{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001248","ANALYSIS_ID":"AN002072","VERSION":"1","CREATED_ON":"September 9, 2019, 1:18 pm"},

"PROJECT":{"PROJECT_TITLE":"The cecal and fecal microbiomes and metabolomes of horses before and after metronidazole administration","PROJECT_SUMMARY":"Metronidazole (15mg/kg BID PO) was given to horses (n=5) with in-dwelling cecal cannulas. The study was suspended after the fifth dose (day 3) due to adverse gastrointestinal effects. Cecal and fecal samples were obtained before and after (Days days -52, -28, -14, 0, 7, 14, 28 and 52) metronidazole administration. DNA was extracted from the cecal and fecal samples, and 16S rRNA genes were sequenced. The bacterial diversity and composition of each sample was determined. Richness and evenness indices were significantly decreased by metronidazole administration in both cecal and fecal samples, but overall composition was only significantly changed in fecal samples on Day 3 (ANOSIM, p=0.008). The most dominant phyla were Bacteroidetes and Firmicutes in all groups examined. In fecal samples, significant changes at the phyla Actinobacteria, Spirochaetes, Lentisphaerae and Verrucomicrobia occurred on Day 3, which correlated with clinical signs of gastrointestinal disease. Analysis of the predicted microbial functions using PICRUSt indicated changes associated with metronidazole in fecal samples. The metabolome was characterized by mass spectrometry-based methods. Fecal, but not cecal metabolites were affected by metronidazole. The fecal metabolites affected represented diverse metabolic pathways such as nucleic acid metabolism, secondary bile metabolism, fatty acid synthesis/degradation/elongation or metabolism and sugar metabolism.","INSTITUTE":"Texas A&M","DEPARTMENT":"Department of Small Animal Clinical Sciences","LABORATORY":"Gastrointestinal Laboratory","LAST_NAME":"Arnold","FIRST_NAME":"Carolyn","ADDRESS":"4474 TAMU","EMAIL":"carnold@cvm.tamu.edu","PHONE":"979 845 3541"},

"STUDY":{"STUDY_TITLE":"The cecal and fecal metabolomes of horses before and after metronidazole administration","STUDY_SUMMARY":"Metronidazole (15mg/kg BID PO) was given to horses (n=5) with in-dwelling cecal cannulas. The study was suspended after the fifth dose (day 3) due to adverse gastrointestinal effects. Cecal and fecal samples were obtained before and after (Days days -52, -28, -14, 0, 7, 14, 28 and 52) metronidazole administration. The metabolome was characterized by mass spectrometry-based methods. Fecal, but not cecal metabolites were affected by metronidazole. The fecal metabolites affected represented diverse metabolic pathways such as nucleic acid metabolism, secondary bile metabolism, fatty acid synthesis/degradation/elongation or metabolism and sugar metabolism.","INSTITUTE":"Texas A&M","DEPARTMENT":"Department of Small Animal Clinical Sciences","LABORATORY":"Gastrointestinal Laboratory","LAST_NAME":"Arnold","FIRST_NAME":"Carolyn","ADDRESS":"4474 TAMU","EMAIL":"carnold@cvm.tamu.edu","PHONE":"979 845 3541"},

