MetaboLightsapplication/xmlftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13753/m_MTBLS13753_LC-MS_positive_reverse-phase_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13753/m_MTBLS13753_LC-MS_negative_reverse-phase_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13753/a_MTBLS13753_LC-MS_negative_reverse-phase_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13753/a_MTBLS13753_LC-MS_positive_reverse-phase_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13753/s_MTBLS13753.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13753/i_Investigation.txtprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS13753<p>Metabolites were identified by matching accurate mass (mass error &lt; 5 ppm), retention time deviation (&lt; 0.2 min), and MS/MS spectra with public databases including the Human Metabolome Database (HMDB), METLIN, and MassBank. For metabolites with MS/MS spectra, fragmentation patterns were compared with database entries using a similarity score threshold of &gt; 0.7. Putative annotations were further validated by comparing with authentic standards where available.</p>MetaboLightsPublicLiquid Chromatography MS - negative - reverse-phaseLiquid Chromatography MS - positive - reverse-phase<p>Separation was performed on an Agilent 1290 Infinity II UHPLC system equipped with an Agilent 1290 Infinity II Multisampler autosampler. Analytes were separated using a Waters ACQUITY UPLC HSS T3 column (100 mm × 2.1 mm, 1.8 μm) protected by a Waters ACQUITY UPLC HSS T3 VanGuard pre-column (5 mm × 2.1 mm, 1.8 μm).</p>miR-9394b from Lactobacillus paracasei extracellular vesicles targets iNOS to reprogram host NO-ornithine metabolism and ameliorate ulcerative colitis.Ding HonghaoHuazhong Agriculture Universitycolonmass spectrometry assay<p>Frozen intestinal tissue (50 mg) was weighed and homogenized in 800 μL of ice-cold methanol/water (8:2, v/v) containing 0.1 mg/L L-2-chlorophenylalanine as an internal standard. The homogenate was vortexed for 3 min, incubated on ice for 10 min, and centrifuged at 12,000 × g at 4°C for 15 min. The supernatant was transferred to a new centrifuge tube, dried under nitrogen gas, and reconstituted in 100 μL of methanol/water (1:1, v/v). The reconstituted solution was filtered through a 0.22 μm organic membrane filter before LC-MS analysis.</p>Mus musculus<p>Raw LC-MS data were converted to mzXML format using ProteoWizard MSConvert. Peak detection, alignment, and peak area integration were performed using XCMS online (https://xcmsonline.scripps.edu/). The parameters were set as follows: centWave method for peak picking (ppm = 15, peakwidth = c(5, 20)), obiwarp for retention time correction, and fillPeaks for missing value imputation. The resulting data matrix was normalized by the sum of peak areas per sample and log10-transformed for statistical analysis.</p>Treatment704676812@qq.comhttps://www.ebi.ac.uk/metabolights/MTBLS13753<p>Mice were euthanized by cervical dislocation, and the entire small intestine and colon were rapidly dissected. The intestinal contents were gently removed with pre-cooled phosphate-buffered saline (PBS), and the intestinal tissue was immediately snap-frozen in liquid nitrogen. Samples were stored at -80°C until metabolite extraction.