{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002014","ANALYSIS_ID":"AN003282","VERSION":"1","CREATED_ON":"November 18, 2021, 8:53 am"},

"PROJECT":{"PROJECT_TITLE":"PolyFerm","PROJECT_SUMMARY":"The increased prevalence of Salmonella spp. resistance in swine spurs the search for alternatives to antibiotics. Microcin J25 (MccJ25), a bacteriocin produced by Escherichia coli, is a potent inhibitor of several pathogenic bacteria including Salmonella enterica. In this study, we aimed to evaluate in vitro the impact of MccJ25 on the metabolic activity of the swine colonic microbiota. The PolyFermS in vitro continuous fermentation model was used with modified Macfarlane medium to simulate the porcine proximal colon. During 35 days of fermentation, a first-stage reactor containing immobilized swine fecal microbiota fed two second-stage control and test reactors operated in parallel and used to test the effectsof MccJ25 on the composition and the metabolic activity of the microbiota. Reuterin, a broad spectrum antimicrobial produced by Limosilactobacillus reuteri and the antibiotic rifampicin were tested for comparison. LC-MS analysis of the cell extracts was used to assess the bacteriocin/antibiotic degradation products and monitor changes in the swine colonic microbiota metabolome.","INSTITUTE":"National Museum of Natural History","LABORATORY":"Communication Molecules and Adaptation of Microorganisms","LAST_NAME":"Zirah","FIRST_NAME":"Severine","ADDRESS":"Museum national d'Histoire naturelle, Unité MCAM UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, FRANCE","EMAIL":"severine.zirah@mnhn.fr","PHONE":"+33(0)1 40 79 31 40"},

"STUDY":{"STUDY_TITLE":"Impact of microcin J25 on the porcine microbiome in a continuous culture model","STUDY_SUMMARY":"The increased prevalence of Salmonella spp. resistance in swine spurs the search for alternatives to antibiotics. Microcin J25 (MccJ25), a bacteriocin produced by Escherichia coli, is a potent inhibitor of several pathogenic bacteria including Salmonella enterica. In this study, we aimed to evaluate in vitro the impact of MccJ25 on the metabolic activity of the swine colonic microbiota. The PolyFermS in vitro continuous fermentation model was used with modified Macfarlane medium to simulate the porcine proximal colon. During 35 days of fermentation, a first-stage reactor containing immobilized swine fecal microbiota fed two second-stage control and test reactors operated in parallel and used to test the effectsof MccJ25 on the composition and the metabolic activity of the microbiota. Reuterin, a broad spectrum antimicrobial produced by Limosilactobacillus reuteri and the antibiotic rifampicin were tested for comparison. LC-MS analysis of the cell extracts was used to assess the bacteriocin/antibiotic degradation products and monitor changes in the swine colonic microbiota metabolome.","INSTITUTE":"National Museum of Natural History","LAST_NAME":"Zirah","FIRST_NAME":"Severine","ADDRESS":"Museum national d'Histoire naturelle, Unité MCAM UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, FRANCE","EMAIL":"severine.zirah@mnhn.fr","PHONE":"+33(0)1 40 79 31 40","NUM_GROUPS":"6"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"swine colonic microbiota","GENDER":"Not applicable"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"SalmoF2_t2_RA2_01_3057",
"Factors":{"group":"Salmo","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"100_Intra_SalmoF2_t2_RA2_01_3057.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t6_RA3_01_3060",
"Factors":{"group":"Salmo","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"101_Intra_SalmoF1_t6_RA3_01_3060.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF1_t-1_RA4_01_3061",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"102_Intra_RifaF1_t-1_RA4_01_3061.cdf","time":"-1","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t6_RA5_01_3062",
"Factors":{"group":"Reut","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"103_Intra_ReutF2_t6_RA5_01_3062.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF1_J16_RA6_01_3063",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"104_Intra_StabF1_J16_RA6_01_3063.cdf","time":"NA","time_stab":"16"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF1_t0_RA7_01_3064",
"Factors":{"group":"Rifa","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"105_Intra_RifaF1_t0_RA7_01_3064.cdf","time":"-","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F2_t0_RA8_01_3065",
"Factors":{"group":"J25","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"106_Intra_J25F2_t0_RA8_01_3065.cdf","time":"-","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F1_t24_RB1_01_3066",
"Factors":{"group":"J25","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"107_Intra_J25F1_t24_RB1_01_3066.cdf","time":"24","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF1_t8_RB2_01_3067",
"Factors":{"group":"Reut","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"108_Intra_ReutF1_t8_RB2_01_3067.cdf","time":"8","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF1_t0_RB3_01_3068",
"Factors":{"group":"Reut","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"109_Intra_ReutF1_t0_RB3_01_3068.cdf","time":"-","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t10_RB4_01_3069",
