About this Dataset

Data From: Lacticaseibacillus Rhamnosus Strain GG (LGG) Regulate Gut Microbial Metabolites, An In Vitro Study Using Three Mature Human Gut Microbial Cultures In A Simulator Of Human Intestinal Microbial Ecosystem (SHIME)

Using the SHIME (an in vitro simulator of the human gut microbiome) we studied changes in the gut metabolome that occurred in response to the administration of the Laticaseibacillus rhamnosus strain GG (LGG). Using fecal inoculum from three healthy human donors, reactors were established representing three colonic regions and both the luminal and mucosal microbiome in those regions. Samples were collected before, during, and after inoculation of the reactors with LGG.

This dataset includes untargeted metabolomics data. Shallow shotgun metagenomic sequencing data can be found in the NCBI Sequence Read Archive associated with BioProject PRJNA893635 : https://www.ncbi.nlm.nih.gov/bioproject/PRJNA893635.

Resources in this dataset:

Resource Title: Batch normalized metabolite peak area data File Name: metabolites_individual_samples_batch_norm_non_imputed.csv
Resource Title: Sample metadata File Name: LGG2_metadata.csv
Organization: Department of Agriculture
Last updated: 2024-03-30T11:19:52.352261
Tags: ars, data-gov, metabolomics, np306, probiotics

Tables

Metabolites Individual Samples Batch Norm Non Imputed 0

@usgov.usda_gov_data_from_lacticaseibacillus_rhamnosus_strain_c8746c53.metabolites_individual_samples_batch_norm_non_imputed_0