</p>MetabolomicsLactobacillus paracaseiExtracellular Vesiclesuntargeted metabolitesLactobacillus paracaseiExtracellular Vesiclesuntargeted metabolites<p>Mass spectrometry analysis was carried out on a Thermo Fisher Q Exactive Focus Orbitrap mass spectrometer, operated with a Dual Jet Stream electrospray ionization (ESI) source. The mass analyzer was an Orbitrap, and data were acquired over a scan m/z range of 50–1000.</p>SM(d18:0/18:1(9Z))BistrisMeAIBO-PhosphoethanolamineDesmethylcerivastatin4-Methoxy-6-[2-[4-(3-methylbut-2-enoxy)phenyl]ethyl]-1,3-benzodioxolePhosphoramide_mustardM275T207Anthraquinone, 1,5-dianilino-Goralatide (acetate)4-Guanidinobutyric acid3-(.beta.-D-Glucopyranosyloxy)-2-methylbutanenitrileL-alpha-glutamyl-L-hydroxyproline(2R)-2-(2,5-Difluorophenyl)pyrrolidine2-Carboxy-1-[5-(2-carboxy-1-pyrrolidinyl)-2-hydroxy-2,4-pentadienylidene]pyrrolidinium5-(o-Nitrobenzylidene)barbituric acidAminocyclopyrachlorMebeverineDG(18:4(6Z,9Z,12Z,15Z)/15:0/0:0)PC(42:8)PC(17:0/17:0)PhysapubescinSophocarpineLeu-ThrBezafibratePE(P-18:1(9Z)/20:5(5Z,8Z,11Z,14Z,17Z))Gly-Pro-Arg4-(4-Amino-3-nitrophenyl)-1(2H)-phthalazinone1-Stearoyl-2-arachidonyl-sn-glycero-3-phosphocholinePodophyllotoxin2-Phthalimidoglutaric acidCarnosineGlycine9,12-Octadecadiynoic acid5-CarbolineArgininePhosphate9H-Carbazole, 2-[(2E)-2-(1-azabicyclo[2.2.2]oct-3-ylidene)-2-fluoroethoxy]-4-{5-Bromo-1H-pyrazolo[3,4-b]pyridin-1-yl}-1-methylpiperidineGlutathionePhenylalanine6,7-Dihydro-5H-cyclopenta[d]pyrimidine-2,4-diamineCar(18:0)19,20-Dihydroxydocosa-4,7,10,13,16-pentaenoylcarnitine3,5-Di-tert-butyl-2-hydroxybenzaldehydeHeptanoylcarnitine (Car(7:0))Cyclo(L-Leu-L-Pip-L-Aoe-D-Phe)Pyrogallol2-Imino-4-methylpiperidine3-DeacetylsalanninFlurandrenolideStachybotrylactamN-Methyl-L-proline4,4'-ThiodianilineGlu-GluNonadeca-10,13-dienoylcarnitineNorleucineNeoandrographolideDrostanolone propionateN-[(4E,8E)-1,3-dihydroxyoctadeca-4,8-dien-2-yl]hexadecanamideMesoporphyrin IXM356T2571-(1Z-Octadecenyl)-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphoethanolamineSTIGMASTA-4,22-DIEN-3-ONECytosine3-Pyridol21-Desacetyldeflazacort1-Docosahexaenoyl-2-stearoyl-sn-glycero-3-phosphocholine[2-(Trifluoromethyl)-1,3-thiazol-4-yl]methanolEthyl 3-hydroxyoctanoate2-{[5,6-Bis(4-methoxyphenyl)furo[2,3-d]pyrimidin-4-yl]amino}ethanolPC(18:0/16:0)2-Docosahexaenoyl-1-palmitoyl-sn-glycero-3-phosphoethanolamine2-Chloro-3-(difluoromethyl)pyridineOrnithine3-MethyladenineArachidyl_carnitineDaidzein_6''-O-acetate5'-Amino-2,3'-bithiophene-4'-carboxamide(2-Amino-4,5,6,7-tetrahydro-1-benzothien-3-yl)(4-methylphenyl)methanonepre-putrebactinProlineRutaecarpineN-Methyl-L-valine3-(4-Methyl-3-pentenyl)thiophene5-Amino-1-(2-pyridinyl)-1H-pyrazole-4-carbonitrileReserpic