"Factors":{"group":"Reut","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"110_Intra_ReutF2_t10_RB4_01_3069.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF1_t10_RB5_01_3070",
"Factors":{"group":"Reut","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"111_Intra_ReutF1_t10_RB5_01_3070.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t6_RB6_01_3071",
"Factors":{"group":"Reut","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"112_Intra_ReutF2_t6_RB6_01_3071.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F2_t12_RB7_01_3072",
"Factors":{"group":"J25","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"113_Intra_J25F2_t12_RB7_01_3072.cdf","time":"12","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F1_t4_RB8_01_3073",
"Factors":{"group":"J25","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"114_Intra_J25F1_t4_RB8_01_3073.cdf","time":"4","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF1_t10_RC1_01_3074",
"Factors":{"group":"Rifa","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"115_Intra_RifaF1_t10_RC1_01_3074.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t2_RC2_01_3075",
"Factors":{"group":"Rifa","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"116_Intra_RifaF2_t2_RC2_01_3075.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF2_J27_RC3_01_3078",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"117_Intra_StabF2_J27_RC3_01_3078.cdf","time":"NA","time_stab":"27"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF1_t0_RC4_01_3079",
"Factors":{"group":"Reut","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"118_Intra_ReutF1_t0_RC4_01_3079.cdf","time":"-","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t2_RC5_01_3080",
"Factors":{"group":"Reut","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"119_Intra_ReutF2_t2_RC5_01_3080.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF1_t2_RC6_01_3081",
"Factors":{"group":"Rifa","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"120_Intra_RifaF1_t2_RC6_01_3081.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF2_t8_RC7_01_3082",
"Factors":{"group":"Salmo","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"121_Intra_SalmoF2_t8_RC7_01_3082.cdf","time":"8","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF2_t6_RC8_01_3083",
"Factors":{"group":"Salmo","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"122_Intra_SalmoF2_t6_RC8_01_3083.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF2_J23_RD1_01_3084",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"122_Intra_StabF2_J23_RD1_01_3084.cdf","time":"NA","time_stab":"23"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t10_RD2_01_3085",
"Factors":{"group":"Reut","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"123_Intra_ReutF2_t10_RD2_01_3085.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F2_t12_RD3_01_3086",
"Factors":{"group":"J25","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"124_Intra_J25F2_t12_RD3_01_3086.cdf","time":"12","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF1_t12_RD4_01_3087",
"Factors":{"group":"Rifa","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"125_Intra_RifaF1_t12_RD4_01_3087.cdf","time":"12","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t2_RD5_01_3088",
"Factors":{"group":"Rifa","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"126_Intra_RifaF2_t2_RD5_01_3088.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t-1_RD6_01_3089",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"127_Intra_SalmoF1_t-1_RD6_01_3089.cdf","time":"-1","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF2_t10_RD7_01_3090",
"Factors":{"group":"Salmo","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"128_Intra_SalmoF2_t10_RD7_01_3090.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t0_RD8_01_3091",
"Factors":{"group":"Salmo","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"129_Intra_SalmoF1_t0_RD8_01_3091.cdf","time":"-","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF2_J27_RE1_01_3092",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"130_Intra_StabF2_J27_RE1_01_3092.cdf","time":"NA","time_stab":"27"}
},
{
"Subject ID":"-",
"Sample ID":"StabF1_J20_RE2_01_3093",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"131_Intra_StabF1_J20_RE2_01_3093.cdf","time":"NA","time_stab":"20"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t6_RE3_01_3096",
"Factors":{"group":"Rifa","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"132_Intra_RifaF2_t6_RE3_01_3096.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F1_t0_RE4_01_3097",
"Factors":{"group":"J25","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"133_Intra_J25F1_t0_RE4_01_3097.cdf","time":"-","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t12_RE5_01_3098",
"Factors":{"group":"Reut","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"134_Intra_ReutF2_t12_RE5_01_3098.cdf","time":"12","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t8_RE6_01_3099",
"Factors":{"group":"Rifa","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"135_Intra_RifaF2_t8_RE6_01_3099.cdf","time":"8","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF2_t6_RE7_01_3100",
"Factors":{"group":"Salmo","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"136_Intra_SalmoF2_t6_RE7_01_3100.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF1_t2_RE8_01_3101",