247.2 kB
48 rows
2 columns

CREATE TABLE metabolites_individual_samples_batch_norm_non_imputed_0 (
  "n__mevalonate_s_1_pyrroline_5_carboxylate_putrescine_s_3ec1444c" VARCHAR  -- ,mevalonate,S-1-pyrroline-5-carboxylate,putrescine,spermidine,1-methyladenine,"cytidine 2',3'-cyclic Monophosphate",alpha-ketoglutarate,kynurenate,3-hydroxyisobutyrate,3-hydroxy-3-methylglutarate,3-phosphoglycerate,3-phosphoserine,cholate,4-hydroxyphenylacetate,"5,6-dihydrothymine",hypoxanthine,guanine,quinolinate,N-formylkynurenine,N('1)-acetylspermidine,"N6,N6,N6-trimethyllysine",N-acetylputrescine,N-formylmethionine,glycolate (hydroxyacetate),"adenosine 3',5'-cyclic Monophosphate (cAMP)",adenosine 5'-monophosphate (AMP),5-methylthioadenosine (MTA),N6-methyladenosine,arachidonate (20:4n6),arginine,aspartate,2-hydroxyphenylacetate,3-(4-hydroxyphenyl)lactate,phenylpyruvate,beta-alanine,carnosine,biotin,succinate,3-hydroxybutyrate (BHBA),cholesterol,choline Phosphate,creatinine,cysteinylglycine,cystine,sphingosine,deoxycholate,cystathionine,homocysteine,sphinganine,fumarate,gamma-glutamylglutamate,glutarate (C5-DC),glycine,glycocholate,guanidinoacetate,histamine,histidine,inosine,myo-inositol,2-aminoadipate,citrulline,leucine,lithocholate,lysine,malate,methionine,methylmalonate (MMA),ethanolamine,nicotinamide,ornithine,orotate,phenylalanine,phosphate,phosphoenolpyruvate (PEP),phytosphingosine,proline,lactate,pyridoxal,riboflavin (Vitamin B2),salicylate,serine,spermine,taurine,urea,uridine,2'-deoxyuridine,trans-urocanate,glutamate,glutamine,threonine,tryptophan,valine,nicotinate,pyridoxamine,glucose,adenosine,betaine,cysteine,dimethylglycine,alanine,tyrosine,malonate,pseudouridine,pyruvate,uracil,xylose,cytidine,arabinose,uridine 5'-monophosphate (UMP),thymidine,thiamin (Vitamin B1),adenine,cytosine,thymine,margarate (17:0),nonadecanoate (19:0),arachidate (20:0),maltose,asparagine,dihydroorotate,heptanoate (7:0),caproate (6:0),pyridoxine (Vitamin B6),pentadecanoate (15:0),trans-4-hydroxyproline,allantoin,galactitol (dulcitol),xanthine,5-oxoproline,picolinate,sarcosine,pantothenate,pipecolate,phosphoethanolamine,glycerate,3-ureidopropionate,N-acetylleucine,N-acetylmethionine,N-acetylvaline,erucate (22:1n9),tryptamine,guanosine,gamma-glutamyltyrosine,alpha-tocopherol,N-acetylalanine,4-acetamidobutanoate,3-aminoisobutyrate,chenodeoxycholate,citrate,"5,6-dihydrouracil",tyramine,urate,ursodeoxycholate,valerate (5:0),oleoyl Ethanolamide,gamma-glutamylglutamine,4-hydroxyphenylpyruvate,butyrate/isobutyrate (4:0),N-acetylneuraminate,N(1)-acetylspermine,phenethylamine,creatine,dihomo-linoleate (20:2n6),gamma-glutamylhistidine,N1-methyladenosine,thymidine 5'-monophosphate,glycerol,choline,anthranilate,gamma-glutamylleucine,nicotinamide Adenine Dinucleotide (NAD+),nicotinamide Ribonucleotide (NMN),beta-hydroxyisovalerate,palmitoyl Ethanolamide,N-palmitoyl-sphingosine (d18:1/16:0),1-palmitoyl-2-oleoyl-GPE (16:0/18:1),1-palmitoyl-2-linoleoyl-GPC (16:0/18:2),1-palmitoyl-2-oleoyl-GPC (16:0/18:1),biopterin,glycochenodeoxycholate,taurocholate,taurodeoxycholate,azelate (C9-DC),methylsuccinate,tricarballylate,ethylmalonate,carnitine,benzoate,3-phenylpropionate (hydrocinnamate),phenylacetate,suberate (C8-DC),3-methyl-2-oxovalerate,methionine Sulfoxide,3-methylhistidine,5-hydroxylysine,4-guanidinobutanoate,5-(2-Hydroxyethyl)-4-methylthiazole,agmatine,cadaverine,2'-deoxyinosine,alpha-lipoate,glucuronate,glycerol 3-phosphate,histidinol,imidazole Lactate,indole,kynurenine,glycerophosphorylcholine (GPC),allo-threonine,N-acetylglutamate,N-acetylmuramate,N-alpha-acetylornithine,xanthosine,ribitol,2-isopropylmalate,glycodeoxycholate,quinate,5-aminovalerate,homoserine,indolelactate,glycylvaline,gamma-glutamylphenylalanine,4-methyl-2-oxopentanoate,"1,2-dipalmitoyl-GPC (16:0/16:0)",alpha-hydroxyisocaproate,maleate,isovalerate (i5:0),1-methylguanidine,2-hydroxyoctanoate,mevalonolactone,3-hydroxyoctanoate,phenyllactate (PLA),N-acetylaspartate (NAA),harmane,acetylcarnitine (C2),isocaproate (i6:0),cysteine S-sulfate,6-hydroxynicotinate,1-palmitoylglycerol (16:0),hesperidin (hesperetin 7-rutinoside),tartronate (hydroxymalonate),oxalate (ethanedioate),erythritol,"2,3-dimethylsuccinate",4-hydroxybenzoate,adipate (C6-DC),naringenin,3-methyl-2-oxobutyrate,8-hydroxyoctanoate,homocitrulline,3-hydroxypalmitate,N-acetylglycine,ribonate,p-cresol,threonate,galactonate,glycerol 2-phosphate,indoleacetate,hesperetin,1-methylhistidine,nicotinic Acid Mononucleotide (NaMN),3-dehydrocholate,7-ketodeoxycholate,6-oxolithocholate,7-ketolithocholate,androsterone Sulfate,indolepropionate,trigonelline (N'-methylnicotinate),dodecanedioate (C12-DC),N-acetyltyrosine,pyridoxate,threonylphenylalanine,gamma-glutamylvaline,O-acetylhomoserine,1-methylguanine,8-hydroxy Guanosine,5-hydroxyhexanoate,propionylglycine,butyrylglycine,2-hydroxyadipate,2-methylbutyrylglycine,pro-hydroxy-pro,"1,3-propanediol",docosadienoate (22:2n6),10-undecenoate (11:1n1),1-methylhistamine,4-imidazoleacetate,1-methyl-4-imidazoleacetate,sebacate (C10-DC),daidzein,N-acetylglutamine,N-acetyltryptophan,N-acetylphenylalanine,N-acetylasparagine,glycylleucine,gamma-glutamyl-epsilon-lysine,1-palmitoyl-GPC (16:0),N-acetylarginine,phenylacetylglycine,N-acetylisoleucine,10-nonadecenoate (19:1n9),N-acetylhistidine,gamma-glutamylglycine,stachydrine,alpha-hydroxyisovalerate,nicotinamide Riboside,ophthalmate,gamma-glutamylmethionine,gamma-glutamylthreonine,p-cresol Sulfate,nicotinate Ribonucleoside,erythronate*,eicosenoate (20:1),linolenate [alpha Or Gamma,
  "n__18_3n3_or_6_isovalerylcarnitine_c5_1_methylurate_1__aa1a1424" VARCHAR  -- (18:3n3 Or 6)],isovalerylcarnitine (C5),1-methylurate,1-methylxanthine,beta-guanidinopropanoate,"N2,N2-dimethylguanosine",N6-carbamoylthreonyladenosine,"5,6-dihydrouridine",3-(3-amino-3-carboxypropyl)uridine*,3-ketosphinganine,5-methyluridine (ribothymidine),isovalerylglycine,3-hydroxydodecanedioate*,7-methylguanine,1-stearoyl-GPE (18:0),N1-Methyl-2-pyridone-5-carboxamide,gamma-glutamylisoleucine*,4-hydroxybutyrate (GHB),phenol Sulfate,3-ureidoisobutyrate,glutamine Degradant*,2-hydroxy-3-methylvalerate,ferulate,homostachydrine*,1-palmitoyl-GPE (16:0),1-oleoyl-GPE (18:1),N-acetylcitrulline,2-hydroxypalmitate,gulonate*,isobutyrylglycine,cholesterol Sulfate,undecanedioate (C11-DC),glycerophosphoethanolamine,glycerophosphoinositol*,3-(3-hydroxyphenyl)propionate,2-dimethylaminoethanol,ectoine,deoxycarnitine,N6-succinyladenosine,N2-acetyllysine,alpha-hydroxycaproate,"3,4-dihydroxybutyrate",hexanoylglutamine,N6-acetyllysine,dihomo-linolenate (20:3n3 Or N6),mannitol/sorbitol,pyrraline,N6-carboxymethyllysine,glycylisoleucine,methylphosphate,dimethylarginine (SDMA + ADMA),N-methylalanine,gamma-glutamylalanine,N-acetylserine,chiro-inositol,alanylleucine,cyclo(leu-pro),cyclo(phe-pro),cyclo(gly-phe),cyclo(gly-pro),N-methylproline,pregnenediol Sulfate (C21H34O5S)*,2-hydroxyglutarate,gamma-CEHC,N-acetyl-beta-alanine,palmitoyl Sphingomyelin (d18:1/16:0),cysteine Sulfinic Acid,"N1,N12-diacetylspermine",ergothioneine,indole-3-carboxylate,4-cholesten-3-one,N-acetyl-cadaverine,S-carboxymethyl-L-cysteine,(12 Or 13)-methylmyristate (a15:0 Or I15:0),maltol,"2R,3R-dihydroxybutyrate",alpha-ketoglutaramate*,piperidine,"2,3-dihydroxyisovalerate",5-(galactosylhydroxy)-L-lysine,formiminoglutamate,hydantoin-5-propionate,sulfate*,4-hydroxyglutamate,pantoate,sedoheptulose,cyclo(his-pro),argininate*,5-aminoimidazole-4-carboxamide,solanidine,2-oxoarginine*,cis-4-decenoate (10:1n6)*,1-methyl-5-imidazoleacetate,glycoursodeoxycholate,tauroursodeoxycholate,ursocholate,3-(4-hydroxyphenyl)propionate,(14 Or 15)-methylpalmitate (a17:0 Or I17:0),1-(1-enyl-palmitoyl)-GPE (P-16:0)*,1-(1-enyl-stearoyl)-GPE (P-18:0)*,enterolactone,2-oxindole-3-acetate,isoleucylglycine,leucylglycine,lysylleucine,valylleucine,N-palmitoyltaurine,N-stearoyltaurine,2-O-methylascorbic Acid,carboxyethyl-GABA,beta-citrylglutamate,ponciretin,trimethylamine N-oxide,N6-methyllysine,dihydroferulate,imidazole