#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; 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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