#METABOLOMICS WORKBENCH jhaffner09_20221007_080112 DATATRACK_ID:3495 STUDY_ID:ST002320 ANALYSIS_ID:AN003787 PROJECT_ID:PR001486
VERSION             	1
CREATED_ON             	October 14, 2022, 7:59 am
#PROJECT
PR:PROJECT_TITLE                 	Untargeted Fecal Metabolomic Analyses Across an Industrialization Gradient
PR:PROJECT_TITLE                 	Reveal Shared Metabolites and Impact of Industrialization on Fecal
PR:PROJECT_TITLE                 	Microbiome-Metabolome Interactions
PR:PROJECT_SUMMARY               	The metabolome is a central determinant of human phenotypes and includes the
PR:PROJECT_SUMMARY               	plethora of small molecules produced by host and microbiome, or taken up from
PR:PROJECT_SUMMARY               	exogenous sources. However, studies of the metabolome have so far focused
PR:PROJECT_SUMMARY               	predominantly on urban, industrialized populations. Through an untargeted
PR:PROJECT_SUMMARY               	metabolomic analysis of 90 fecal samples from human individuals from Africa and
PR:PROJECT_SUMMARY               	the Americas—the birthplace and the last continental expansion of our species,
PR:PROJECT_SUMMARY               	respectively—we characterized a shared human fecal metabolome. The majority of
PR:PROJECT_SUMMARY               	detected metabolite features were ubiquitous across populations, despite any
PR:PROJECT_SUMMARY               	geographic, dietary, or behavioral differences. Such shared metabolite features
PR:PROJECT_SUMMARY               	included hyocholic acid and cholesterol. However, any characterization of the
PR:PROJECT_SUMMARY               	shared human fecal metabolome is insufficient without exploring the influence of
PR:PROJECT_SUMMARY               	industrialization. Here, we show chemical differences along an industrialization
PR:PROJECT_SUMMARY               	gradient, where the degree of industrialization correlates with metabolomic
PR:PROJECT_SUMMARY               	changes. We identified differential metabolite features like amino
PR:PROJECT_SUMMARY               	acid-conjugated bile acids and urobilin as major metabolic correlates of these
PR:PROJECT_SUMMARY               	behavioral shifts. Additionally, co-analyses with over 5,000 publicly available
PR:PROJECT_SUMMARY               	human fecal samples and co-occurrence probability analyses with the gut
PR:PROJECT_SUMMARY               	microbiome highlight connections between the human fecal metabolome and gut
PR:PROJECT_SUMMARY               	microbiome. Our results indicate that industrialization significantly influences
PR:PROJECT_SUMMARY               	the human fecal metabolome, but diverse human lifestyles and behavior still
PR:PROJECT_SUMMARY               	maintain a shared human fecal metabolome. This study represents the first
PR:PROJECT_SUMMARY               	characterization of the shared human fecal metabolome through untargeted
PR:PROJECT_SUMMARY               	analyses of populations along an industrialization gradient.
