large-scale untargeted metabolomics data for metabolite discovery.PMID:39554097 | PMC:PMC11565975 | DOI:10.1101/2024.10.31.621412

bioRxiv [Preprint]. 2024 Oct 28:2024.10.27.620437. doi: 10.1101/2024.10.27.620437.ABSTRACTIn multiple sclerosis (MS) the circulating metabolome is dysregulated, with indole lactate (ILA) being one of the most significantly reduced metabolites. We demonstrate that oral supplementation of ILA impacts key MS disease processes in two preclinical models. ILA reduces neuroinflammation by dampening immune cell activation/ infiltration; and promotes remyelination and in vitro oligodendrocyte differentiation through the aryl hydrocarbon receptor (AhR). Supplementation of ILA, a reductive indole metabolite, restores the gut microbiome's oxidative/reductive metabolic balance by lowering circulating indole acetate (IAA), an oxidative indole metabolite, that blocks remyelination and oligodendrocyte maturation. The ILA-induced reduction in circulating IAA is linked to changes in IAA-producing gut microbiota taxa and pathways that are also dysregulated in MS. Notably, a lower ILA:IAA ratio correlates with worse MS outcomes. Overall, these findings identify ILA as a new potential anti-inflammatory remyelinating agent and provide novel insights into the role of gut dysbiosis-related metabolic alterations in MS progression.PMID:39554063 | PMC:PMC11565924 | DOI:10.1101/2024.10.27.620437