"Factors":{"group":"Reut","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"137_Intra_ReutF1_t2_RE8_01_3101.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t-1_BA1_01_3102",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"138_Intra_SalmoF1_t-1_BA1_01_3102.cdf","time":"-1","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t-1_BA2_01_3103",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"139_Intra_RifaF2_t-1_BA2_01_3103.cdf","time":"-1","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t4_BA3_01_3104",
"Factors":{"group":"Reut","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"140_Intra_ReutF2_t4_BA3_01_3104.cdf","time":"4","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF2_t12_BA4_01_3105",
"Factors":{"group":"Salmo","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"141_Intra_SalmoF2_t12_BA4_01_3105.cdf","time":"12","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF2_J28_BA5_01_3106",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"142_Intra_StabF2_J28_BA5_01_3106.cdf","time":"NA","time_stab":"28"}
},
{
"Subject ID":"-",
"Sample ID":"J25F2_t6_BA6_01_3107",
"Factors":{"group":"J25","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"143_Intra_J25F2_t6_BA6_01_3107.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF1_t0_BA7_01_3108",
"Factors":{"group":"Rifa","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"144_Intra_RifaF1_t0_BA7_01_3108.cdf","time":"-","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF1_t2_BA8_01_3109",
"Factors":{"group":"Rifa","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"145_Intra_RifaF1_t2_BA8_01_3109.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t12_BB1_01_3110",
"Factors":{"group":"Rifa","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"146_Intra_RifaF2_t12_BB1_01_3110.cdf","time":"12","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF1_t-1_BB2_01_3111",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"147_Intra_ReutF1_t-1_BB2_01_3111.cdf","time":"-1","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF1_t4_BB3_01_3114",
"Factors":{"group":"Rifa","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"148_Intra_RifaF1_t4_BB3_01_3114.cdf","time":"4","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t10_BB4_01_3115",
"Factors":{"group":"Salmo","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"149_Intra_SalmoF1_t10_BB4_01_3115.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t-1_BB5_01_3116",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"150_Intra_ReutF2_t-1_BB5_01_3116.cdf","time":"-1","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF1_J28_BB6_01_3117",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"151_Intra_StabF1_J28_BB6_01_3117.cdf","time":"NA","time_stab":"28"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t6_BB7_01_3118",
"Factors":{"group":"Rifa","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"152_Intra_RifaF2_t6_BB7_01_3118.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t0_BB8_01_3119",
"Factors":{"group":"Reut","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"153_Intra_ReutF2_t0_BB8_01_3119.cdf","time":"-","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF2_t10_BC1_01_3120",
"Factors":{"group":"Salmo","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"154_Intra_SalmoF2_t10_BC1_01_3120.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF1_t2_BC2_01_3121",
"Factors":{"group":"Reut","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"155_Intra_ReutF1_t2_BC2_01_3121.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F2_t24_BC3_01_3122",
"Factors":{"group":"J25","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"156_Intra_J25F2_t24_BC3_01_3122.cdf","time":"24","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F1_t0_BC4_01_3123",
"Factors":{"group":"J25","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"157_Intra_J25F1_t0_BC4_01_3123.cdf","time":"-","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F1_t10_BC5_01_3124",
"Factors":{"group":"J25","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"158_Intra_J25F1_t10_BC5_01_3124.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F1_t2_BC6_01_3125",
"Factors":{"group":"J25","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"159_Intra_J25F1_t2_BC6_01_3125.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF1_J27_BC7_01_3126",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"160_Intra_StabF1_J27_BC7_01_3126.cdf","time":"NA","time_stab":"27"}
},
{
"Subject ID":"-",
"Sample ID":"J25F1_t6_BC8_01_3127",
"Factors":{"group":"J25","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"161_Intra_J25F1_t6_BC8_01_3127.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF1_t6_BD1_01_3128",
"Factors":{"group":"Rifa","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"162_Intra_RifaF1_t6_BD1_01_3128.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF1_t-1_BD2_01_3129",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"163_Intra_ReutF1_t-1_BD2_01_3129.cdf","time":"-1","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t4_BD3_01_3132",
"Factors":{"group":"Reut","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"164_Intra_ReutF2_t4_BD3_01_3132.cdf","time":"4","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F1_t2_BD4_01_3133",
