#METABOLOMICS WORKBENCH jessepeach_20230528_133308 DATATRACK_ID:4049 STUDY_ID:ST002723 ANALYSIS_ID:AN004414 PROJECT_ID:PR001689 VERSION 1 CREATED_ON June 4, 2023, 11:08 pm #PROJECT PR:PROJECT_TITLE A systems-level approach for disentangling complex interactions among the gut PR:PROJECT_TITLE microbiome, anti-inflammatory food metabolomic signatures, and human PR:PROJECT_TITLE inflammation phenotypes PR:PROJECT_SUMMARY The goal of this project is to elucidate interactions among the gut microbiome, PR:PROJECT_SUMMARY anti-inflammatory food metabolomic signatures, and human inflammation PR:PROJECT_SUMMARY phenotypes. Inflammation plays both direct and indirect roles in the development PR:PROJECT_SUMMARY of type 2 diabetes (T2D), atherogenic cardiovascular diseases, and other causes PR:PROJECT_SUMMARY of morbidity and mortality. In preliminary USDA-NIFA funded studies, we found PR:PROJECT_SUMMARY that individuals of distinct low and high inflammation phenotypes have distinct PR:PROJECT_SUMMARY metabolomic signatures in their blood. Anthocyanins and fiber of bioactive PR:PROJECT_SUMMARY components of foods that have been shown to lower inflammation. However, there PR:PROJECT_SUMMARY is tremendous inter-individual variability in bioavailability of anthocyanins PR:PROJECT_SUMMARY and production of phenolic and aromatic metabolites in the colon that depends, PR:PROJECT_SUMMARY at least in part, on digestive metabolism by microorganisms (the microbiota) in PR:PROJECT_SUMMARY the gut. Fiber which acts as a prebiotic to enrich favorable gut microbes and as PR:PROJECT_SUMMARY a fermentation substrate to produce favorable or unfavorable metabolites PR:PROJECT_SUMMARY according to the unique makeup of the gut microbiota. However, little is known PR:PROJECT_SUMMARY about the complex interactions among the gut microbiome, anti-inflammatory food PR:PROJECT_SUMMARY metabolomic signatures, and human inflammation phenotypes. We propose a of human PR:PROJECT_SUMMARY mechanistic clinical trials and mice humanized with fecal microbiome transplants PR:PROJECT_SUMMARY to disentangle these complex interactions. To determine the metabolomic PR:PROJECT_SUMMARY signatures anti-inflammatory foods and key bioactive components and determine PR:PROJECT_SUMMARY associations with constituents of the gut microbiome (Aim 1A), we will measure PR:PROJECT_SUMMARY in a human cohort the makeup of the gut microbiome and metabolomic changes PR:PROJECT_SUMMARY induced by acute (3 d) ingestion of 1) chokeberry and chokeberry anthocyanins PR:PROJECT_SUMMARY (n=75), and 2) lentils and lentil fiber (n=75). To determine whether these foods PR:PROJECT_SUMMARY are related to the metabolomic signatures of low versus high inflammation PR:PROJECT_SUMMARY phenotypes (Aim 1B), we will compare the metabolites and associated metabolic PR:PROJECT_SUMMARY pathways of chokeberry, chokeberry anthocyanins, lentils, and lentil fiber to PR:PROJECT_SUMMARY those associated with low and high inflammation phenotypes. To determine the PR:PROJECT_SUMMARY impact of inter-individual variability of the gut microbiome on metabolomic PR:PROJECT_SUMMARY signatures (Aim 2A), we will humanize mice with a diverse collection of human PR:PROJECT_SUMMARY gut microbiomes and determine whether the makeup of the microbiome predicts PR:PROJECT_SUMMARY features (metabolites) of chokeberry/anthocyanin, lentils/fiber metabolomic PR:PROJECT_SUMMARY signatures. Findings from these experiments directly address the PAR-18-727 PR:PROJECT_SUMMARY program area priority of “identification and validation of food and nutrient PR:PROJECT_SUMMARY specific metabolic signatures that correlate with nutrient quality and efficacy PR:PROJECT_SUMMARY and provide insights to develop synergistic foodprebiotic based therapies to PR:PROJECT_SUMMARY convert humans from high to low inflammation phenotypes to reduce disease risk PR:PROJECT_SUMMARY and severity. PR:INSTITUTE Montana State University PR:LAST_NAME Jesse PR:FIRST_NAME Peach PR:ADDRESS PO Box 173400, Bozeman, MT 59717 PR:EMAIL jessepeach@gmail.com PR:PHONE 406-595-3100 #STUDY ST:STUDY_TITLE INFLAMMATORY STIMULUS IN HUMANIZED MOUSE MODELS REVEALS THE ANTIOXIDANT EFFECTS ST:STUDY_TITLE OF ARONIA SUPPLEMENTATION ST:STUDY_SUMMARY INFLAMMATORY STIMULUS IN HUMANIZED MOUSE MODELS REVEALS THE ANTIOXIDANT EFFECTS ST:STUDY_SUMMARY OF ARONIA SUPPLEMENTATION