"SUBJECT":{"SUBJECT_TYPE":"Other","SUBJECT_SPECIES":"Equus caballus","TAXONOMY_ID":"9796"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD0_030",
"Factors":{"organ":"fecal","Day":"D0","Treatment":"No"}
},
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD0_031",
"Factors":{"organ":"fecal","Day":"D0","Treatment":"No"}
},
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD0_032",
"Factors":{"organ":"fecal","Day":"D0","Treatment":"No"}
},
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD0_033",
"Factors":{"organ":"fecal","Day":"D0","Treatment":"No"}
},
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD28_034",
"Factors":{"organ":"fecal","Day":"D28","Treatment":"Yes"}
},
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD3_031",
"Factors":{"organ":"fecal","Day":"D3","Treatment":"Yes"}
},
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD7_032",
"Factors":{"organ":"fecal","Day":"D7","Treatment":"Yes"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD0_017",
"Factors":{"organ":"fecal","Day":"D0","Treatment":"No"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD-14_016",
"Factors":{"organ":"fecal","Day":"D-14","Treatment":"No"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD14_020",
"Factors":{"organ":"fecal","Day":"D14","Treatment":"Yes"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD-28_015",
"Factors":{"organ":"fecal","Day":"D-28","Treatment":"No"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD28_021",
"Factors":{"organ":"fecal","Day":"D28","Treatment":"Yes"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD3_018",
"Factors":{"organ":"fecal","Day":"D3","Treatment":"Yes"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD7_019",
"Factors":{"organ":"fecal","Day":"D7","Treatment":"Yes"}
},
{
"Subject ID":"Ernie",
"Sample ID":"ErnieD0_024",
"Factors":{"organ":"fecal","Day":"D0","Treatment":"No"}
},
{
"Subject ID":"Ernie",
"Sample ID":"ErnieD-14_023",
"Factors":{"organ":"fecal","Day":"D-14","Treatment":"No"}
},
{
"Subject ID":"Ernie",
"Sample ID":"ErnieD14_027",
"Factors":{"organ":"fecal","Day":"D14","Treatment":"Yes"}
},
{
"Subject ID":"Ernie",
"Sample ID":"ErnieD-28_022",
"Factors":{"organ":"fecal","Day":"D-28","Treatment":"No"}
},
{
"Subject ID":"Ernie",
"Sample ID":"ErnieD3_025",
"Factors":{"organ":"fecal","Day":"D3","Treatment":"Yes"}
},
{
"Subject ID":"Ernie",
"Sample ID":"ErnieD7_026",
"Factors":{"organ":"fecal","Day":"D7","Treatment":"Yes"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD0_003",
"Factors":{"organ":"fecal","Day":"D0","Treatment":"No"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD-14_002",
"Factors":{"organ":"fecal","Day":"D-14","Treatment":"No"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD14_006",
"Factors":{"organ":"fecal","Day":"D14","Treatment":"Yes"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD-28_001",
"Factors":{"organ":"fecal","Day":"D-28","Treatment":"No"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD28_007",
"Factors":{"organ":"fecal","Day":"D28","Treatment":"Yes"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD3_004",
"Factors":{"organ":"fecal","Day":"D3","Treatment":"Yes"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD7_005",
"Factors":{"organ":"fecal","Day":"D7","Treatment":"Yes"}
},
{
"Subject ID":"Steve",
"Sample ID":"SteveD0_010",
"Factors":{"organ":"fecal","Day":"D0","Treatment":"No"}
},
{
"Subject ID":"Steve",
"Sample ID":"SteveD-14_009",
"Factors":{"organ":"fecal","Day":"D-14","Treatment":"No"}
},
{
"Subject ID":"Steve",
"Sample ID":"SteveD14_013",
"Factors":{"organ":"fecal","Day":"D14","Treatment":"Yes"}
},
{
"Subject ID":"Steve",
"Sample ID":"SteveD-28_008",
"Factors":{"organ":"fecal","Day":"D-28","Treatment":"No"}
},
{
"Subject ID":"Steve",
"Sample ID":"SteveD28_014",
"Factors":{"organ":"fecal","Day":"D28","Treatment":"Yes"}
},
{
"Subject ID":"Steve",
"Sample ID":"SteveD3_011",
"Factors":{"organ":"fecal","Day":"D3","Treatment":"Yes"}
},
{
"Subject ID":"Steve",
"Sample ID":"SteveD7_012",
"Factors":{"organ":"fecal","Day":"D7","Treatment":"Yes"}
},
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD0_058",
"Factors":{"organ":"cecal","Day":"D0","Treatment":"No"}
},
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD-14_057",
"Factors":{"organ":"cecal","Day":"D-14","Treatment":"No"}
},
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD14_060",
"Factors":{"organ":"cecal","Day":"D14","Treatment":"Yes"}
},
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD-28_056",
"Factors":{"organ":"cecal","Day":"D-28","Treatment":"No"}
},
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD28_061",
"Factors":{"organ":"cecal","Day":"D28","Treatment":"Yes"}
},
{
"Subject ID":"Alvin",
"Sample ID":"AlvinD7_059",
"Factors":{"organ":"cecal","Day":"D7","Treatment":"Yes"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD0_047",
"Factors":{"organ":"cecal","Day":"D0","Treatment":"Yes"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD-14_046",
"Factors":{"organ":"cecal","Day":"D-14","Treatment":"No"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD14_049",
"Factors":{"organ":"cecal","Day":"D14","Treatment":"Yes"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD-28_045",
"Factors":{"organ":"cecal","Day":"D-28","Treatment":"No"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD28_050",
"Factors":{"organ":"cecal","Day":"D28","Treatment":"Yes"}
},
{
"Subject ID":"Billy",
"Sample ID":"BillyD7_048",
"Factors":{"organ":"cecal","Day":"D7","Treatment":"Yes"}
},
{
"Subject ID":"Ernie",
"Sample ID":"ErnieD0_053",
"Factors":{"organ":"cecal","Day":"D0","Treatment":"Yes"}
},
{
"Subject ID":"Ernie",
"Sample ID":"ErnieD-14_052",
"Factors":{"organ":"cecal","Day":"D-14","Treatment":"No"}
},
{
"Subject ID":"Ernie",
"Sample ID":"ErnieD14_055",
"Factors":{"organ":"cecal","Day":"D14","Treatment":"Yes"}
},
{
"Subject ID":"Ernie",
"Sample ID":"ErnieD-28_051",
"Factors":{"organ":"cecal","Day":"D-28","Treatment":"No"}
},
{
"Subject ID":"Ernie",
"Sample ID":"ErnieD7_054",
"Factors":{"organ":"cecal","Day":"D7","Treatment":"Yes"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD0_037",
"Factors":{"organ":"cecal","Day":"D0","Treatment":"No"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD-14_036",
"Factors":{"organ":"cecal","Day":"D-14","Treatment":"No"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD14_039",
"Factors":{"organ":"cecal","Day":"D14","Treatment":"Yes"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD-28_035",
"Factors":{"organ":"cecal","Day":"D-28","Treatment":"No"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD28_040",
"Factors":{"organ":"cecal","Day":"D28","Treatment":"Yes"}
},
{
"Subject ID":"Frank",
"Sample ID":"FrankD7_038",
"Factors":{"organ":"cecal","Day":"D7","Treatment":"Yes"}
},
{
"Subject ID":"Steve",
"Sample ID":"SteveD0_042",
"Factors":{"organ":"cecal","Day":"D0","Treatment":"No"}
},
{
"Subject ID":"Steve",
"Sample ID":"SteveD-14_041",
"Factors":{"organ":"cecal","Day":"D-14","Treatment":"No"}
},
{
"Subject ID":"Steve",
"Sample ID":"SteveD14_043",
"Factors":{"organ":"cecal","Day":"D14","Treatment":"Yes"}
},
{
"Subject ID":"Steve",
"Sample ID":"SteveD28_044",
"Factors":{"organ":"cecal","Day":"D28","Treatment":"No"}
},
{
"Subject ID":"Steve",
"Sample ID":"SteveD7_062",
"Factors":{"organ":"cecal","Day":"D7","Treatment":"Yes"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cecal and fecal samples were obtained before and after (Days days -52, -28, -14, 0, 7, 14, 28 and 52) metronidazole administration.","SAMPLE_TYPE":"Feces"},