PR:INSTITUTE                     	University of Oklahoma, Department of Anthropology
PR:LABORATORY                    	Laboratories of Molecular Anthropology and Microbiome Research
PR:LAST_NAME                     	Haffner
PR:FIRST_NAME                    	Jacob
PR:ADDRESS                       	101 David L. Boren Blvd., Norman, Oklahoma, 73019, USA
PR:EMAIL                         	jacob.haffner@ou.edu
PR:PHONE                         	405-325-7381
#STUDY
ST:STUDY_TITLE                   	Untargeted Fecal Metabolomic Analyses Across an Industrialization Gradient
ST:STUDY_TITLE                   	Reveal Shared Metabolites and Impact of Industrialization on Fecal
ST:STUDY_TITLE                   	Microbiome-Metabolome Interactions
ST:STUDY_SUMMARY                 	The metabolome is a central determinant of human phenotypes and includes the
ST:STUDY_SUMMARY                 	plethora of small molecules produced by host and microbiome, or taken up from
ST:STUDY_SUMMARY                 	exogenous sources. However, studies of the metabolome have so far focused
ST:STUDY_SUMMARY                 	predominantly on urban, industrialized populations. Through an untargeted
ST:STUDY_SUMMARY                 	metabolomic analysis of 90 fecal samples from human individuals from Africa and
ST:STUDY_SUMMARY                 	the Americas—the birthplace and the last continental expansion of our species,
ST:STUDY_SUMMARY                 	respectively—we characterized a shared human fecal metabolome. The majority of
ST:STUDY_SUMMARY                 	detected metabolite features were ubiquitous across populations, despite any
ST:STUDY_SUMMARY                 	geographic, dietary, or behavioral differences. Such shared metabolite features
ST:STUDY_SUMMARY                 	included hyocholic acid and cholesterol. However, any characterization of the
ST:STUDY_SUMMARY                 	shared human fecal metabolome is insufficient without exploring the influence of
ST:STUDY_SUMMARY                 	industrialization. Here, we show chemical differences along an industrialization
ST:STUDY_SUMMARY                 	gradient, where the degree of industrialization correlates with metabolomic
ST:STUDY_SUMMARY                 	changes. We identified differential metabolite features like amino
ST:STUDY_SUMMARY                 	acid-conjugated bile acids and urobilin as major metabolic correlates of these
ST:STUDY_SUMMARY                 	behavioral shifts. Additionally, co-analyses with over 5,000 publicly available
ST:STUDY_SUMMARY                 	human fecal samples and co-occurrence probability analyses with the gut
ST:STUDY_SUMMARY                 	microbiome highlight connections between the human fecal metabolome and gut
ST:STUDY_SUMMARY                 	microbiome. Our results indicate that industrialization significantly influences
ST:STUDY_SUMMARY                 	the human fecal metabolome, but diverse human lifestyles and behavior still
ST:STUDY_SUMMARY                 	maintain a shared human fecal metabolome. This study represents the first
ST:STUDY_SUMMARY                 	characterization of the shared human fecal metabolome through untargeted
ST:STUDY_SUMMARY                 	analyses of populations along an industrialization gradient.
ST:INSTITUTE                     	University of Oklahoma
ST:LAST_NAME                     	Haffner
ST:FIRST_NAME                    	Jacob
ST:ADDRESS                       	101 David L. Boren Blvd, Norman, OK, 73019
ST:EMAIL                         	jacob.haffner@ou.edu
ST:PHONE                         	405-325-7381
ST:NUM_GROUPS                    	6
ST:TOTAL_SUBJECTS                	90
ST:NUM_MALES                     	29
ST:NUM_FEMALES                   	47
#SUBJECT
SU:SUBJECT_TYPE                  	Human
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
SU:AGE_OR_AGE_RANGE              	5-77
SU:WEIGHT_OR_WEIGHT_RANGE        	NA
SU:HEIGHT_OR_HEIGHT_RANGE        	NA
SU:GENDER                        	Male and female
SU:HUMAN_LIFESTYLE_FACTORS       	Urban industrial; Rural industrial; Rural traditional; Isolated traditional
SU:HUMAN_ALCOHOL_DRUG_USE        	NA
SU:HUMAN_NUTRITION               	NA
SU:HUMAN_INCLUSION_CRITERIA      	NA
SU:HUMAN_EXCLUSION_CRITERIA      	NA
#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           	-	NO01	Population:Norman | Industrialization_Category:Urban Industrial | Sex:M | Age:23 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO01.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO02	Population:Norman | Industrialization_Category:Urban Industrial | Sex:F | Age:37 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO02.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO03	Population:Norman | Industrialization_Category:Urban Industrial | Sex:M | Age:40 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO03.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO04	Population:Norman | Industrialization_Category:Urban Industrial | Sex:M | Age:26 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO04.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO05	Population:Norman | Industrialization_Category:Urban Industrial | Sex:M | Age:28 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO05.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO06	Population:Norman | Industrialization_Category:Urban Industrial | Sex:M | Age:28 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO06.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO07	Population:Norman | Industrialization_Category:Urban Industrial | Sex:F | Age:32 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO07.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO08	Population:Norman | Industrialization_Category:Urban Industrial | Sex:F | Age:32 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO08.