ST:INSTITUTE Montana State University ST:LAST_NAME Peach ST:FIRST_NAME Jesse ST:ADDRESS PO Box 173400, Bozeman, MT 59717 ST:EMAIL jessepeach@gmail.com ST:PHONE 406-595-3100 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - Blank Donor:Blank | Treatment:Blank | Time:Blank RAW_FILE_NAME=2021_01_29_HF_MurSerum_02_Blank2.d SUBJECT_SAMPLE_FACTORS - 52 Donor:7 | Treatment:Control | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_03_114_52.d SUBJECT_SAMPLE_FACTORS - 11 Donor:1 | Treatment:Aronia | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_04_114_11.d SUBJECT_SAMPLE_FACTORS - 56 Donor:7 | Treatment:Control | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_05_114_56.d SUBJECT_SAMPLE_FACTORS - 66 Donor:Extraction Blank | Treatment:Extraction Blank | Time:Extraction Blank RAW_FILE_NAME=2021_01_29_HF_MurSerum_06_114_66.d SUBJECT_SAMPLE_FACTORS - 65 Donor:7 | Treatment:Control | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_08_114_65.d SUBJECT_SAMPLE_FACTORS - 19 Donor:1 | Treatment:Control | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_09_114_19.d SUBJECT_SAMPLE_FACTORS - 7 Donor:1 | Treatment:Aronia | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_10_114_07.d SUBJECT_SAMPLE_FACTORS - 36 Donor:7 | Treatment:Aronia | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_11_114_36.d SUBJECT_SAMPLE_FACTORS - 31 Donor:7 | Treatment:Aronia | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_13_114_31.d SUBJECT_SAMPLE_FACTORS - 29 Donor:1 | Treatment:Control | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_14_114_29.d SUBJECT_SAMPLE_FACTORS - 63 Donor:7 | Treatment:Control | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_15_114_63.d SUBJECT_SAMPLE_FACTORS - 60 Donor:7 | Treatment:Control | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_16_114_60.d SUBJECT_SAMPLE_FACTORS - 14 Donor:1 | Treatment:Aronia | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_19_114_14.d SUBJECT_SAMPLE_FACTORS - 50 Donor:7 | Treatment:Aronia | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_20_114_50.d SUBJECT_SAMPLE_FACTORS - 30 Donor:1 | Treatment:Control | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_21_114_30.d SUBJECT_SAMPLE_FACTORS - 34 Donor:7 | Treatment:Aronia | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_22_114_34.d SUBJECT_SAMPLE_FACTORS - 49 Donor:7 | Treatment:Aronia | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_24_114_49.d SUBJECT_SAMPLE_FACTORS - 33 Donor:7 | Treatment:Aronia | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_25_114_33.d SUBJECT_SAMPLE_FACTORS - 68 Donor:7 | Treatment:Aronia | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_26_114_68.d SUBJECT_SAMPLE_FACTORS - 53 Donor:7 | Treatment:Control | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_27_114_53.d SUBJECT_SAMPLE_FACTORS - 10 Donor:1 | Treatment:Aronia | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_29_114_10.d SUBJECT_SAMPLE_FACTORS - 67 Donor:Extraction Blank | Treatment:Extraction Blank | Time:Extraction Blank RAW_FILE_NAME=2021_01_29_HF_MurSerum_30_114_67.d SUBJECT_SAMPLE_FACTORS - 54 Donor:7 | Treatment:Control | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_32_114_54.d SUBJECT_SAMPLE_FACTORS - 24 Donor:1 | Treatment:Control | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_33_114_24.d SUBJECT_SAMPLE_FACTORS - 62 Donor:7 | Treatment:Control | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_35_114_62.d SUBJECT_SAMPLE_FACTORS - 45 Donor:7 | Treatment:Aronia | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_36_114_45.d SUBJECT_SAMPLE_FACTORS - 6 Donor:1 | Treatment:Aronia | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_37_114_06.d SUBJECT_SAMPLE_FACTORS - 22 Donor:1 | Treatment:Control | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_38_114_22.d SUBJECT_SAMPLE_FACTORS - 18 Donor:1 | Treatment:Control | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_40_114_18.d SUBJECT_SAMPLE_FACTORS - 20 Donor:1 | Treatment:Control | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_41_114_20.d SUBJECT_SAMPLE_FACTORS - 4 Donor:1 | Treatment:Aronia | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_42_114_04.d SUBJECT_SAMPLE_FACTORS - 13 Donor:1 | Treatment:Aronia | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_43_114_13.d SUBJECT_SAMPLE_FACTORS - 38 Donor:7 | Treatment:Aronia | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_45_114_38.d SUBJECT_SAMPLE_FACTORS - 25 Donor:1 | Treatment:Control | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_46_114_25.d SUBJECT_SAMPLE_FACTORS - 59 Donor:7 | Treatment:Control | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_47_114_59.d SUBJECT_SAMPLE_FACTORS - 39 Donor:7 | Treatment:Aronia | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_48_114_39.d SUBJECT_SAMPLE_FACTORS - 35 Donor:7 | Treatment:Aronia | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_51_114_35.d SUBJECT_SAMPLE_FACTORS - 48 Donor:7 | Treatment:Aronia | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_52_114_48.d SUBJECT_SAMPLE_FACTORS - 41 Donor:7 | Treatment:Aronia | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_53_114_41.d SUBJECT_SAMPLE_FACTORS - 8 Donor:1 | Treatment:Aronia | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_54_114_08.d SUBJECT_SAMPLE_FACTORS - 46 Donor:7 | Treatment:Aronia | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_56_114_46.d SUBJECT_SAMPLE_FACTORS - 51 Donor:7 | Treatment:Control | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_57_114_51.d SUBJECT_SAMPLE_FACTORS - 55 Donor:7 | Treatment:Control | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_60_114_55.d SUBJECT_SAMPLE_FACTORS - 15 Donor:1 | Treatment:Aronia | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_61_114_15.d SUBJECT_SAMPLE_FACTORS - 21 Donor:1 | Treatment:Control | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_62_114_21.d SUBJECT_SAMPLE_FACTORS - 23 Donor:1 | Treatment:Control | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_62_114_23.d SUBJECT_SAMPLE_FACTORS - 16 Donor:1 | Treatment:Control | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_63_114_16.d SUBJECT_SAMPLE_FACTORS - 44 Donor:7 | Treatment:Aronia | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_63_114_44.d SUBJECT_SAMPLE_FACTORS - 43 Donor:7 | Treatment:Aronia | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_64_114_43.d SUBJECT_SAMPLE_FACTORS - 47 Donor:7 | Treatment:Aronia | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_64_114_47.d SUBJECT_SAMPLE_FACTORS - 64 Donor:7 | Treatment:Control | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_64_114_64.d SUBJECT_SAMPLE_FACTORS - 12 Donor:1 | Treatment:Aronia | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_65_114_12.d SUBJECT_SAMPLE_FACTORS - 28 Donor:1 | Treatment:Control | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_65_114_28.d SUBJECT_SAMPLE_FACTORS - 32 Donor:7 | Treatment:Aronia | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_65_114_32.d SUBJECT_SAMPLE_FACTORS - 37 Donor:7 | Treatment:Aronia | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_65_114_37.d SUBJECT_SAMPLE_FACTORS - 9 Donor:1 | Treatment:Aronia | Time:6 RAW_FILE_NAME=2021_01_29_HF_MurSerum_66_114_09.d SUBJECT_SAMPLE_FACTORS - 17 Donor:1 | Treatment:Control | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_66_114_17.d SUBJECT_SAMPLE_FACTORS - 26 Donor:1 | Treatment:Control | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_66_114_26.d SUBJECT_SAMPLE_FACTORS - 40 Donor:7 | Treatment:Aronia | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_66_114_40.d SUBJECT_SAMPLE_FACTORS - 57 Donor:7 | Treatment:Control | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_66_114_57.d SUBJECT_SAMPLE_FACTORS - 1 Donor:1 | Treatment:Aronia | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_67_114_01.d SUBJECT_SAMPLE_FACTORS - 5 Donor:1 | Treatment:Aronia | Time:8 RAW_FILE_NAME=2021_01_29_HF_MurSerum_67_114_05.d SUBJECT_SAMPLE_FACTORS - 61 Donor:7 | Treatment:Control | Time:0 RAW_FILE_NAME=2021_01_29_HF_MurSerum_68_114_61.d SUBJECT_SAMPLE_FACTORS - 3 Donor:1 | Treatment:Aronia | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_69_114_03.d SUBJECT_SAMPLE_FACTORS - 42 Donor:7 | Treatment:Aronia | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_70_114_42.d SUBJECT_SAMPLE_FACTORS - 58 Donor:7 | Treatment:Control | Time:4 RAW_FILE_NAME=2021_01_29_HF_MurSerum_71_114_58.d SUBJECT_SAMPLE_FACTORS - 2 Donor:1 | Treatment:Aronia | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_73_114_02.d SUBJECT_SAMPLE_FACTORS - 27 Donor:1 | Treatment:Control | Time:2 RAW_FILE_NAME=2021_01_29_HF_MurSerum_74_114_27.d #COLLECTION CO:COLLECTION_SUMMARY Two human stool donors were selected based on