"Factors":{"group":"J25","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"165_Intra_J25F1_t2_BD4_01_3133.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F2_t8_BD5_01_3134",
"Factors":{"group":"J25","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"166_Intra_J25F2_t8_BD5_01_3134.cdf","time":"8","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t12_BD6_01_3135",
"Factors":{"group":"Rifa","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"167_Intra_RifaF2_t12_BD6_01_3135.cdf","time":"12","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF1_J22_BD7_01_3136",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"168_Intra_StabF1_J22_BD7_01_3136.cdf","time":"NA","time_stab":"22"}
},
{
"Subject ID":"-",
"Sample ID":"J25F1_t24_BD8_01_3137",
"Factors":{"group":"J25","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"169_Intra_J25F1_t24_BD8_01_3137.cdf","time":"24","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF1_t8_BE1_01_3138",
"Factors":{"group":"Rifa","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"170_Intra_RifaF1_t8_BE1_01_3138.cdf","time":"8","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF2_J23_BE2_01_3139",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"171_Intra_StabF2_J23_BE2_01_3139.cdf","time":"NA","time_stab":"23"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t4_BE3_01_3140",
"Factors":{"group":"Rifa","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"172_Intra_RifaF2_t4_BE3_01_3140.cdf","time":"4","time_stab":"NA"}
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{
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"Sample ID":"J25F2_t24_BE4_01_3141",
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{
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"Sample ID":"StabF1_J22_BE5_01_3142",
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"Additional sample data":{"RAW_FILE_NAME":"174_Intra_StabF1_J22_BE5_01_3142.cdf","time":"NA","time_stab":"22"}
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{
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"Sample ID":"ReutF1_t12_BE6_01_3143",
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"Additional sample data":{"RAW_FILE_NAME":"175_Intra_ReutF1_t12_BE6_01_3143.cdf","time":"12","time_stab":"NA"}
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{
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"Sample ID":"ReutF1_t4_BE7_01_3144",
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"Additional sample data":{"RAW_FILE_NAME":"176_Intra_ReutF1_t4_BE7_01_3144.cdf","time":"4","time_stab":"NA"}
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{
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"Sample ID":"StabF1_J17_BE8_01_3145",
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},
{
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"Sample ID":"StabF2_J16_GA1_01_3146",
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"Additional sample data":{"RAW_FILE_NAME":"178_Intra_StabF2_J16_GA1_01_3146.cdf","time":"NA","time_stab":"16"}
},
{
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{
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"Sample ID":"SalmoF1_t8_GA3_01_3150",
"Factors":{"group":"Salmo","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"180_Intra_SalmoF1_t8_GA3_01_3150.cdf","time":"8","time_stab":"NA"}
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{
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"Factors":{"group":"Rifa","ferm":"F2"},
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{
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{
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},
{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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},
{
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{
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{
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},
{
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"Sample ID":"J25F1_t8_BC5_01_2986",
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{
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},
{
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},
{
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},
{
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"Sample ID":"RifaF1_t24_BD1_01_2990",
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},
{
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{
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},
{
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{
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{
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"Sample ID":"RifaF1_t12_BD6_01_2997",
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},
{
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{
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{
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},
{
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"Sample ID":"SalmoF1_t12_BE2_01_3001",
"Factors":{"group":"Salmo","ferm":"F1"},
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{
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"Sample ID":"SalmoF2_t-1_BE3_01_3004",
"Factors":{"group":"Stab","ferm":"F2"},