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO09	Population:Norman | Industrialization_Category:Urban Industrial | Sex:F | Age:34 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO09.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO10	Population:Norman | Industrialization_Category:Urban Industrial | Sex:M | Age:41 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO10.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO11	Population:Norman | Industrialization_Category:Urban Industrial | Sex:M | Age:26 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO11.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO12	Population:Norman | Industrialization_Category:Urban Industrial | Sex:F | Age:27 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO12.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO13	Population:Norman | Industrialization_Category:Urban Industrial | Sex:M | Age:35 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO13.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO19	Population:Norman | Industrialization_Category:Urban Industrial | Sex:F | Age:32 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO19.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO20	Population:Norman | Industrialization_Category:Urban Industrial | Sex:M | Age:26 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO20.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO21	Population:Norman | Industrialization_Category:Urban Industrial | Sex:M | Age:23 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO21.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO22	Population:Norman | Industrialization_Category:Urban Industrial | Sex:M | Age:26 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO22.mzXML
SUBJECT_SAMPLE_FACTORS           	-	NO23	Population:Norman | Industrialization_Category:Urban Industrial | Sex:F | Age:26 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=United States; RAW_FILE_NAME=NO23.mzXML
SUBJECT_SAMPLE_FACTORS           	-	GU1	Population:Guayabo | Industrialization_Category:Rural Industrial | Sex:F | Age:52 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=1GU.mzXML
SUBJECT_SAMPLE_FACTORS           	-	GU2	Population:Guayabo | Industrialization_Category:Rural Industrial | Sex:F | Age:19 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=2GU.mzXML
SUBJECT_SAMPLE_FACTORS           	-	GU4	Population:Guayabo | Industrialization_Category:Rural Industrial | Sex:F | Age:40 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=4GU.mzXML
SUBJECT_SAMPLE_FACTORS           	-	GU6	Population:Guayabo | Industrialization_Category:Rural Industrial | Sex:NA | Age:6 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=6GU.mzXML
SUBJECT_SAMPLE_FACTORS           	-	GU7	Population:Guayabo | Industrialization_Category:Rural Industrial | Sex:NA | Age:9 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=7GU.mzXML
SUBJECT_SAMPLE_FACTORS           	-	GU10	Population:Guayabo | Industrialization_Category:Rural Industrial | Sex:F | Age:58 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=10GU.mzXML
SUBJECT_SAMPLE_FACTORS           	-	GU11	Population:Guayabo | Industrialization_Category:Rural Industrial | Sex:NA | Age:7 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=11GU.mzXML
SUBJECT_SAMPLE_FACTORS           	-	GU12	Population:Guayabo | Industrialization_Category:Rural Industrial | Sex:NA | Age:16 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=12GU.mzXML
SUBJECT_SAMPLE_FACTORS           	-	GU13	Population:Guayabo | Industrialization_Category:Rural Industrial | Sex:F | Age:41 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=13GU.mzXML
SUBJECT_SAMPLE_FACTORS           	-	GU17	Population:Guayabo | Industrialization_Category:Rural Industrial | Sex:F | Age:51 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=17GU.mzXML
SUBJECT_SAMPLE_FACTORS           	-	GU19	Population:Guayabo | Industrialization_Category:Rural Industrial | Sex:F | Age:24 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=19GU.mzXML
SUBJECT_SAMPLE_FACTORS           	-	GU20	Population:Guayabo | Industrialization_Category:Rural Industrial | Sex:F | Age:63 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=20GU.mzXML
SUBJECT_SAMPLE_FACTORS           	-	1TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:F | Age:61 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=1TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	2TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:F | Age:40 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=2TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	3TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:NA | Age:5 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=3TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	4TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:F | Age:40 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=4TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	6TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:F | Age:31 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=6TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	10TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:NA | Age:8 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=10TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	11TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:M | Age:39 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=11TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	14TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:F | Age:77 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=14TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	16TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:F | Age:38 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=16TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	17TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:NA | Age:7 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=17TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	18TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:NA | Age:13 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=18TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	26TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:F | Age:36 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=26TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	27TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:NA | Age:13 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=27TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	31TM	Population:Tambo de Mora | Industrialization_Category:Rural Industrial | Sex:NA | Age:28 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=31TM.mzXML
SUBJECT_SAMPLE_FACTORS           	-	TM10_01	Population:Boulkiemd� | Industrialization_Category:Rural Traditional | Sex:M | Age:55 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=Burkina Faso; RAW_FILE_NAME=BF10_01.mzXML
SUBJECT_SAMPLE_FACTORS           	-	TM13_01	Population:Boulkiemd� | Industrialization_Category:Rural Traditional | Sex:M | Age:53 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=Burkina Faso; RAW_FILE_NAME=BF13_01.mzXML
SUBJECT_SAMPLE_FACTORS           	-	TM23_02	Population:Boulkiemd� | Industrialization_Category:Rural Traditional | Sex:F | Age:51 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=Burkina Faso; RAW_FILE_NAME=BF23_02.mzXML
SUBJECT_SAMPLE_FACTORS           	-	TM01_01	Population:Boulkiemd� | Industrialization_Category:Rural Traditional | Sex:M | Age:55 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=Burkina Faso; RAW_FILE_NAME=BF01_01.mzXML
SUBJECT_SAMPLE_FACTORS           	-	TM09_02	Population:Boulkiemd� | Industrialization_Category:Rural Traditional | Sex:F | Age:32 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=Burkina Faso; RAW_FILE_NAME=BF09_02.mzXML
SUBJECT_SAMPLE_FACTORS           	-	TM11_04	Population:Boulkiemd� | Industrialization_Category:Rural Traditional | Sex:F | Age:40 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=Burkina Faso; RAW_FILE_NAME=BF11_04.mzXML
SUBJECT_SAMPLE_FACTORS           	-	TM17_02	Population:Boulkiemd� | Industrialization_Category:Rural Traditional | Sex:F | Age:35 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=Burkina Faso; RAW_FILE_NAME=BF17_02.mzXML
SUBJECT_SAMPLE_FACTORS           	-	TM20_03	Population:Boulkiemd� | Industrialization_Category:Rural Traditional | Sex:F | Age:37 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=Burkina Faso; RAW_FILE_NAME=BF20_03.mzXML
SUBJECT_SAMPLE_FACTORS           	-	TM22_03	Population:Boulkiemd� | Industrialization_Category:Rural Traditional | Sex:M | Age:29 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=Burkina Faso; RAW_FILE_NAME=BF22_03.mzXML
SUBJECT_SAMPLE_FACTORS           	-	TM25_03	Population:Boulkiemd� | Industrialization_Category:Rural Traditional | Sex:F | Age:38 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=Burkina Faso; RAW_FILE_NAME=BF25_03.mzXML
SUBJECT_SAMPLE_FACTORS           	-	TM29_01	Population:Boulkiemd� | Industrialization_Category:Rural Traditional | Sex:M | Age:73 | Time_Kept_on_Ice_before_Frozen:Within 1 day	Country_of_Origin=Burkina Faso; RAW_FILE_NAME=BF29_01.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO01	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:36 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO01.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO03	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:M | Age:6 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO03.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO09	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:NA | Age:13 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO09.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO10	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:M | Age:10 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO10.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO11	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:M | Age:36 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO11.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO12	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:35 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO12.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO13	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:9 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO13.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO14	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:34 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO14.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO15	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:63 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO15.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO16	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:NA | Age:11 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO16.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO17	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:7 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO17.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO18	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:M | Age:11 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO18.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO21	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:M | Age:10 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO21.