Metabolite identification was performed using the R XCMS package. The acquired MS/MS spectral data were matched against the mzCloud, Human Metabolome Database (HMDB), MassBank, LipidMaps, Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and an in-house database.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["Chromatographic separation was performed on a Vanquish UHPLC system (Thermo Fisher Scientific, Waltham, MA, USA) using an ACQUITY UPLC HSS T3 reverse-phase column (2.1 × 150 mm, 1.8 µm; Waters). The mobile phases consisted of 0.1% formic acid in water and 0.1% formic acid in acetonitrile for the positive ion mode, and 5 mM ammonium formate in water and acetonitrile for the negative ion mode. The flow rate was 0.25 mL/min, the column temperature was 40 °C, and the injection volume was 2 µL.
"],"publication":["Integrated cecal microbiota and metabolome analyses reveal stage-specific microbiota-metabolite associations underlying host responses during Eimeria tenella infection in Wenchang chickens."],"submitter_affiliation":["Jiangsu Institute of Poultry Science"],"submitter_name":["LI Jianmei"],"organism_part":["cecum"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Cecal content samples were thawed on ice. Metabolites were extracted using pre-chilled methanol/acetonitrile (1:1, v/v). A constant volume of internal standard solution was added to all samples prior to extraction; however, the exact identity and concentration of the internal standard were not documented. After centrifugation, the supernatants were collected. Pooled quality control (QC) samples were prepared by pooling equal aliquots of all samples. No solvent blank or external standard information was recorded.
"],"organism":["Gallus gallus"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15811"],"author":["Jianmei Li. Jiangsu Institute of Poultry Science. jianmeili157@sina.com."],"data_transformation_protocol":["Raw data were converted to mzXML format by MSConvert (ProteoWizard v3.0.8789) and processed using the R XCMS package for peak detection, retention time correction, and alignment. Multivariate statistical analyses, including principal component analysis (PCA) and orthogonal partial least-squares discriminant analysis (OPLS-DA), were performed using the R package ropls (version 1.6.2). Differential metabolites were screened using a two-tiered strategy: P < 0.05 and VIP > 1.0 for 2 dpi; VIP > 1.0, |log2 fold change| > 1, and FDR-adjusted P < 0.05 for 4 dpi and 7 dpi.
"],"study_factor":["Treatment","Breed","Time point"],"submitter_email":["jianmeili157@sina.com"],"sample_collection_protocol":["Cecal content samples were collected from three chicken breeds—Wenchang chicken (WCC), recessive white feather chicken (RWFC), and white ear yellow chicken (WEYC)—at 26 days of age. For each breed, 60 birds were randomly allocated into two groups: an infected group (n = 30) and a non-infected control group (n = 30), with 5 replicate pens of 6 birds each. The infected group was orally inoculated with 1 mL PBS containing 50,000 sporulated E. tenella oocysts, while the control group received an equivalent volume of PBS. At 2, 4, and 7 days post-infection (dpi), one bird was randomly selected from each replicate pen per group per breed (n = 5 per group per time point per breed). Birds were euthanized by CO2 inhalation followed by cervical dislocation. Immediately after euthanasia, cecal contents were collected and snap-frozen in liquid nitrogen. All samples were stored at −80 °C until metabolomics analysis. A total of 90 cecal content samples (3 breeds × 2 groups × 3 time points × 5 replicates) were collected for metabolomics analysis.