"TREATMENT":{"TREATMENT_SUMMARY":"Metronidazole (15mg/kg BID PO) was given to horses (n=5) with in-dwelling cecal cannulas. The study was suspended after the fifth dose (day 3) due to severe adverse gastrointestinal effects."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Samples were stored at −80 °C until shipped on dry ice to the West Coast Metabolomics Core (University of California, Davis, CA, USA) using an untargeted approach.(20) Samples were homogenized and extracted. Following resuspension in methanol/chloroform, samples were derivatized by methoxyamine hydrochloride in pyridine and subsequently by N-methyl-N-trimethylsilyltrifluoroacetamide for trimethylsilylation of acidic protons."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 6890N","COLUMN_NAME":"Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Leco Pegasus III GC TOF","INSTRUMENT_TYPE":"GC-TOF","MS_TYPE":"MALDI","ION_MODE":"POSITIVE","MS_COMMENTS":"Raw data files are preprocessed directly after data acquisition and stored as ChromaTOF-specific *.peg files, as generic *.txt result files and additionally as generic ANDI MS *.cdf files. ChromaTOF vs. 2.32 is used for data preprocessing without smoothing, 3 s peak width, baseline subtraction just above the noise level, and automatic mass spectral deconvolution and peak detection at signal/noise levels of 5:1 throughout the chromatogram. Apex masses are reported for use in the BinBase algorithm. Result *.txt files are exported to a data server with absolute spectra intensities and further processed by a filtering algorithm implemented in the metabolomics BinBase database.","MS_RESULTS_FILE":"ST001248_AN002072_Results.txt UNITS:peak intensity Has m/z:Yes Has RT:Yes RT units:Seconds"}

}