MetaboLights

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ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12816/m_MTBLS12816_LC-MS_negative_reverse-phase_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12816/m_MTBLS12816_LC-MS_positive_reverse-phase_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12816/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12816/s_MTBLS12816.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12816/a_MTBLS12816_LC-MS_negative_reverse-phase_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12816/a_MTBLS12816_LC-MS_positive_reverse-phase_metabolite_profiling.txtprimaryOK200ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12816The metabolites were identified by searching database,  with the main databases being HMDB (http://www.hmdb.ca/) and Metlin ( https://metlin.scripps.edu/). MetaboLightsPublicLiquid Chromatography MS - negative - reverse phaseLiquid Chromatography MS - positive - reverse phaseChromatographic separation of metabolites was carried out on a Thermo UHPLC-Q Exactive system equipped with an ACQUITY HSS T3 column (100 mm × 2.1 mm i.d., 1.8 µm; Waters, Milford, USA). The mobile phases consisted of solvent A (0.1% formic acid in water:acetonitrile, 95:5, v/v) and solvent B (0.1% formic acid in acetonitrile:isopropanol:water, 47.5:47.5:5, v/v/v). The injection volume was 2.0 µL, with a flow rate of 0.4 mL/min, and the column temperature was maintained at 40°C. Unravelling the interaction between the phageome and bacteriome in the rumen and its role in influencing metabolome dynamics in dairy cows at different lactation stages.Northwest A&F Universitymengya wangrumenmass spectrometryApproximately 100 μL of rumen fluid was transferred into a 1.5-mL centrifuge tube containing 400 μL of a solution composed of acetonitrile and methanol (1:1, v/v), supplemented with 0.02 mg/mL of the internal standard L-2-chlorophenylalanine. The samlpes were mixed by vortex for 30 seconds and ultrasonication at 40 kHz for 30 minutes at 5°C, followed by placing them at -20°C for 30 minutes to precipitate proteins. The samples were centrifuged at 13,000 × g for 15 minutes at 4°C. After being taken out, the supernatant was blown dry using nitrogen. The concentrated product was re-solubilized in 100 μL of water/acetonitrile (1:1, v/v), and extracted in an ultrasonic bath at 5°C with the ultrasonic frequency of 40 kHz for 5 minutes. After centrifuging the mixture, the supernatant was then carefully transferred to sample vials for LCMS analysis.CattleThe pretreatment of LC/MS raw data was performed by Progenesis QI (Waters Corporation, Milford, USA) software, and a three-dimensional data matrix in CSV format was exported. The information in this three-imensional matrix included: sample information, metabolite name and mass