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{
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"Sample ID":"StabFM_J16_BE4_01_3005",
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{
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"Sample ID":"J25F2_t10_BE5_01_3006",
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{
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"Sample ID":"J25F1_t-1_BE6_01_3007",
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{
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"Sample ID":"SalmoF2_t2_BE7_01_3008",
"Factors":{"group":"Salmo","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"57_Intra_SalmoF2_t2_BE7_01_3008.cdf","time":"2","time_stab":"NA"}
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{
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"Sample ID":"StabF1_J23_BE8_01_3009",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"58_Intra_StabF1_J23_BE8_01_3009.cdf","time":"NA","time_stab":"23"}
},
{
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"Sample ID":"ReutF2_t2_GA1_01_3010",
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},
{
"Subject ID":"-",
"Sample ID":"StabFM_J12_GA2_01_3011",
"Factors":{"group":"Stab","ferm":"FM"},
"Additional sample data":{"RAW_FILE_NAME":"60_Intra_StabFM_J12_GA2_01_3011.cdf","time":"NA","time_stab":"12"}
},
{
"Subject ID":"-",
"Sample ID":"J25F2_t-1_GA3_01_3014",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"61_Intra_J25F2_t-1_GA3_01_3014.cdf","time":"-1","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF2_t12_GA4_01_3015",
"Factors":{"group":"Salmo","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"62_Intra_SalmoF2_t12_GA4_01_3015.cdf","time":"12","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabFM_J10_GA5_01_3016",
"Factors":{"group":"Stab","ferm":"FM"},
"Additional sample data":{"RAW_FILE_NAME":"63_Intra_StabFM_J10_GA5_01_3016.cdf","time":"NA","time_stab":"10"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t6_GA6_01_3017",
"Factors":{"group":"Salmo","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"64_Intra_SalmoF1_t6_GA6_01_3017.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF1_J27_GA7_01_3018",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"65_Intra_StabF1_J27_GA7_01_3018.cdf","time":"NA","time_stab":"27"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t10_GA8_01_3019",
"Factors":{"group":"Rifa","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"66_Intra_RifaF2_t10_GA8_01_3019.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F2_t2_GB1_01_3020",
"Factors":{"group":"J25","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"67_Intra_J25F2_t2_GB1_01_3020.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF1_t6_GB2_01_3021",
"Factors":{"group":"Reut","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"68_Intra_ReutF1_t6_GB2_01_3021.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F2_t2_GB3_01_3024",
"Factors":{"group":"J25","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"69_Intra_J25F2_t2_GB3_01_3024.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t10_GB4_01_3025",
"Factors":{"group":"Salmo","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"70_Intra_SalmoF1_t10_GB4_01_3025.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t12_GB5_01_3026",
"Factors":{"group":"Reut","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"71_Intra_ReutF2_t12_GB5_01_3026.cdf","time":"12","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF2_J16_GB6_01_3027",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"72_Intra_StabF2_J16_GB6_01_3027.cdf","time":"NA","time_stab":"16"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF1_t10_GB7_01_3028",
"Factors":{"group":"Reut","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"73_Intra_ReutF1_t10_GB7_01_3028.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F1_t10_GB8_01_3029",
"Factors":{"group":"J25","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"74_Intra_J25F1_t10_GB8_01_3029.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t2_GC1_01_3030",
"Factors":{"group":"Salmo","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"75_Intra_SalmoF1_t2_GC1_01_3030.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F2_t-1_GC2_01_3031",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"76_Intra_J25F2_t-1_GC2_01_3031.cdf","time":"-1","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t0_GC3_01_3032",
"Factors":{"group":"Rifa","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"77_Intra_RifaF2_t0_GC3_01_3032.cdf","time":"-","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF1_t8_GC4_01_3033",
"Factors":{"group":"Reut","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"78_Intra_ReutF1_t8_GC4_01_3033.cdf","time":"8","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t10_GC5_01_3034",
"Factors":{"group":"Rifa","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"79_Intra_RifaF2_t10_GC5_01_3034.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t2_GC6_01_3035",
"Factors":{"group":"Salmo","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"80_Intra_SalmoF1_t2_GC6_01_3035.cdf","time":"2","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F1_t12_GC7_01_3036",