"],"omics_type":["Metabolomics"],"study_design":["Thermo Scientific Vanquish UHPLC System","pooled quality control sample","Metabolomics","infection","untargeted analysis","Thermo Scientific Q Exactive HF-X","Time Series","cecum","Gallus gallus","experimental sample"],"curator_keywords":["Thermo Scientific Vanquish UHPLC System","pooled quality control sample","Metabolomics","infection","untargeted analysis","Thermo Scientific Q Exactive HF-X","Time Series","cecum","Gallus gallus","experimental sample"],"mass_spectrometry_protocol":["Mass spectrometry detection was performed on a Q Exactive HFX Orbitrap mass spectrometer (Thermo Fisher Scientific, Waltham, MA, USA) equipped with an electrospray ionization (ESI) source. Data were acquired in alternating positive and negative ionization modes over an m/z range of 100–1000. The key parameters were set as follows: spray voltage, +3.50 kV for the positive mode and -2.50 kV for the negative mode; sheath gas pressure, 30 arb; auxiliary gas flow, 10 arb; capillary temperature, 325 °C. The exact resolution setting for full MS scans was not recorded in the original laboratory records.
"],"metabolite_name":["Schaftoside","(2S,5S)-trans-Carboxymethylproline","1-Hexadecylthio-2-hexadecanoylamino-1,2-dideoxy-sn-glycero-3-phosphocholine","Corticosterone","Prostaglandin G2","Deoxyribose","Lipoxin B4","Riboflavin","Bufadienolide","Alantolactone","Cephalosporin C","Aspartame","11-O-Demethyl-17-O-deacetylvindoline","Imidazolelactic acid","gamma-Aminobutyric acid","Ectoine","N-a-Acetylcitrulline","Aminoglutethimide","N1,N12-Diacetylspermine","Juvenile hormone III","Kinetin","L-Histidine","Ketoleucine","Vulgaxanthin I","2-Keto-6-acetamidocaproate","Reserpine","Cholest-4-en-3-one","Nicotinate D-ribonucleoside","Besonprodil","L-2-Amino-6-oxoheptanedioate","O-Succinyl-L-homoserine","D-Gulono-1,4-lactone","Biotin","L-Homophenylalanine","Bz-Arg-OEt","4,4'-Dihydroxy-alpha-methylstilbene","Quadrone","L-Proline","1-Methylxanthine","Benzoate","(R)-mandelic Acid","Methylimidazole acetaldehyde","N1-Acetylspermidine","Ursolic acid","3-Hydroxyanthranilic acid","N-Acetyl-D-tryptophan","5-Hydroxyindoleacetic acid","Neocembrene","Glucosamine","Triacetate lactone","5-Nitro-2-(3-phenylpropylamino)benzoic acid","Hydroxykynurenine","9-cis-Retinoic acid","Prostaglandin E2","alpha-Tocopherol","Pilocarpine","1,2,3-Trihydroxybenzene","N2-Succinyl-L-ornithine","cis-4-Hydroxy-D-proline","Ureidopropionic acid","Jasmone","Tetrahydrodipicolinate","6beta-Hydroxytestosterone","Oleic acid","9,10,13-TriHOME","13S-hydroxyoctadecadienoic acid","Taurohyocholate","Lacto-N-biose I","(R)-Pantolactone","Abscisic alcohol","Aflatoxin G2","Propafenone","(2S)-Liquiritigenin","L-beta-Phenylalanine","Isoalantolactone","N-Acetyl-L-glutamate 5-semialdehyde","Pregnanediol","Glutathione","12,13-DHOME","7-Dehydrodesmosterol","5-Hydroxylysine","Allopregnanolone","Isophorone","Temazepam","7,8-Diaminononanoate","Perillyl alcohol","L-Formylkynurenine","Isoetharine","Linatine","Methylselenopyruvate","Dihydrocapsaicin","4-Acetamidobenzoic