acidPC(35:4)[4-Amino-2-(ethylamino)-1,3-thiazol-5-yl](4-chlorophenyl)methanoneBis(2,4,6-trimethylphenyl)phosphine1-(alpha-linolenoyl)-sn-glycero-3-phosphoethanolaminePiperanineIsoleucineAlanyl-ProlineHarmalineLPI(20:4)PC(31:0)1-Cyclohexyl-3-(3,4-dichlorophenyl)ureaN-Acetylglucosaminylasparagine5-[[17-(5,6-dihydroxy-6-methylheptan-2-yl)-3,12-dihydroxy-4,4,10,13,14-pentamethyl-2,3,5,6,7,11,12,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-2-yl]oxy]-3-hydroxy-3-methyl-5-oxopentanoic acidHEPESCyromazineArg-AspArachidonateArgininosuccinic acidN-Ethyl-6,7-dimethoxy-4-quinazolinamineCytidine 5'-diphosphocholine (CDP-choline)DHA ethyl esterHypotaurine[2-Amino-1-(2-chlorophenyl)ethyl]dimethylaminePhenylalanylphenylalanineSpecioside5,6,7,8-Tetrahydrothieno[2,3-b]quinolin-4-amineAnnosquamosin_Bsn-Glycerol 3-phosphateDL-Threonine methyl esterLNTEthyl 5-(2-chloroacetyl)-2,4-dimethyl-1H-pyrrole-3-carboxylateHistidinePC(16:0/16:0)Resazurin2-(Naphthalen-1-yl)-1H-1,3-benzodiazoleInositol_cyclic_phosphateCytidine monophosphate N-acetylneuraminic acidPC(42:10)9(10)-Epoxy-12Z-octadecenoic acidRutamarinSpectinomycin1-(1Z-Octadecenyl)-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphoethanolamineOctanoylcarnitine (Car(8:0))1-Deoxymannojirimycin (hydrochloride)LysineMethyl 4-(trifluoromethyl)benzoylacetateSM(d18:1/17:0)4-Aminobenzoic acidNigroxanthin(3.beta.,5.Xi.,9.Xi.)-23,28-Dihydroxyoleana-11,13(18)-dien-3-yl hexopyranosyl-(1->4)-6-deoxyhexopyranosyl-(1->4)hexopyranosyl-(1->3)hexopyranoside2-Fluoro-7H-purin-6-amineN-[(4E,8Z)-1,3-dihydroxyoctadeca-4,8-dien-2-yl]hexadecanamide_1-glucosideErgothioneine1,2-Dipalmitoleoyl-sn-glycero-3-phosphoethanolamine8-ChloroisoquinolineArg-GlyMan2a1-Lignoceroyl-2-hydroxy-sn-glycero-3-phosphocholinePhloionolic_acidQuinmeracCer(d18:1/16:0)4-Amino-1,2-benzenediolGanodosteroneDEHP1,2-Diarachidonoyl-sn-glycero-3-phosphocholineGlucose 1-phosphateKynurenine2-Hydroxypyridine3-Aminoadipic acid2-DeoxysepiapterinPE(22:6(4Z,7Z,10Z,13Z,16Z,19Z)/P-16:0)1-(Pyrimidin-2-yl)-1,4-diazepaneCytidine 5'-monophosphate (CMP)AlanineGlcCer(d18:1/16:0)AspartateEtobenzanid1-(1Z-Octadecenyl)-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphocholineFructose 6-phosphateFormiminoglutamic acidPS(18:4(6Z,9Z,12Z,15Z)/22:0)ValineAsparagine5beta-Pregnane-3alpha,17alpha,20alpha-triolOleoyl ethylamideOctenoyl-carnitineN-EthylguanidineAmprolium cation24-epi-brassinolidePC(22:2)Arg-Phe3-[Hexadecyl(dimethyl)ammonio]-1-propanesulfonateLysoPC(22:6(4Z,7Z,10Z,13Z,16Z,19Z))PC(12:0/12:0)Tyr-PheGlu-AspDG(18:3(6Z,9Z,12Z)/15:0/0:0)1-Aminopropan-2-olPC(20:2(11Z,14Z)/20:5(5Z,8Z,11Z,14Z,17Z))DonhexocinAdenylyl(3'-5')cytidine2-(10-Heptadecenyl)-6-hydroxybenzoic_acidColnelenic_acidNaproxenNandroloneTestosterone_phenylpropionatePhenacetin6-(Thiophen-3-yl)imidazo[2,1-b][1,3]thiazoleSpinacoside_DTanshinone I.beta.