VERSION             	1
CREATED_ON             	June 4, 2023, 11:08 pm
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
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
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Mus musculus
SU:TAXONOMY_ID                   	10090
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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
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)
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.  
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.
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
AN:ANALYSIS_TYPE                 	MS
MS:INSTRUMENT_NAME               	Agilent 6530 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