acid","3-(2-Hydroxyphenyl)propanoic acid","4-Amino-5-hydroxymethyl-2-methylpyrimidine","17beta-Acetamidoandrost-4-en-3-one","(R)-Laudanidine","Vitamin D3","Guanosine","Sinapyl alcohol","Quillaic acid","Ascorbate","Erucic acid","Delta-12-Prostaglandin J2","Indoleacetaldehyde","8-Amino-7-oxononanoate","gamma-Glutamyltyramine","Pyridoxamine 5'-phosphate","trans-Isoasarone","2-Biphenylol","21-Hydroxypregnenolone","4-Acetamido-2-aminobutanoic acid","Biliverdin","Aminoadipic acid","N,N-Dimethylsphingosine","Apiole","Mupirocin","Prostaglandin D3","4-Methoxybenzaldehyde","FMLP","6'-Oxolividamine","7a,12a-Dihydroxy-5b-cholestan-3-one","Hecogenin","trans-trans-Muconic acid","(R) 2,3-Dihydroxy-3-methylvalerate","Cis-zeatin","6-Tuliposide A","Soyasapogenol B 3-O-D-glucuronide","Fenuron","Retrorsine","1-Oleoylglycerophosphocholine","Androstenedione","Ornithine","4-Hydroxyphenylacetaldehyde","(R)-10-Hydroxystearate","Indole","Equol","Lovastatin","Methylprednisolone acetate","4-Methylbenzaldehyde","Diazinon","4-(beta-D-Glucosyloxy)benzoate","gamma-L-Glutamyl-D-alanine","Isocitric acid","6-Keto-prostaglandin F1a","3-Indoleacetonitrile","(5-L-Glutamyl)-L-glutamate","L-Carnitine","3alpha,7alpha-Dihydroxy-12-oxo-5beta-cholanate","Emetine","Cerulenin","Swainsonine","Thiamine","Cyclopentolate","Diethylpropion","D-Lysopine","Adenosine","Nitrendipine","L-Glutamic gamma-semialdehyde","Acetamidopropanal","Acetylphosphate","5-Acetamidovalerate","Prostaglandin B2","3-Dehydroshikimate","2-Hydroxycinnamic acid","Linoleic acid","Cycloheximide","Carfentanil","Sulfamerazine","Campesterol","Nornicotine","L-Dopa","Aflatoxin B1","3-Methyl-L-tyrosine","Argininosuccinic acid","Methyleugenol","2,3-Dinor-8-iso prostaglandin F2alpha","Betamethasone","Isopentenyl adenosine","Hypotaurine","L-Phenylalanine","Stearidonic acid","5-Methylcytosine","9-Riburonosyladenine","8,9-EET","HC-toxin","N-Butyryl-L-homoserine lactone","Dihydrobiochanin A","Isoproterenol","Clomipramine","N-Acetyl-D-galactosamine","Metoclopramide","(9Z,12Z)-(8R)-Hydroxyoctadeca-9,12-dienoic acid","Oleanolic acid","Morphinone","Butein","4-(Glutamylamino) butanoate","Indole-3-acetaldehyde oxime","Ecgonine","Ophthalmate","Spermidine","Cortexolone","3-Dehydrosphinganine","Sphingosine","Triethylamine","beta-Zearalenol","2-Naphthylamine","2,5-Dioxopentanoate","Folinic acid","Nicotinamide riboside","5(S)-HpETE","Tyrosine methylester","2-Isopropyl-3-oxosuccinate","Dehydroepiandrosterone sulfate","Acetaminophen","L-Cystathionine","5-Dehydroavenasterol","Cyclobenzaprine","N(omega)-Hydroxyarginine","alpha-Spinasterol","Phenylacetaldehyde","Metanephrine","N(6)-Methyllysine","Geranyl acetate","Cyclopeptine","Paspalicine","N-Desmethylcitalopram","Methostenol","1-O-Vanilloyl-beta-D-glucose","N-Demethylindolmycin","Pyridoxal 5'-phosphate","Bufotalin","3-Methoxyanthranilate","Guanine","Coleonol","5'-Methylthioadenosine","(S)-4-Hydroxymandelate","Octadecanamide","8,11,14-Eicosatrienoic