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO41	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:NA | Age:54 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO41.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO53	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:44 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO53.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO61	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:20 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO61.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO63	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:6 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO63.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO66	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:M | Age:11 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO66.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO67	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:26 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO67.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO68	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:M | Age:7 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO68.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO69	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:NA | Age:9 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO69.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO70	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:40 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO70.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO72	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:5 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO72.mzXML
SUBJECT_SAMPLE_FACTORS           	-	HCO74	Population:Tunapuco | Industrialization_Category:Rural Traditional | Sex:F | Age:36 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=HCO74.mzXML
SUBJECT_SAMPLE_FACTORS           	-	SM01	Population:Matses | Industrialization_Category:Isolated Traditional | Sex:M | Age:30 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=SM01.mzXML
SUBJECT_SAMPLE_FACTORS           	-	SM02	Population:Matses | Industrialization_Category:Isolated Traditional | Sex:F | Age:25 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=SM02.mzXML
SUBJECT_SAMPLE_FACTORS           	-	SM03	Population:Matses | Industrialization_Category:Isolated Traditional | Sex:M | Age:10 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=SM03.mzXML
SUBJECT_SAMPLE_FACTORS           	-	SM10	Population:Matses | Industrialization_Category:Isolated Traditional | Sex:F | Age:6 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=SM10.mzXML
SUBJECT_SAMPLE_FACTORS           	-	SM23	Population:Matses | Industrialization_Category:Isolated Traditional | Sex:M | Age:7 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=SM23.mzXML
SUBJECT_SAMPLE_FACTORS           	-	SM28	Population:Matses | Industrialization_Category:Isolated Traditional | Sex:F | Age:52 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=SM28.mzXML
SUBJECT_SAMPLE_FACTORS           	-	SM29	Population:Matses | Industrialization_Category:Isolated Traditional | Sex:F | Age:50 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=SM29.mzXML
SUBJECT_SAMPLE_FACTORS           	-	SM33	Population:Matses | Industrialization_Category:Isolated Traditional | Sex:F | Age:5 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=SM33.mzXML
SUBJECT_SAMPLE_FACTORS           	-	SM37	Population:Matses | Industrialization_Category:Isolated Traditional | Sex:M | Age:12 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=SM37.mzXML
SUBJECT_SAMPLE_FACTORS           	-	SM39	Population:Matses | Industrialization_Category:Isolated Traditional | Sex:F | Age:40 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=SM39.mzXML
SUBJECT_SAMPLE_FACTORS           	-	SM41	Population:Matses | Industrialization_Category:Isolated Traditional | Sex:M | Age:6 | Time_Kept_on_Ice_before_Frozen:Within 4 days	Country_of_Origin=Peru; RAW_FILE_NAME=SM41.mzXML
#COLLECTION
CO:COLLECTION_SUMMARY            	Fecal material was deposited into polypropylene containers and then put on ice.
CO:COLLECTION_SUMMARY            	Samples were kept in ice while in the field until arriving at research
CO:COLLECTION_SUMMARY            	facilities equipped with freezers. The Norman samples were kept in ice after
CO:COLLECTION_SUMMARY            	collection and frozen at the laboratory within 24 hours. The Peruvian samples
CO:COLLECTION_SUMMARY            	were secured similarly to the Norman samples. After collection, samples were
CO:COLLECTION_SUMMARY            	stored on ice for four days until arriving at Lima, Peru. Samples were frozen
CO:COLLECTION_SUMMARY            	and sent to the laboratory in Norman, Oklahoma. Boulkiemdé samples were
CO:COLLECTION_SUMMARY            	collected similarly to Norman and Peruvian samples. After collection,
CO:COLLECTION_SUMMARY            	Boulkiemdé samples were frozen at -20 °C within 24 hours and kept frozen
CO:COLLECTION_SUMMARY            	overnight. Samples were thawed the following evening to extract DNA, refrozen at
CO:COLLECTION_SUMMARY            	-20 °C, and kept frozen until shipped to the laboratory in Norman, Oklahoma.
CO:COLLECTION_SUMMARY            	Upon arrival, 2 g of fecal material was extracted from each sample for anaerobic
CO:COLLECTION_SUMMARY            	culturing. Following this 2 g aliquoting, samples were frozen at -80 °C until
CO:COLLECTION_SUMMARY            	use for this project. The Norman, Tunapuco, and Matses samples had previously
CO:COLLECTION_SUMMARY            	been aliquoted and underwent 16S rRNA gene sequencing for an earlier study.