"Factors":{"group":"J25","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"81_Intra_J25F1_t12_GC7_01_3036.cdf","time":"12","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF2_J17_GC8_01_3037",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"82_Intra_StabF2_J17_GC8_01_3037.cdf","time":"NA","time_stab":"17"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t0_GD1_01_3038",
"Factors":{"group":"Salmo","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"83_Intra_SalmoF1_t0_GD1_01_3038.cdf","time":"-","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F1_t6_GD2_01_3039",
"Factors":{"group":"J25","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"84_Intra_J25F1_t6_GD2_01_3039.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF1_t24_GD3_01_3042",
"Factors":{"group":"Reut","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"85_Intra_ReutF1_t24_GD3_01_3042.cdf","time":"24","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF2_t4_GD4_01_3043",
"Factors":{"group":"Salmo","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"86_Intra_SalmoF2_t4_GD4_01_3043.cdf","time":"4","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF2_J20_GD5_01_3044",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"87_Intra_StabF2_J20_GD5_01_3044.cdf","time":"NA","time_stab":"20"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t24_GD6_01_3045",
"Factors":{"group":"Salmo","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"88_Intra_SalmoF1_t24_GD6_01_3045.cdf","time":"24","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF1_t10_GD7_01_3046",
"Factors":{"group":"Rifa","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"89_Intra_RifaF1_t10_GD7_01_3046.cdf","time":"10","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF1_J28_GD8_01_3047",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"90_Intra_StabF1_J28_GD8_01_3047.cdf","time":"NA","time_stab":"28"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t24_GE1_01_3048",
"Factors":{"group":"Salmo","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"91_Intra_SalmoF1_t24_GE1_01_3048.cdf","time":"24","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t24_GE2_01_3049",
"Factors":{"group":"Reut","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"92_Intra_ReutF2_t24_GE2_01_3049.cdf","time":"24","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF1_t6_GE3_01_3050",
"Factors":{"group":"Rifa","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"93_Intra_RifaF1_t6_GE3_01_3050.cdf","time":"6","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"J25F2_t4_GE4_01_3051",
"Factors":{"group":"J25","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"94_Intra_J25F2_t4_GE4_01_3051.cdf","time":"4","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF1_J17_GE5_01_3052",
"Factors":{"group":"Stab","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"95_Intra_StabF1_J17_GE5_01_3052.cdf","time":"NA","time_stab":"17"}
},
{
"Subject ID":"-",
"Sample ID":"RifaF2_t24_GE6_01_3053",
"Factors":{"group":"Rifa","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"96_Intra_RifaF2_t24_GE6_01_3053.cdf","time":"24","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"SalmoF1_t4_GE7_01_3054",
"Factors":{"group":"Salmo","ferm":"F1"},
"Additional sample data":{"RAW_FILE_NAME":"97_Intra_SalmoF1_t4_GE7_01_3054.cdf","time":"4","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"ReutF2_t8_GE8_01_3055",
"Factors":{"group":"Reut","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"98_Intra_ReutF2_t8_GE8_01_3055.cdf","time":"8","time_stab":"NA"}
},
{
"Subject ID":"-",
"Sample ID":"StabF2_J19_RA1_01_3056",
"Factors":{"group":"Stab","ferm":"F2"},
"Additional sample data":{"RAW_FILE_NAME":"99_Intra_StabF2_J19_RA1_01_3056.cdf","time":"NA","time_stab":"19"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The PolyFermS in vitro continuous fermentation model was used here with modified Macfarlane medium to simulate the porcine proximal colon. During 35 days of fermentation, a first-stage reactor containing immobilized swine fecal microbiota fed two second-stage control and test reactors operated in parallel and used to test the effects of MccJ25 on the metabolic activity of the microbiota.","SAMPLE_TYPE":"Bacterial cells","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Performed simultaneously in TR1 and TR2, the four treatments consisted of adding by adding Salmonella enterica subsp. enterica serovar Newport ATCC 6962 alone at an initial concentration of 107 cfu/mL to each reactor, followed by adding the bacteria at this cell density along with each tested antimicrobial: 0.4 mM MccJ25, 4 mM reuterin or 0.6 mM rifampicin."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"The metabolites were extracted from swine colonic microbiota in methanol/chloroform/water. The aqueous phase was collected.","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Low pH polar","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000 RS","COLUMN_NAME":"Acclaim Polar Advantage II column (Thermo)"},

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

"MS":{"INSTRUMENT_NAME":"Bruker Maxis II ETD","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Proprietary analytical software for MS acquisition Data processing with xcms (R package)","MS_RESULTS_FILE":"ST002014_AN003282_Results.txt UNITS:m/z Has m/z:Yes Has RT:Yes RT units:Minutes"}

}