acid","1-Linoleoylglycerophosphocholine","Rivastigmine","gamma-Amino-gamma-cyanobutanoate","Tropate","N1,N8-Bis(4-coumaroyl)spermidine","8-Isoprostane","m-Cresol","Alprenolol","beta-Hydroxyarginine","Creatinine","Riboflavin reduced","Methyl hexadecanoic acid","Pyridoxine","(2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinate","Myriocin","N-Acetylarylamine","Retinol","Emodin","7-Methylguanine","D-synephrine","Formiminoglutamic acid","Oxethazaine","Norcodeine","2-Phenylacetamide","11,12,15-THETA","N-Glucosylnicotinate","Atrazine","Thiabendazole","Acetylcholine chloride","(+)-7-Isojasmonic acid","Quinestrol","Etiocholanedione","Isohelenol","Capsaicin","2-Deoxystreptamine","Cortisol","Bilirubin","Nicotinamide ribotide","Glycocholic acid","24-Methylenecycloartanol","Pipecolic acid","Nopaline","9(S)-HPOT","Myristicin","Mirtazapine","7-Dehydrocholesterol","1-Hydroxy-2-naphthoate","(13E)-11a-Hydroxy-9,15-dioxoprost-13-enoic acid","N-Methylhydantoin","N6-Acetyl-N6-hydroxy-L-lysine","Glutethimide","Hesperetin","Beta-Tyrosine","beta-Alanyl-L-arginine","1,3-Dihydro-(2H)-indol-2-one","4-Phenylbutyrate","L-Methionine S-oxide","6-Amino-6-deoxyfutalosine","L-2,4-diaminobutyric acid","Cytidine","Anandamide","Bisphenol A","Dyphylline","N-Acetyl-L-aspartic acid","N2-Malonyl-D-tryptophan","N-Methylserotonin","gamma-Glutamylalanine","4-Fluoro-L-threonine","4-Oxoglutaramate","3-Methoxy-4-hydroxyphenylglycolaldehyde","3-Dehydro-2-deoxyecdysone","Isoquinoline","Zolpidem","5-Guanidino-3-methyl-2-oxopentanoate","Mesobilirubinogen","Pyridostigmine","L-Lysine","(2R,3R)-3-Methylglutamyl-5-semialdehyde-N6-lysine","Gamabufogenin","Androstanedione","Beta-Carboline","Asiatic acid","14-Dihydroxycornestin","2,4-Dihydroxypteridine","Prostaglandin I2","Cafestol","Sodium deoxycholate","Dioxacarb","7-Methyluric acid","Thymol","Eugenol","Misoprostol","Dodecanoic acid","androst-5-ene-3,17-dione","alpha-D-Galactosyl-1,3-beta-D-galactosyl-1,4-N-acetyl-D-glucosamine","2-Amino-2-deoxy-D-gluconate","Thyrotropin releasing hormone","2-Hydroxy-3-oxoadipate","(+)-Sesamin","Sphinganine","Phosphohydroxypyruvic acid","2-Hydroxyestrone","4-Amino-4-deoxychorismate","Cadaverine","Butyryl-L-carnitine","3-Ketosphingosine","Traumatic Acid","Thymine","Dobutamine","Docosatetraenoyl Ethanolamide","Oleoylethanolamide","Tigogenin","4,5-Dihydroorotic acid","6'-Oxogentamicin X2","1-Methyladenosine","Qing Hau Sau","Pirimiphos-ethyl","D-Ribose","Maltol","N-Carbamoylputrescine","Progesterone","(4Z,7Z,10Z,13Z,16Z,19Z)-Docosahexaenoic acid ethyl ester","Pyrimidodiazepine","beta-Alanyl-L-lysine","1-Methylhistamine","Taurine","Naringenin","9,10-EOT","Genistin","L-Alanyl-gamma-D-glutamyl-L-lysine","2-Methoxy-17beta-estradiol","O-Phosphoethanolamine","Formylanthranilic acid","1-(3,4-Dihydroxyphenyl)-5-hydroxy-3-decanone","N-Methyl-2-pyrrolidinone","Lithocholic acid","(R)-2-O-Sulfolactate","Megestrol acetate","3-Dehydroecdysone","D-Ribose 5-phosphate","(R,S)-Coclaurine","4'-Oxonebramine","L-Threonine","2-Aminophenol","p-Synephrine","Glutathionylspermidine","4a-Methylzymosterol","Agmatine","Myristoleic