spectral response intensity. Internal standard peaks, as well as any known false positive peaks (including noise, column bleed, and derivatized reagent peaks), were removed from the data matrix, deredundant and peak pooled.Grouphttps://www.ebi.ac.uk/metabolights/MTBLS128161550057124@qq.comRumen fluid samples were collected using oral stomach tubes prior to morning feeding during the peak (70 DIM), early mid- (120 DIM), and later mid-lactation (150 DIM). The initial 100 mL of rumen fluid from each cow was discarded to prevent saliva contamination, and the next 50 mL of rumen fluid was filtered through four layers of sterile cheesecloth in an environment with a steady CO2 flux. After sampling from each cow, the rumen fluid was promptly packaged and temporarily stored in liquid nitrogen and finally transferred to -80 for storage.Metabolomicslactationuntargeted metabolitesRumenlactationuntargeted metabolitesRumenThe mass spectrometric data were collected using a Thermo UHPLC-Q Exactive Mass Spectrometer equipped with an electrospray ionization (ESI) source operating in positive mode and negative mode.The optimal conditions were set as followed: source temperature at 400℃; sheath gas flow rate at 40 arb; Aux gas flow rate at 10 arb; ion-spray voltage floating (ISVF) at -2800V in negative mode and 3500V in positive mode, respectively; Normalized collision energy, 20-40-60 eV rolling for MS/MS. Full MS resolution was 70000, and MS/MS resolution was 17500. Data acquisition was performed with the Data Dependent Acquisition (DDA) mode. The detection was carried out over a mass range of 70-1050 m/z.Tetrahydroharmol(10betaH,11xi)-11-Hydroxy-13-nor-6-eremophilen-8-one4-HydroxynonenalCarissanolLPE(18:2)DehydrooreadoneEdulisin I3,3-Dimethylglutaric acid(+)-Galeon2-BenzoxazololN-DihydroferuloyltyraminePhaseolus eDiosbulbinoside DHypogeic acidStearoylcarnitineDeoxyinosine12-Oxo-20-trihydroxy-leukotriene B41-(11Z-eicosenoyl)-glycero-3-phosphate5,8-Dihydroxy-3-(4-hydroxybenzyl)-7-methoxy-4-chromanone 8-acetateThreoninyl-PhenylalanineLysoPE(0:0/18:1(11Z))Ethyl (2E)-3-(4-hydroxyphenyl)prop-2-enoateVanillic acid 4-sulfate3-(1,1-Dimethylallyl)scopoletin 7-glucosideDL-o-Tyrosine(R)-S-lactoylglutathionate(1-)Simmondsin 2'-ferulateN-Cyclopropyl-trans-2-cis-6-nonadienamide[4]-Gingerdiol 3,5-diacetatePI(18:1(11Z)/20:4(5Z,8Z,11Z,14Z))Alpha-ZearalenolGamma-CEHCValyl-ValineGuanidylic acid (guanosine monophosphate)Doxepin N-oxide glucuronideSyringic acidSorbitan stearateCerP(d18:1/12:0)2-{[hydroxy(2,3,4-trimethoxyphenyl)methylidene]amino}acetic acid1-OleoylglycerophosphoserineTaraxinic acid glucosyl ester(+)-threo-2-Amino-3,4-dihydroxybutanoic acid5-Hydroxyindoleacetic acidMonic acidKaempferol-3-O-alpha-L-arabinosideCorosinMarindinin4,11,13,15-Tetrahydroridentin BTetrahydrodipicolinate6''-O-AcetyldaidzinOleic