Propionate,tyrosol,phenylalanylglycine,phenylalanylalanine,tyrosylglycine,tryptophylglycine,valylglycine,prolylglycine,N-palmitoylglycine,mannonate*,phenylacetylphenylalanine,"N6,N6-dimethyladenosine",lanthionine,N-methyltaurine,N-propionylmethionine,pterin,tryptophol,dimethyl Sulfone,o-Tyrosine,2-piperidinone,indolin-2-one,"2,8-quinolinediol Sulfate",3-hydroxyadipate,1-methyl-beta-carboline-3-carboxylic Acid,6-oxopiperidine-2-carboxylate,N-delta-acetylornithine,2-aminoheptanoate,N-formylanthranilic Acid,3-methoxytyramine Sulfate,methionine Sulfone,"cyclo(phe-pro) (L,D)*",1-(1-enyl-oleoyl)-GPE (P-18:1)*,fructosyllysine,ferulic Acid 4-sulfate,N-acetylmethionine Sulfoxide,N-acetyltaurine,acetylagmatine,2-keto-3-deoxy-gluconate,isovaleryltryptophan,alpha-CEHC Sulfate,"sphingomyelin (d18:1/24:1, D18:2/24:0)*","5alpha-androstan-3alpha,17beta-diol Monosulfate (2)",N-formylphenylalanine,arabonate/xylonate,ribulose/xylulose,N-acetylhistamine,vanillactate,"sphingomyelin (d18:1/20:0, D16:1/22:0)*",behenoyl Sphingomyelin (d18:1/22:0)*,lignoceroyl Sphingomyelin (d18:1/24:0),3-hydroxyhexanoate,N-acetylkynurenine (2),arabitol/xylitol,N-acetylglucosamine/N-acetylgalactosamine,citraconate/glutaconate,linoleoyl Ethanolamide,cyclo(his-phe),"sphingomyelin (d18:1/17:0, D17:1/18:0, D19:1/16:0)",2-hydroxybutyrate/2-hydroxyisobutyrate,2-methylcitrate/homocitrate,palmitoyl Dihydrosphingomyelin (d18:0/16:0)*,tricosanoyl Sphingomyelin (d18:1/23:0)*,1-stearoyl-2-linoleoyl-GPC (18:0/18:2)*,gamma-tocopherol/beta-tocopherol,N-palmitoyl-sphinganine (d18:0/16:0),thioproline,isovalerylphenylalanine*,2-acetamidobutanoate,isocitric Lactone,2-methylserine,glycocholate Glucuronide (1),glycosyl-N-palmitoyl-sphingosine (d18:1/16:0),4-acetamidobenzoate,3-methylglutarate/2-methylglutarate,2'-O-methyluridine,2-hydroxybehenate,N-(2-hydroxypalmitoyl)-sphingosine (d18:1/16:0(2OH)),glycerophosphoserine*,"ceramide (d18:1/14:0, D16:1/16:0)*","ceramide (d18:1/17:0, D17:1/18:0)*","ceramide (d18:1/20:0, D16:1/22:0, D20:1/18:0)*",arachidoylcarnitine (C20)*,"N,N,N-trimethyl-5-aminovalerate",2-methylbutyryltryptophan*,2-hydroxyarachidate*,cytidine 2' Or 3'-monophosphate (2' Or 3'-CMP),lyxonate,dodecenedioate (C12:1-DC)*,hexadecenedioate (C16:1-DC)*,octadecenedioate (C18:1-DC),3-formylindole,diacetylspermidine*,glutamine Conjugate Of C6H10O2 (2)*,N-carbamoylvaline,3-amino-2-piperidone,"N,N-dimethylalanine",3-indoleglyoxylic Acid,2-hydroxysebacate,enterolactone Sulfate,"N6,N6-dimethyllysine",gamma-CEHC Sulfate,cholic Acid Glucuronide,deoxycholic Acid Glucuronide,lithocholate Sulfate (1),"N,N-dimethyl-5-aminovalerate",12-ketolithocholate,"cyclo(his-pro) (D,L)*",hydroxypalmitoyl Sphingomyelin (d18:1/16:0(OH))**,carboxymethylarginine,pregnenetriol Sulfate*,"hydroxy-N6,N6,N6-trimethyllysine*",N-carboxymethylalanine,(S)-a-amino-omega-caprolactam,2-hydroxy-4-(methylthio)butanoic Acid,pentose Acid*,N-butyryl-phenylalanine,N-isobutyryl-phenylalanine,N-butyryl-leucine,N-butyryl-isoleucine,N-carbamoylputrescine,S-carboxyethylcysteine,dibutyl Sulfosuccinate,4-quinolinecarboxylic Acid,chenodeoxycholic Acid Sulfate (1),deoxycholic Acid 12-sulfate*,4-chlorobenzoic Acid,"2,4-di-tert-butylphenol",butyrylputrescine/isobutyrylputrescine,flunixin,"N,N-dimethyl-pro-pro",oxindolylalanine,X-11787,X-11979,X-12013,X-12100,X-12680,X-13007,X-13507,X-13684,X-14056,X-14254,X-14263,X-14351,X-14383,X-14416,X-14422,X-14454,X-14904,X-15136,X-15245,X-15853,X-15854,X-15956,X-17010,X-17749,X-17808,X-17843,X-17877,X-17960,X-17969,X-18887,X-19751,X-19929,X-20172,X-20718,X-20728,X-20747,X-21286,X-21796,X-23481,X-23482,X-23639,X-23737,X-23739,X-23745,X-23908,X-24137,X-24139,X-24142,X-24144,X-24147,X-24152,X-24153,X-24160,X-24174,X-24425,X-24456,X-24608,X-24931,X-25007,X-25009,X-25010,X-25011,X-25012,X-25013,X-25036,X-25037,X-25041,X-25042,X-25045,X-25047,X-25053,X-25054,X-25057,X-25071,X-25076,X-25082,X-25083,X-25089,X-25095,X-25100,X-25103,X-25109,X-25521,X-25536,X-25737,X-25743,X-25817,X-25836,X-25837,X-25940,X-25948,X-25957,X-26094,X-26097,X-26127
);