-Alanine, N-[2-[(3-hexylphenyl)amino]-2-oxoethyl]-[2-[4-methyl-2-(2-methylpropanoyloxy)phenyl]oxiran-2-yl]methyl 2-methylpropanoateLotaustralinHeptanedioic acid, 1-(2-cyclopentylidenehydrazide)Cyclo(glycylleucylvalylleucylprolylseryl)(4-Oxo-1,2,3-benzotriazin-3(4H)-yl)acetic acidN-Cyclohexyl-N'-[3-(trifluoromethyl)phenyl]urea3-(3-(1,2-Dihydroxy-1,2-dihexanoyl)thiopropane)inositol-4,5-diphosphate1-(1Z-Octadecenyl)-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphocholineNeryl_glucoside4-[4-(Trifluoromethoxy)phenoxy]piperidineGlutamatePC(18:1(9Z)/18:3(9Z,12Z,15Z))CytidineCarnitineHydroxyprolyl-Gamma-glutamatePro-AspN-Nervonoyl-D-erythro-sphingosylphosphorylcholineTriciribineN-Methyltetrahydro-2H-pyran-4-amineAmericinePC(38:6)N-Succinimidyl 4-[4-(dimethylamino)phenylazo]benzoateTercatain2-PiperidoneGly-ThrTyr-ValCefalexin3-Hydroxystigmast-5-en-7-one5-(Galactosylhydroxy)-L-lysineLeucineN-Butyl-3,4-dichlorobenzamideLactose-lysineLysoPC(22:1(13Z))4-(4-Methyl-1-piperazinyl)butanoic acidPC(38:3)(1S,3R)-1-Aminocyclopentane-1,3-dicarboxylic acidDocosatetraenoylcarnitine(S)-Nerolidol_3-O-[a-L-rhamnopyranosyl-(1->2)-b-D-glucopyranoside](aspartyl)adenylateArg-AlaL-?Leucyl-?L-?alanine2,2-Dimethyl-N-[3-(trifluoromethyl)phenyl]propanamide8-Carboxy-3-methylflavone4-[(6-Aminopyrimidin-4-yl)amino]benzenesulfonamideButralin5-[2-(4-Chlorophenyl)hydrazin-1-ylidene]-2,2-dimethyl-1,3-dioxane-4,6-dioneAlbendazoleN-BenzoylaminopurinePC(14:1(9Z)/16:1(9Z))LysoPE(24:0/0:0)falsemiR-9394b from Lactobacillus paracasei extracellular vesicles targets iNOS to reprogram host NO-ornithine metabolism and ameliorate ulcerative colitis<p>Background Probiotics have attracted considerable interest for ulcerative colitis (UC); however, their efficacy is highly strain-specific and the underlying molecular mechanisms remain incompletely understood.</p><p>Results Accumulating evidence indicates that bacterial extracellular vesicles (BEVs) function as important effector carriers by delivering regulatory cargos to host cells. In this study, we investigated lactobacilli isolated from infant intestinal contents and screened four strains in a DSS-induced murine colitis model. Oral administration of Lactobacillus paracasei (LPC) or its extracellular vesicles (LPC-EVs) markedly alleviated colitis severity, as evidenced by reduced histopathological damage, restoration of intestinal epithelial barrier integrity, and suppression of TLR4/NF-κB–associated inflammatory responses. Untargeted metabolomics further demonstrated that LPC-EVs reshaped host arginine metabolism, characterized by increased ornithine levels. In vitro assays showed efficient uptake of LPC-EVs by intestinal epithelial cells; their bioactivity was markedly diminished or abolished after RNase treatment, supporting an RNA cargo–dependent mechanism. miRNA sequencing identified miR-9394b as a highly enriched candidate key cargo in LPC-EVs. Mechanistic analyses suggested that miR-9394b can target inducible nitric oxide synthase (iNOS), thereby suppressing excessive nitric oxide (NO) production, enhancing ornithine availability, and promoting epithelial repair.</p><p>Conclusion In this study, we report for the first time that the Lactobacillus paracasei–EV–miR-9394b–iNOS/NO–ornithine metabolic regulatory axis contributes to UC amelioration, providing mechanistic and theoretical support for EV cargos targeting host metabolism and promoting mucosal repair.</p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