acidKinetin-7-N-glucosideGlutaric acidPolysorbate 20{[1-(4-methoxyphenyl)pentan-3-yl]oxy}sulfonic acid4-Hydroxycinnamyl aldehydeEpoxymurin ADL-Benzylsuccinic acidL-beta-aspartyl-L-alanineAlpha-Ionol O-[arabinosyl-(1->6)-glucoside]SativanN-Acetylglutamic acidLysoPE(15:0/0:0)Gamma-Glutamyltyrosine3,4-Dihydroxymandelaldehyde8-Hydroxy-5,6-octadienoic acidLactucinD-glycero-L-galacto-OctuloseN-Acetylvanilalanine(1R,2S,3R)-2-Acetyl-4(5)-(1,2,3,4-tetrahydroxybutyl)imidazoleAvocadyne 2-acetateCaffeic acid1-Hydroxy-3-nonanone4-Methoxybenzyl acetate11-alpha-O-beta-D-Glucopyranosyl-16alpha-O-methylneoquassinProline betaineN-lactoyl-Leucine2-Ethyl-2-Hydroxybutyric acid2-(Methoxymethyl)furanPyridoxal (Vitamin B6)PalmitaldehydeKainic acid3-Hydroxydodecanedioic acidValyl-Isoleucine4-Pyridoxic acidCorchoroside BThreoninyl-SerinePS(16:0/18:2(9Z,12Z))1-StearoylglycerophosphoglycerolRibothymidinePE(14:0/18:1(11Z))Erucic acidP-Tolyl SulfateXanthurenic acid(R)-2-Hydroxy-7,8-dimethoxy-2H-1,4-benzoxazin-3(4H)-one 2-glucoside3beta-3,24-Dihydroxy-9(11),12-oleanadien-30-oic acidMacaridine4-Methoxycinnamic acidCrocin 3Dihydro-3-coumaric acid3-hydroxy-3-(2-hydroxyphenyl)propanalVanillic acid4,6,7-trihydroxy-2H-chromen-2-one9,10,16-trihydroxy palmitic acidHexadecanedioic acidCotinine glucuronideLysoPE(14:0/0:0)HelenalinPSOROMIC ACIDProstaglandin D3MupirocinEriojaposide BL-FucoseMethylisopelletierineHomoarecoline1-(2-Furyl)butan-3-one15-hydroxyicosanoic acidAmphibine HIsorhamnetin13,14-Dihydro-15-keto-PGE2Glutaminylhydroxyproline(R)-11,12,13-Trinor-1(5),6,9-guaiatrien-8-oneFA(18:2(OH3))CRESOPYRINE17-phenyl-18,19,20-trinor-prostaglandin D2Asparaginyl-ValineN-Acetyl-DL-tryptophanEnterodiolNeryl rhamnosyl-glucosideLPC(18:2)GlutamylprolineProstaglandin G2 2-glyceryl EsterLysoPE(0:0/20:3(11Z,14Z,17Z))Acetaldehyde butyl phenethyl acetalMesnaTovophyllin BDulcitol3,4-Dimethyl-5-pentyl-2-furanpropanoic acidIsopentyl gentiobiosideValyl-Tyrosine3-Sulfinoalanine6-Acetyl-2,3-dihydro-2-(hydroxymethyl)-4(1H)-pyridinone4-Hydroxyproline galactosidePA(8:0/13:0)Valyl-AspartateDihydrocoumaroyl Hexoside2(R)-hydroxydocosanoic acidCodeine N-oxidePS(14:0/16:0)Antibiotic CJ 15544Dihydroxyphenylacetic acidSorbitan palmitateDextrorphan O-glucuronide8-(1-hydroxy-2-methoxypropan-2-yl)-2H-furo[2,3-h]chromen-2-oneLPC(18:1)Jasmolone glucoside6-Hydroxy-R-acenocoumarolIsovalerylglutamic acidN-Acetyl-L-glutamic acid(R)-2,7-Dihydroxy-2H-1,4-benzoxazin-3(4H)-oneUric acid(R)-2-Hydroxycaprylic acidAmericanol7-hydroxy-6-(4-hydroxy-3-methylbut-2-en-1-yl)-8-methoxy-2H-chromen-2-oneN-Acetyl-D-phenylalanine2,3-Dinor-6-keto-prostaglandin F1 aTaxiphyllin3-Hydroxytetradecanedioic acidL-Tyrosine4'-Dihydroabscisic acid(Z)-3-Oxo-2-(2-pentenyl)-1-cyclopenteneacetic acidHydroxysuberic acid20-Carboxy-leukotriene B4PS(15:0/18:1(11Z))L-PhenylalanineIsoeugenol