their inflammation profile which CO:COLLECTION_SUMMARY occurred prior to gut microbial community profiling. Female germ- free (GF) CO:COLLECTION_SUMMARY C57BL/6J mice, originally purchased from the Jackson Laboratory (Bar Harbor, ME) CO:COLLECTION_SUMMARY were housed and bred at the American Association for the Accreditation of CO:COLLECTION_SUMMARY Laboratory Animal Care-accredited Animal Resource Center at Montana State CO:COLLECTION_SUMMARY University. Mice were held in individually ventilated cages with sterile bedding CO:COLLECTION_SUMMARY before and after fecal transplantation from selected human stool donors. Two CO:COLLECTION_SUMMARY female mice received an inoculation with fecal material from a human donor CO:COLLECTION_SUMMARY categorized as having low or high systemic inflammation based on serum levels of CO:COLLECTION_SUMMARY six proinflammatory cytokines. Human donor stool slurry aliquots were CO:COLLECTION_SUMMARY administered to GF mice through oral gavage. Sexually mature male GF C57BL/6J CO:COLLECTION_SUMMARY mice were added to each cage approximately one week after transplantation. Male CO:COLLECTION_SUMMARY mice removed prior to birth of pups. Pups from the inoculated dams were CO:COLLECTION_SUMMARY co-housed by sex (3 – 5 mice/cage) with different microbial inoculations CO:COLLECTION_SUMMARY placed in separate isolators. Mice from each microbial inoculation were assigned CO:COLLECTION_SUMMARY to one of two juice groups: Aronia (ARO LO , = 3, ARO HI , n=5), or a CO:COLLECTION_SUMMARY sugar-matched juice (CON LO ,n=3, CON HI , n = 3). Weekly measurements of body CO:COLLECTION_SUMMARY weight and food and fluid intake were recorded. Blood samples were collected at CO:COLLECTION_SUMMARY the same interval into serum separating tubes. Whole blood was allowed to clot CO:COLLECTION_SUMMARY for 15 minutes before centrifugation at 1200 RPM for 15 minutes with resulting CO:COLLECTION_SUMMARY serum aliquoted and stored at -80ºC until analysis. After T8 sample collection, CO:COLLECTION_SUMMARY mice were euthanized via rapid CO 2 asphyxiation. CO:SAMPLE_TYPE Blood (serum) #TREATMENT TR:TREATMENT_SUMMARY At baseline (T0), regular drinking water was replaced with ARO or CON juice to TR:TREATMENT_SUMMARY begin a two-week familiarization period with the juice. ARO mice received an TR:TREATMENT_SUMMARY unpasteurized blend of Aronia juice, and CON mice received a sugar-matched TR:TREATMENT_SUMMARY beverage containing water, sorbitol, glucose, and fructose. The mice were housed TR:TREATMENT_SUMMARY in cages with free access to their respective juice. During the familiarization TR:TREATMENT_SUMMARY period, all mice received standard chow (LabDiet 5013).  After the 2-week TR:TREATMENT_SUMMARY familiarization period (T2), mice began a 6-week high-fat diet, delivered ad TR:TREATMENT_SUMMARY libitum concomitant with juice consumption. The HFD (Teklad TD.96132) was chosen TR:TREATMENT_SUMMARY to induce obesity and present an inflammatory stimulus (Duan et al., 2018) . The TR:TREATMENT_SUMMARY HFD mimics a Western style diet and consisted of 40.6% fat, 40.7% carbohydrate, TR:TREATMENT_SUMMARY and 18.7% protein and was particularly rich in sugars and trans-fatty acids. All TR:TREATMENT_SUMMARY chow provided was sterilized via autoclaving or irradiation. A total of 150 mL TR:TREATMENT_SUMMARY of juice was provided per cage each week. Juice was refilled three times each TR:TREATMENT_SUMMARY week.   #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Samples were stored at -80 until ready for analysis. A liquid extraction was SP:SAMPLEPREP_SUMMARY completed with a protein precipitation. Samples were then concentrated and SP:SAMPLEPREP_SUMMARY stored dry until LCMS analysis. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent 1290 Infinity II CH:COLUMN_NAME Waters ACQUITY UPLC BEH HILIC (150 x 2.1mm,1.7um) CH:SOLVENT_A Water with 0.1% formic acid CH:SOLVENT_B Acetonitrile with 0.1% formic acid CH:FLOW_GRADIENT Linear 45-70%A CH:FLOW_RATE 0.4mL/min CH:COLUMN_TEMPERATURE 40 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6530 QTOF MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Mass Hunter to acquire data. Processed with msconvert and mzMine. Annotation MS:MS_COMMENTS with SIRIUS software. MS:MS_RESULTS_FILE ST002723_AN004414_Results.txt UNITS:area Has m/z:Yes Has RT:Yes RT units:Minutes #END