acid","L-Leucine","Trigonelline","beta-Carotene","gamma-Glutamyl-beta-aminopropiononitrile","(10S)-Juvenile hormone III diol","Palmitoylethanolamide","(R)-4-Hydroxymandelate","Cytisine","3''-Deamino-3''-oxonicotianamine","Prednisone","Catechol","Clostebol","Retinoyl b-glucuronide","Leukotriene E4","1-palmitoylglycerophosphocholine","N(omega)-Nitro-L-arginine methyl ester","Porphobilinogen","Glutamylglutamic acid","Tyrosol","Nalbuphine","(3S,4S)-3-Hydroxytetradecane-1,3,4-tricarboxylate","Pentoxifylline","Cortisol 21-acetate","Antibiotic JI-20B","Antibiotic JI-20A","Ubiquinone-1","13-L-Hydroperoxylinoleic acid","Dopaquinone","Undecanoic acid","Gabapentin","Calcitriol","Phenelzine","Sinapoyl aldehyde","Ethyl icosapentate","Fenfluramine","Pyrrole-2-carboxylic acid","Imidazole-4-acetate","Carnosine","Prilocaine","(R)-Methylmalonate semialdehyde","Neostigmine","Demethylated antipyrine","Lincomycin","Quinaldic acid","Se-Methylselenocysteine","Xanthoxic acid","2-Keto-glutaramic acid","Taraxerol","Methoxamine","Cyclizine","Tetracaine","Benzoylagmatine","Sotalol","Niacinamide","Tentoxin","Diaminopimelic acid","Dopamine","Serotonin","Deoxyuridine","Brevianamide F","(S)-1-Phenylethanol","4-Guanidinobutanoic acid","Cholesterol","Epiandrosterone","Zeranol","Soyasapogenol A","Soyasapogenol B","Flutamide","Pentaporphyrin I","Gitogenin","Anhydroglycinol","Racemethionine","5,6-Dihydro-5-fluorouracil","8-Hydroxyquinoline","2-Dehydropantoate","Nicotianamine","Indolelactic acid","Yamogenin","Tryptamine","meso-2,6-Diaminoheptanedioate","N-Acetylserotonin","8-HETE","(+)-Demethoxyaschantin","L-Kynurenine","Ropivacaine","10-Nitrolinoleic acid","cis-9,10-Epoxystearic acid","Harmine","Hellebrigenin","5-Aminolevulinic acid","Phytosphingosine","2-Methylserine","Cytosine","beta-Zearalanol","Fisetin","Xanthoxin","Mibefradil","Levamisole","Ergocalciferol","2-Acetamidofluorene","17a-Estradiol","Coumarin","Spermine","N-Acetyl-beta-glucosaminylamine","2-Dehydro-3-deoxy-L-rhamnonate","7-Oxodeoxycholate","2-Phenylethanol","17-HYDROXYPROGESTERONE","2-Hydroxy-3-(4-hydroxyphenyl)propenoic acid","Palmitoyl ethanolamide","L-Arginine","Nevirapine","Ethirimol","Enterolactone","4-Hydroxy-2-quinolone","epsilon-(gamma-L-Glutamyl)-L-lysine","N8-Acetylspermidine","Indole-3-acetate","Galactosylsphingosine","Lenacil","1,1-Dimethylbiguanide","N5-(L-1-Carboxyethyl)-L-ornithine","Nicotinic acid mononucleotide","N-Succinyl-L,L-2,6-diaminopimelate","2-Hydroxybutyric acid","Quinolinic acid","beta-D-3-Ribofuranosyluric acid","(S)-N-Methylcoclaurine","p-Octopamine","Malonoben","Homocitrulline","Diphenhydramine","Choline sulfate","5-KETE","Gamma-Tocotrienol","2-Hydroxyphenethylamine","dAMP","Allocystathionine","Cortisone","9(S)-HOT","Cinchonidine","Citraconic acid","Repaglinide","Inosine","Purine","S-Methyl-L-methionine","Norepinephrine","Lumichrome","Dimethylglycine","L-Histidine trimethylbetaine","1D-1-Guanidino-3-amino-1,3-dideoxy-scyllo-inositol","Levonordefrin","Methylimidazoleacetic