formate(S,E)-ZearalenoneFlacourtinTetradecanedioic acidLysoPC(17:0)LPE(16:0)Hydroxysebacic acidGlycylproline(R)-1-O-[b-D-Apiofuranosyl-(1->2)-b-D-glucopyranoside]-1,3-octanediolPS(14:0/18:0)PC(P-16:0/14:1(9Z))Kudzusaponin SA2Methyl (3x,10R)-dihydroxy-11-dodecene-6,8-diynoate 10-glucosideIsoleucyl-Aspartate1-Isopropyl citrateAegelinolAcetyl-DL-LeucineTrans-EKODE-(E)-Ib6-MethoxymelleinPE(15:0/22:2(13Z,16Z))DTDP-4-acetamido-4,6-dideoxy-D-galactose2-Isopropylmalic acidN-Palmitoylsphingosine3,4,5-trihydroxy-6-[(4-oxo-2-phenyl-4H-chromen-3-yl)oxy]oxane-2-carboxylic acidAraliasaponin II2-{[(2,4-dihydroxy-5-methoxyphenyl)(hydroxy)methylidene]amino}acetic acidTrans-Grandmarin(2R,2'R)-3,3'-disulfanediylbis(2-acetamidopropanoic acid)Ascorbic Acid6-(4-ethyl-3-hydroxyphenoxy)-3,4,5-trihydroxyoxane-2-carboxylic acidFuranofukininN-acetyl-L-2-aminoadipate(2-)Acetyl-DL-Valine(3,4,5,6-tetrahydroxyoxan-2-yl)methyl acetateMolybdopterin precursor ZSecoeremopetasitolide AAlanyl-HydroxyprolineChlorogenoquinone(3beta,17alpha,23R)-17,23-Epoxy-3,29-dihydroxy-27-norlanost-8-ene-15,24-dioneCyclocalopin FSuberic acidN-Acetyl-4-O-acetylneuraminic acidUmbelliferone2-hydroxyhexadecanoic acidDehydrocurdioneIndole-3-carboxilic acid-O-sulphateDehydrocyanaropicrin5-HydroxyindoleacetaldehydeTetraethylene glycol6-HydroxyenterolactoneTrans-Zeatin-O-glucoside riboside(R)-6'-O-(4-Geranyloxy-2-hydroxycinnamoyl)-marmin1-(2,3-Dihydro-1H-pyrrolizin-5-yl)-1,4-pentanedione(3R,5Z)-5-Octene-1,3-diolRitalinic acidIxabepilone(E)-Suberenol5-Phenyl-1,3-oxazinane-2,4-dione1-heptadecanoyl-glycero-3-phosphateXanthosineNb-ArachidoyltryptamineMelledonal C1-Methoxy-3-(4-hydroxyphenyl)-2E-propenal 4'-glucosideUridine 5'-monophosphateMelledonal ACitric acidPolyethylene, oxidized5-[(4-Hydroxypheny)ethenyl]-2-(3-methyl-1-butenyl)-1,3-benzenediolGamma-Glutamylalanine[(3-methylbut-2-en-1-yl)oxy]sulfonic acid3-Formyl-6-hydroxyindole(E)-10-Hydroxy-8-decenoic acidPE(18:3(9Z,12Z,15Z)/20:3(8Z,11Z,14Z))Gyrocyanin3-Galactosyllactose3-Isopropenylpentanedioic acidMedicagenic acidBilirubin5-HydroxyflavoneDonhexocin(R)-Pelletierine19-Hydroxy-PGE2Cis-10-Hydroxylinalyl oxide 7-glucosideCrispolide3,4-Methylene suberic acidBenzoyl glucuronide (Benzoic acid)Pyridoxine (Vitamin B6)Vignatic acid APS(18:1(9Z)/0:0)DG(13:0/16:0/0:0)1-Octen-3-yl primeverosideJasmonic acidGamma-Glutamyl-S-methylcysteine sulfoxide4-Acetamidobutanoic acidDG(15:0/18:0/0:0)4',5,6-Trimethylscutellarein 7-glucosideHebevinoside VLotaustralin5-(3',4'-Dihydroxyphenyl)-gamma-valerolactonePelargonidinAdrenochromeBiotripyrrin-bGinsenoside Rh3(3beta,5alpha,6alpha,22E,24R)-Ergosta-7,9(11),22-triene-3,5,6-triol3alpha-HydroxyoreadonePonatinibLysoPC(18:0)Methyl (2R*,3S*)-2,3-dihydro-3-hydroxy-2-isopropenyl-5-benzofurancarboxylate3-O-trans-Feruloyleuscaphic