CO:SAMPLE_TYPE                   	Feces
CO:COLLECTION_LOCATION           	United States; Peru; Burkina Faso
CO:VOLUMEORAMOUNT_COLLECTED      	Variable; 50mg used for experimental analyses
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	The sample preparation protocol used for this project was adapted from a global
TR:TREATMENT_SUMMARY             	metabolite extraction protocol with proven success (Want et al. 2013). Samples
TR:TREATMENT_SUMMARY             	were thawed and 500 μl of chilled LC-MS grade water (Fisher Scientific) was
TR:TREATMENT_SUMMARY             	added to 50 mg of fecal material. Next, a TissueLyzer homogenized samples at 25
TR:TREATMENT_SUMMARY             	Hz for three minutes. Following homogenization, chilled LC-grade methanol
TR:TREATMENT_SUMMARY             	(Fisher Scientific) spiked with 4 μM sulfachloropyridazine as the internal
TR:TREATMENT_SUMMARY             	standard (IS) was added, bringing the total concentration to 50% methanol. The
TR:TREATMENT_SUMMARY             	TissueLyzer homogenized samples again at 25 Hz for three minutes, followed by
TR:TREATMENT_SUMMARY             	overnight incubation at 4 °C. The next day, samples were centrifuged at 16,000
TR:TREATMENT_SUMMARY             	x g at 4 °C for ten minutes. Aqueous supernatant was then removed and dried
TR:TREATMENT_SUMMARY             	using a SpeedVac vacuum concentrator. Dried extracts were frozen at -80 °C
TR:TREATMENT_SUMMARY             	until the day of MS analysis. Immediately prior to MS analysis, extracts were
TR:TREATMENT_SUMMARY             	resuspended in 150 μl chilled LC-MS methanol:water (1:1) spiked with 1 μg/ml
TR:TREATMENT_SUMMARY             	sulfadimethoxine as a second IS. After resuspension, samples were diluted to a
TR:TREATMENT_SUMMARY             	1:10 ratio. Diluted samples were sonicated using a Fisher Scientific Ultrasonic
TR:TREATMENT_SUMMARY             	Cleaning Bath at maximum power for ten minutes. Supernatants were spun briefly
TR:TREATMENT_SUMMARY             	to remove any particulates, then loaded into a 96-well plate for MS analysis.
TR:TREATMENT_SUMMARY             	One well contained only 150 μl of the resuspension solution to serve as blank
TR:TREATMENT_SUMMARY             	control.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	The sample preparation protocol used for this project was adapted from a global
SP:SAMPLEPREP_SUMMARY            	metabolite extraction protocol with proven success (Want et al. 2013). Samples
SP:SAMPLEPREP_SUMMARY            	were thawed and 500 μl of chilled LC-MS grade water (Fisher Scientific) was
SP:SAMPLEPREP_SUMMARY            	added to 50 mg of fecal material. Next, a TissueLyzer homogenized samples at 25
SP:SAMPLEPREP_SUMMARY            	Hz for three minutes. Following homogenization, chilled LC-grade methanol
SP:SAMPLEPREP_SUMMARY            	(Fisher Scientific) spiked with 4 μM sulfachloropyridazine as the internal
SP:SAMPLEPREP_SUMMARY            	standard (IS) was added, bringing the total concentration to 50% methanol. The
SP:SAMPLEPREP_SUMMARY            	TissueLyzer homogenized samples again at 25 Hz for three minutes, followed by
SP:SAMPLEPREP_SUMMARY            	overnight incubation at 4 °C. The next day, samples were centrifuged at 16,000
SP:SAMPLEPREP_SUMMARY            	x g at 4 °C for ten minutes. Aqueous supernatant was then removed and dried
SP:SAMPLEPREP_SUMMARY            	using a SpeedVac vacuum concentrator. Dried extracts were frozen at -80 °C
SP:SAMPLEPREP_SUMMARY            	until the day of MS analysis. Immediately prior to MS analysis, extracts were
SP:SAMPLEPREP_SUMMARY            	resuspended in 150 μl chilled LC-MS methanol:water (1:1) spiked with 1 μg/ml
SP:SAMPLEPREP_SUMMARY            	sulfadimethoxine as a second IS. After resuspension, samples were diluted to a
SP:SAMPLEPREP_SUMMARY            	1:10 ratio. Diluted samples were sonicated using a Fisher Scientific Ultrasonic
SP:SAMPLEPREP_SUMMARY            	Cleaning Bath at maximum power for ten minutes. Supernatants were spun briefly
SP:SAMPLEPREP_SUMMARY            	to remove any particulates, then loaded into a 96-well plate for MS analysis.