acid","(R)-3-Ureidoisobutyrate","N-Acetyl-L-phenylalanine","(3S)-3,6-Diaminohexanoate","16-Feruloyloxypalmitate","9,10-Dihydroxystearate","Arachidonic acid","Carnosol","Chitobiose","4a-Carbinolamine tetrahydrobiopterin","Subaphylline","Illudin M","7,8-Dihydropteroic acid","(S)-Norlaudanosoline","Saccharopine","Diethylstilbestrol","Coniferyl aldehyde","trans-1,2-Dihydrobenzene-1,2-diol","Tyramine","Resolvin D2","(S)-5-Amino-3-oxohexanoate","3-Epiecdysone","(3S)-6-Acetamido-3-aminohexanoate","Allocholic acid","Tetrahydropteridine","(S)-3-Hydroxy-N-methylcoclaurine","4-Hydroxybenzoic acid","5,6-DHET","L-Methionine","Dillapiol","Dihydrouracil","Melezitose","(R)-5,6-Dihydrothymine","Ciliatine","Quercetin","Antipyrine","N-Acetylhistamine","Methyldopa","24,25-Dihydrolanosterol","Glycerophosphocholine","Theophylline","13(S)-HpOTrE","Ergothioneine","1-Aminocyclopropanecarboxylic acid","Ethynodiol Diacetate","2,3-Dinor-8-iso prostaglandin F1alpha","Capecitabine","Nalidixic Acid","N-Acetylornithine","5-Amino-2-oxopentanoic acid","Propazine","6-Hydroxymelatonin","Neocnidilide","17a-Hydroxypregnenolone","Picolinic acid","Ancymidol","Aspartylglycosamine","Apigenin","Prephenate","N7-Methylguanosine","Cinobufotalin","3-Amino-4-hydroxybenzoate","Ecdysone","Pyridoxamine","8,9-DiHETrE","4-Hydroxycinnamoylagmatine","N-Acetylhistidine","3,4-Methylenedioxyamphetamine","Orciprenaline","(S)-Reticuline","2-Oxoarginine","N-Acetylputrescine","Aurachin B","O-Acetylcarnitine","Mannitol 1-phosphate","Androsterone","Tocainide","S-Adenosylmethionine","Glycyrrhetinate","4a-Carboxy-4b-methyl-5a-cholesta-8,24-dien-3b-ol","Protriptyline","Imperatorin","Gentamicin X2","L-Pyrrolysine","3-(3,4-Dihydroxyphenyl)pyruvate","2-Hydroxy-6-pentadecylbenzoic acid","Acetylcholine","L-4-Hydroxyphenylglycine","L-Lysine 1,6-lactam","Khellin","Methaqualone","Capsidiol","Isochavicol","Kyotorphin","N-Acetylmuramate","Acetylcysteine","Methyl isobutyl ketone","Homatropine","26-Hydroxyecdysone","Nandrolone","Baclofen","Asymmetric dimethylarginine","Tryptophanol","D-Octopine","(24R,24(1)R)-Fucosterol epoxide","8-Hydroxyguanine","Docosanedioate","5,7-Dihydroxyisoflavone","Dulcin","11,14,15-THETA","Betulin","5-Oxo-1,2-campholide","18-Hydroxycorticosterone","Benzaldehyde","(2S)-Flavanone","1-Pyrroline-2-carboxylic acid","Phosphorylcholine","Methyl (indol-3-yl)acetate","Exemestane","3-Methylindole","Bufalin","Methyl jasmonate","Confertifolin","Iminoarginine","Quinidine","Palmitoyl-L-carnitine","L-Aspartic acid","Procaine","Dyclonine","Ethyl oleate","N(6)-[(Indol-3-yl)acetyl]-L-lysine","2'-Deoxyadenosine","Sarsasapogenin","N-Alpha-acetyllysine","3,3',4'5-Tetrahydroxystilbene","L-Targinine","(2R,3R)-3-Methylornithinyl-N6-lysine","All-trans-hexaprenyl diphosphate","N-Acetyl-L-2-amino-6-oxopimelate","Oxycodone","2-Deoxy-scyllo-inosose","Lacto-N-tetraose","Leucocyanidin","Oxazepam","Ribavirin","Citalopram","N2-Succinyl-L-arginine","Senecionine","O-Acetyl-L-homoserine","Bitertanol","Dihydrothymine","Parthenin","2,3-Butanediol","Medroxyprogesterone","2-Aminobenzoic