acid(4R,5S,7R,11x)-11,12-Dihydroxy-1(10)-spirovetiven-2-one 12-glucosideGanosporelactone BSedanonic acidPyroglutamyl-IsoleucineArginyl-AsparagineLPC(16:0)L-GlutamateAcidissiminol epoxideDIPROTIN A7,8-Dihydrovomifoliol 9-[apiosyl-(1->6)-glucoside]12-Oxo-2,3-dinor-10,15-phytodienoic acidThymolAllysineA-L-threo-4-Hex-4-enopyranuronosyl-D-galacturonic acidCis-5-TetradecenoylcarnitineTriazolopropionic acidDehydrochorismic acidAc-Ser-Asp-Lys-Pro-OHGoyaglycoside gPyridine N-oxide glucuronideHydroxybuprenorphineRiboflavin (Vitamin B2)Strobilurin ADIHYDRO-beta-TUBAIC ACID8-{[3-(hydroxymethyl)-3-methyloxiran-2-yl]methyl}-7-methoxy-2H-chromen-2-oneTraumatic Acid7-Methoxy-2-methylisoflavoneBeta-D-Xylopyranosyl-(1->5)-alpha-L-arabinofuranosyl-(1->5)-L-arabinoseErinapyrone AAnnomutacinDodecylbenzenesulfonic acidPE-NMe(16:0/20:3(5Z,8Z,11Z))APC9,10-DiHOME3,4,5,6-Tetrahydrohippuric acid13,14-dihydro Prostaglandin F1alpha{[1-(2-hydroxyphenyl)-3-oxopropan-2-yl]oxy}sulfonic acid(3beta,17alpha,23S,24S)-17,23-Epoxy-3,24,29-trihydroxy-27-norlanost-8-en-15-onePhenylalanyl-AsparagineEthisteroneN-AcetylgalactosamineNaringenin9-(2,3-dihydroxypropoxy)-9-oxononanoic acid12-epi Leukotriene B3Janthitrem FAflatoxin Ex2B1(1beta,2beta,5beta)-p-Menth-3-ene-1,2,5-triolOchratoxin ADTMP13'-Hydroxy-gamma-tocotrienolCytochalasin Ppho5-Hydroxyvalproic acidLysoPA(18:0e/0:0)N-Linoleoyl GABAAdenosine 3'-monophosphate(3beta,5alpha,9alpha,22E,24R)-3,5,9-Trihydroxy-23-methylergosta-7,22-dien-6-oneIsokaempferideFA(18:1(OH3))N-acetyl-S-(3-oxo-3-carboxy-n-propyl)cysteineDolichosteroneAnabasine2-Hydroxy-22-methyltetracosanoic acid4-Hydroxyhippuric acid2'-Oxoaloesol 7-glucosideIsoleucyl-TryptophanLeu-Leu-LeuN-lactoyl-phenylalaninePrednisoneN-(1-Deoxy-1-fructosyl)tryptophanEnoxoloneDopamine glucuronide(4-ethenyl-2,6-dihydroxyphenyl)oxidanesulfonic acid(2S,4R)-p-Mentha-1(7),5-dien-2-ol acetate(S)-Nerolidol 3-O-[a-L-rhamnopyranosyl-(1->2)-b-D-glucopyranoside]DopaquinoneLubiminolD-N-(Carboxyacetyl)alanineDiphenol glucuronide5-Butyl-3,4-dimethyl-2-furanundecanoic acidCis-Resveratrol 3-O-glucuronide6-FormylumbelliferoneN-acetylaspartateHistidinyl-MethionineHistidinyl-Gamma-glutamatePhenylacetylaspartic acidDemethylated antipyrineGentisic acid1-HeptadecanoylglycerophosphoethanolamineCholesterol glucuronide4-{[3-(hydroxymethyl)-3-methyloxiran-2-yl]methoxy}-7H-furo[3,2-g]chromen-7-one8-Propanoylneosolaniol(3beta,5alpha,6alpha,7alpha,22E,24R)-5,6-Epoxyergosta-8,14,22-triene-3,7-diolCanesceinC75Cyclocalopin C1Aspirin1-(4-methoxy-1-benzofuran-5-yl)ethan-1-oneIsoleucylisoleucine13'-Carboxy-gamma-tocotrienol3-AcetamidobutanalCinncassiol C24-ethenyl-6-methoxybenzene-1,3-diolFerulic acid3-(5-Methyl-2-furanyl)butanalTocopheronic acid6-(3-ethenylphenoxy)-3,4,5-trihydroxyoxane-2-carboxylic acid(S)-17-Hydroxy-9,11,13,15-octadecatetraynoic