SP:SAMPLEPREP_SUMMARY            	One well contained only 150 μl of the resuspension solution to serve as blank
SP:SAMPLEPREP_SUMMARY            	control.
SP:EXTRACT_STORAGE               	On ice
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	None (Direct infusion)
CH:INSTRUMENT_NAME               	ThermoFisher Scientific Vanquish Flex Binary LC System
CH:COLUMN_NAME                   	Kinetex C18 core-shell column (50 x 2.1 mm, 1.7 μM particle size, 100 Å pore
CH:COLUMN_NAME                   	size)
CH:FLOW_GRADIENT                 	12.5 min runtime gradient
CH:COLUMN_TEMPERATURE            	40
CH:METHODS_FILENAME              	C18_RP_Pos_QEPlus_20180403_12.5mint_ddMS2.meth
CH:SOLVENT_A                     	LC-MS grade water with 0.1% formic acid
CH:SOLVENT_B                     	LC-MS grade acetonitrile with 0.1% formic acid
CH:INTERNAL_STANDARD             	Sulfadimethoxine
CH:SAMPLE_INJECTION              	5 uL randomized order
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive Plus Orbitrap
MS:INSTRUMENT_TYPE               	Triple quadrupole
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	LC was performed on a ThermoFisher Scientific Vanquish Flex Binary LC System
MS:MS_COMMENTS                   	with a Kinetex C18 core-shell column (50 x 2.1 mm, 1.7 μM particle size, 100 Å
MS:MS_COMMENTS                   	pore size). LC column was kept at 40 °C and the sample compartment was held at
MS:MS_COMMENTS                   	10 °C. The LC System was coupled to a ThermoFisher Scientific Q Exactive Plus
MS:MS_COMMENTS                   	Hybrid Quadrupole-Orbitrap Mass Spectrometer for MS/MS analysis. For the LC
MS:MS_COMMENTS                   	mobile phase, Solvent A was LC-MS grade water (Fisher Scientific) with 0.1%
MS:MS_COMMENTS                   	formic acid and Solvent B was LC-MS grade acetonitrile (Fisher Scientific) with
MS:MS_COMMENTS                   	0.1% formic acid. Elution gradient started at 5% Solvent B for one minute,
MS:MS_COMMENTS                   	increased to 100% Solvent B until minute nine, held at 100% Solvent B for two
MS:MS_COMMENTS                   	minutes, dropped to 5% Solvent B over 30 seconds, and 5% Solvent B for one
MS:MS_COMMENTS                   	minute as re-equilibration. Samples were injected in random order with an
MS:MS_COMMENTS                   	injection volume of 5 μl. After elution, electrospray ionization was conducted
MS:MS_COMMENTS                   	with spray voltage of 3.8 kV, auxiliary gas flow rate of 10, auxiliary gas
MS:MS_COMMENTS                   	temperature at 350 °C, sheath gas flow rate at 35, and sweep gas flow at 0.
MS:MS_COMMENTS                   	Capillary temperature was 320 °C and S-lens RF was 50 V. MS1 scan range was
MS:MS_COMMENTS                   	100-1,500 m/z, MS1 resolution was set to 35,000 and MS1 AGC target to 1e6. MS1
MS:MS_COMMENTS                   	data were obtained in positive mode and MS2 data were obtained using
MS:MS_COMMENTS                   	data-dependent acquisition. In each cycle, 5 MS/MS scans of the most abundant
MS:MS_COMMENTS                   	ion were recorded. Both MS1 and MS2 injection times were set at 100 ms. MS2
MS:MS_COMMENTS                   	resolutions were set to 17,500, MS2 AGC target was set to 5e5, and the inclusion
MS:MS_COMMENTS                   	window to 2 m/z. MS/MS was conducted at an apex trigger of 2-8 seconds and an
MS:MS_COMMENTS                   	exclusion window of 10 seconds. MS/MS collision energy gradually increased from
MS:MS_COMMENTS                   	20-40%.
MS:CAPILLARY_TEMPERATURE         	320°C
MS:IONIZATION                    	ESI
MS:MS_RESULTS_FILE               	ST002320_AN003787_Results.txt	UNITS:Peak area	Has m/z:Yes	Has RT:Yes	RT units:Minutes
#END