acid","L-2-Hydroxyglutaric acid","p-Aminobenzoic acid","(R)-b-aminoisobutyric acid","L-4-Hydroxyphenylglycyl-L-arginine","5alpha-Ergosta-7,22-diene-3beta,5-diol","11b-Hydroxyandrost-4-ene-3,17-dione","Epinephrine","Metaxalone","N-Methyl-L-glutamic acid","Dethiobiotin","Clozapine","Rutin","Deoxycholic acid","N1-Acetylspermine","Anisomycin","Estrone","Mestranol","(2R,5S)-2,5-Diaminohexanoate"],"additional_accession":[]},"is_claimable":false,"name":"UHPLC-MS/MS Untargeted Metabolomics Profiling of Cecal Content in Three Chicken Breeds","description":"This study applied an untargeted metabolomics approach to analyze cecal content samples from three chicken breeds (Wenchang chicken, White-ear Yellow chicken, and Recessive White chicken) using UHPLC-MS/MS (Vanquish UHPLC coupled with Q Exactive HFX Orbitrap). A total of 90 samples (30 per breed) plus 8 pooled QC samples were analyzed. Metabolites were extracted with methanol/acetonitrile (1:1, v/v), and data were acquired in positive and negative ionization modes. Raw data were converted to mzXML format by MSConvert (ProteoWizard v3.0.8789) and processed using the R XCMS package for peak detection, retention time correction, and alignment. Metabolites were annotated against HMDB, MassBank, LipidMaps, mzCloud, KEGG, and an in-house database. Data normalization was performed using QC-RLSC (LOESS signal correction), and features with QC RSD > 30% were filtered out. Multivariate statistics (PCA and OPLS-DA) were conducted using the R package ropls to distinguish metabolic profiles. Differential metabolites were screened using a two-tiered strategy: for 2 dpi, P < 0.05 and VIP > 1.0 were used; for 4 dpi and 7 dpi, VIP > 1.0, |log2FC| > 1, and FDR-adjusted P < 0.05 were applied. Pathway enrichment analysis was performed using MetaboAnalyst; no pathway reached P < 0.05, and pathways with P < 0.2 were considered as trends.
Breed name mapping: In the commercial dataset folders, breeds are abbreviated as WCJ (Wenchang chicken), BEJ (White-ear Yellow chicken), and YXB (Recessive White chicken). These correspond to WCC, WEYC, and RWFC, respectively, as used in this study and the manuscript.
Note: The associated manuscript analyzes and reports conclusions based exclusively on the Wenchang chicken breed; data from the other two breeds (YXB and BEJ) are included for project-level transparency. They have not been used in the analyses presented in this manuscript.
Data source clarification: The manuscript analyses are based on the 2023 commercial metabolomics report, which was generated from the complete original raw data at that time. The raw data recovered in 2026 are deposited in MetaboLights (MTBLS15811) and in the Zenodo record for archival and transparency purposes. A small number of recovered files have reduced scan counts due to the original corruption; however, all files can be opened, and this does not affect the manuscript conclusions, which rely on the 2023 commercial report.
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