acidOsthenol(5alpha,8beta,9beta)-5,9-Epoxy-3,6-megastigmadien-8-ol3-Hydroxy-2H-pyran-2-one6-Methoxy-2(3H)-benzoxazoloneFarnesylcysteineCitalopram propionic acidIndolelactic acid2-Methoxy-4-(4-methyl-1,3-dioxolan-2-yl)phenol(Z)-Resveratrol 3-(4''-sulfoglucoside)Abu-Trp-OHAdipostatin A1,2-Di-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphateY-Linolenic acidSinapic acid11,13-Dihydrotaraxinic acid glucosyl ester11Z-Eicosenoic acid6-Hydroxy-1H-indole-3-acetamide(S)-Edulinine5-Hexyldihydro-5-methyl-2(3H)-furanone5,7-Dihydroxy-4'-methoxy-8-methylflavanone9-Oxo-nonanoic acid(3b,9R)-5-Megastigmene-3,9-diol 9-[apiosyl-(1->6)-glucoside]TUBAIC ACID2-Deoxy-L-ribono-1,4-lactone(S)-9-Hydroxy-10-undecenoic acid2-Acetyl-1-methylpyrrole9-OxoasimicinonePalmitoyl glucuronideGallic acid2',7-Dihydroxy-4'-methoxy-8-prenylflavan 2',7-diglucoside5-(2-Methylpropyl)tetrahydro-2-oxo-3-furancarboxylic acid(9S,10S)-9,10-dihydroxyoctadecanoate2''-O-trans-p-CoumaroylastragalinDumetorine2-ISOPRENYL-3-HYDROXY-5-METHYL-a-PYRONEWithangulatin AProstaglandin E2 ethanolamideAdipic acid(R)-lipoic acid(17alpha,23S)-Epoxy-28,29-dihydroxy-27-norlanost-8-ene-3,24-dioneTG(8:0/8:0/i-19:0)MethylgallateEremopetasitenin B2Erythro-5-hydroxy-L-lysinium(1+)Phenylglucuronide3-Hydroxypicolinic acid(4S,8R)-8,9-Dihydroxy-p-menth-1(6)-en-2-oneCis-4-Hydroxycyclohexylacetic acidN-lactoyl-TyrosineLeucyl-phenylalanineLysoPA(0:0/16:0)Phenylalanyl-TryptophanAlanyl-Threonine4-Hydroxycyclohexylcarboxylic acid5,7-dihydroxy-2-(4-hydroxyphenyl)-8-(3,4,5-trihydroxyoxan-2-yl)-4H-chromen-4-one(S)-2-Hydroxy-2-phenylacetonitrile O-b-D-allopyranosideMEDICA 16Hexyl glucoside(1xi,3xi)-1,2,3,4-Tetrahydro-1-methyl-beta-carboline-3-carboxylic acidDihydro-2-methoxy-2-methyl-3(2H)-thiophenone2beta,9xi-Dihydroxy-8-oxo-1(10),4,11(13)-germacratrien-12,6alpha-olideAdenine5-Aminosalicylic??acidMG(0:0/14:1(9Z)/0:0)N2-Acetyl-L-ornithineElatoside GJimenezinBlumenol C O-[apiosyl-(1->6)-glucoside]Taraxacoside2-{9-hydroxy-2-oxo-2H,8H,9H-furo[2,3-h]chromen-8-yl}propan-2-yl acetateInosine7-hydroxy-3-(hydroxymethyl)-1H-isochromen-1-oneTryptophyl-Valine1-MethylinosineDihydroprudomenin3-METHYLORSELLINIC ACIDLucidenic acid N2,3-dinor Prostaglandin E1(Z)-13-Hexadecenoic acidGanoderiol IN-Deschlorobenzoyl indomethacin2-(4-ethyl-3-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol5-Pentyltetrahydro-2-oxo-3-furancarboxylic acidMelibioseMelledonol3,4-Methylenesebacic acid6-(hydroxymethyl)-7-methoxy-2H-chromen-2-oneMarmesin rhamnoside12-Hydroxy-13-O-D-glucuronoside-octadec-9Z-enoateOleoyl glycine5-Hydroxy-p-mentha-6,8-dien-2-oneN-(1-Deoxy-1-fructosyl)leucineHovenidulcigenin AMarshrinIsosativan7(14)-Bisabolene-2,3,10,11-tetrolTanacetinN-Acetyl-DL-methionineHawkinsinSebacic acidIsopetasoside1-Phenyl-6,7-dihydroxy-isochromanArginyl-Hydroxyproline3-DehydroquinateWithanolide BNanaomycin(R)-1-O-b-D-glucopyranosyl-1,3-octanediolMethionyl-SerineL-Menthyl (R,S)-3-hydroxybutyrate(2-Methoxyethoxy)propanoic acidL-alpha-PhosphatidylethanolamineN,N'-diacetylchitobioseNeocnidilide2,5-Dimethyl-3(2H)-furanonePyroglutamic acidCavipetin E isomer 16-Hydroxypentadecanedioic acidBetavulgaroside II(S)-alpha-Amino-4-carboxy-3-furanpropanoic acidMaysin 3'-methyl etherHydroxyphenyllactic acidP-Acetamidophenol (Acetaminophen, Tylenol)SuccinylacetoneCappariloside A2-Hydroxyacorenone2-MethylguanosineAscorbyl palmitate8-Deoxy-11,13-dihydroxygrosheimin5-Methoxysalicylic acidValechlorin1-[(5-Amino-5-carboxypentyl)amino]-1-deoxyfructose6-(2-amino-2-carboxyethyl)-4-hydroxybenzothiazoleL-(-)-PhenylalanineCis-6-Nitro-p-mentha-1(7),2-dieneDeoxyguanosineFA(18:2(OH2))GingerolMangalkanyl glucosideN-Acetyl-L-alanineCoprocholic acidP-Cresol glucuronide(5-ethenyl-2-hydroxyphenyl)oxidanesulfonic acidIsopulegone caffeateDaidzin 4'-O-glucuronideIsosakuranetinAH 6809PE(18:4(6Z,9Z,12Z,15Z)/P-16:0)4-(2-Aminophenyl)-2,4-dioxobutanoic acid6-Oxopiperidine-2-carboxylic acidPisatoside2,4,7-Decatrienoic acidPS(14:0/14:0)FA(18:1(OH1))Nicotinamide N-oxide1-eicosanoyl-glycero-3-phosphateHAEMATOMMIC ACIDAcacetinArmexifolinL-Aspartic AcidN-PropionylmethionineGamma-L-Glutamyl-L-pipecolic acidNonate(¡À)-Enterolactone2,2'-(3-methylcyclohexane-1,1-diyl)diacetic acidGlycochenodeoxycholic acid 3-glucuronideTetracyclineCinchonain Id 7-glucoside3'-Hydroxy-4',5,6,7,8-pentamethoxyflavoneProstaglandin D1 AlcoholThreoninyl-TyrosineIsocitrateLucyin AS-Methyl benzenecarbothioate(2S,3'S)-alpha-Amino-2-carboxy-5-oxo-1-pyrrolidinebutanoic acidN5-Acetyl-N2-gamma-L-glutamyl-L-ornithineThreoninyl-Valine6-(2-Hydroxyethoxy)-6-oxohexanoic acidIsopentyl beta-D-glucosideCarvacrol(3,4,5,6-tetrahydroxyoxan-2-yl)methyl 3-(4-hydroxy-3-methoxyphenyl)prop-2-enoateN-Methoxyspirobrassinol methyl ether3-Oxotetradecanoic acid12-Keto-leukotriene B43-Oxooctanoic acidPG(a-13:0/i-12:0)Egonol glucosidePurpurenin2-octenoylglycine2-Carboxy-4-dodecanolideSpirolide BDeoxyadenosine monophosphateSalicyluric acid(3beta,22E,24R)-3-Hydroxyergosta-5,8,22-trien-7-one1a,1b-dihomo-PGE1LysoPC(P-18:1(9Z))Deoxycholic acid2-Hydroxymyristic Acid(¡À)9-HpODEPisumic acid2-(Ethylamino)-4,5-dihydroxybenzamide[6]-Gingerdiol 3,5-diacetateLubiprostoneHydroxyisonobilin3-Isovalidene-3alpha,4-dihydrophthalide{[4-(4-hydroxy-3-methoxyphenyl)butan-2-yl]oxy}sulfonic acid12a-Hydroxy-3-oxocholadienic acidFA(12:1(OH1))3-Hydroxyadipic acid 3,6-lactone28-Homobrassinolide5-MethoxytryptopholCMPFfalseUnravelling the interaction between the phageome and bacteriome in the rumen and its role in influencing metabolome dynamics in dairy cows at different lactation stagesBackground: Although the roles of rumen microbiome in milk yield and milk protein synthesis have been widely recognized, knowledge on how ruminal microbiome dynamic changes affect these two traits during the whole lactation is lacking. Phages have been shown to affect the microbiota, but little is known about the shift patterns of ruminal phages and if they may modulate rumen microbiome during lactation. Herein, a longitudinal study was performed to identify the potential roles of ruminal phageome and bacteriome interactions, and metabolic function shift in affecting milk yield and protein content using metagenomic and metabolomic profiling of rumen microbiome from the peak, early and later mid-lactation stages.Results: A total of 780 ruminal bacterial phages were identified, which exhibited two primary shifting patterns: 1) decreasing then increasing; 2) decreasing then stabilizing through the lactation. Bacteriome also showed first increasing then stabilizing or continuously decline besides exhibiting two similar shifting patterns to those of phages. By associating the differentially abundant phages with their host bacteria, we observed that significantly increased Lactococcus phage BM13, Corynebacterium phage P1201 and Campylobacter phage CJIE4-5 in peak lactation, along with Lactobacillus phage Lv-1 in early and later mid-lactation, and they were positively correlated with the relative abundance of their hosts. However, significantly increased Bacillus phage BCU4 and the Enterococcus phage phiNASRA1 in early mid-lactation were negatively related to their host abundance. In terms of bacteria, such as Ruminococcus flavefaciens and Faecalibacterium sp. CAG 74 had the highest abundance in peak lactation, whereas most Prevotella species were more abundant in early and later mid-lactation. Notably, ruminal carbohydrate and amino acid metabolism functions were enhanced in early mid-lactation. Further structural equation model and network analysis revealed that abundant Bacillus phage BCU4 and Enterococcus phage phiNASRA1 in early mid-lactation were associated with increased relative abundance of Prevotella species, possibly due to a reduction in Bacillus cereus and Enterococcus faecalis. Additionally, these Prevotella species exhibited positive relationships with rumen metabolites, such as L-phenylalanine, phenylacetylglycine, N-acetyl-D-phenylalanine, as well as propionate content, which contributed to the improved milk protein yield.Conclusions: This study revealed the bacteriome and phageome interactions at different lactation stages, and the key phages and bacteria regulating the rumen function and metabolism thus contributing to the milk traits of cows. The potential regulatory roles of phages in affecting the rumen bacteriome suggest that they can be powerful targets for future interventions to improve rumen functions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