#METABOLOMICS WORKBENCH rennylan_20240907_125332 DATATRACK_ID:5179 STUDY_ID:ST003508 ANALYSIS_ID:AN005762 PROJECT_ID:PR002154
VERSION             	1
CREATED_ON             	October 2, 2024, 7:01 pm
#PROJECT
PR:PROJECT_TITLE                 	Associations Between Maternal Microbiome, Metabolome and Incidence of Low-Birth
PR:PROJECT_TITLE                 	Weight in Guatemalan Participants from the Women First Trial
PR:PROJECT_SUMMARY               	Low birth weight (babies born at less than 2,500 grams) affects approximately 15
PR:PROJECT_SUMMARY               	to 20 percent of global births annually and is associated with poor child
PR:PROJECT_SUMMARY               	development. The goal of this study was to examine relationships between
PR:PROJECT_SUMMARY               	maternal microbial taxa, fecal metabolites, and maternal anthropometry on
PR:PROJECT_SUMMARY               	incidence of LBW in resource-limited settings. This was a secondary analysis of
PR:PROJECT_SUMMARY               	the Women First trial conducted in a semi-rural region of Guatemala. Maternal
PR:PROJECT_SUMMARY               	weight was measured at 12 and 34 weeks (wk) of gestation. Infant anthropometry
PR:PROJECT_SUMMARY               	measures were collected within 48 h of delivery. Maternal fecal samples at 12
PR:PROJECT_SUMMARY               	and 34 wk were used for microbiome (16S rRNA gene amplicon sequencing) and
PR:PROJECT_SUMMARY               	metabolomics analysis (34 wk only). Linear mixed models using the MaAslin2
PR:PROJECT_SUMMARY               	package were utilized to assess changes in microbiome associated with LBW.
PR:PROJECT_SUMMARY               	Predictive models using gradient boosted machines (XGBoost) were developed using
PR:PROJECT_SUMMARY               	the H2o.ai engine. No differences in β-diversity were observed at either time
PR:PROJECT_SUMMARY               	point between mothers with LBW infants relative to normal weight (NW) infants.
PR:PROJECT_SUMMARY               	Simpson diversity at 12 and 34 wk was lower in mothers with LBW infants. Notable
PR:PROJECT_SUMMARY               	differences in genus-level abundance between LBW and NW mothers (p< 0.05) were
PR:PROJECT_SUMMARY               	observed at 12 weeks with increasing abundances of Barnesiella,
PR:PROJECT_SUMMARY               	Faecalibacterium, Sutterella, and Bacterioides. At 34 weeks, there were lower
PR:PROJECT_SUMMARY               	abundances of Magasphaera, Phascolarctobacterium, and Turicibacter and higher
PR:PROJECT_SUMMARY               	abundances of Bacteriodes, and Fusobacterium in mothers with LBW infants. Fecal
PR:PROJECT_SUMMARY               	metabolites related to bile acids, tryptophan metabolism and fatty acid related
PR:PROJECT_SUMMARY               	metabolites changed in mothers with LBW infants. Classification models to
PR:PROJECT_SUMMARY               	predict LBW based on maternal anthropometry and predicted microbial functions
PR:PROJECT_SUMMARY               	showed moderate performance. Collectively, the findings indicate that less
PR:PROJECT_SUMMARY               	beneficial gut microbes and circulating metabolites of the mother is associated
PR:PROJECT_SUMMARY               	with low birth weight infants compared to normal weight. Future research should
PR:PROJECT_SUMMARY               	target functional and predictive roles of the maternal gut microbiome in infant
PR:PROJECT_SUMMARY               	birth outcomes including birthweight.
PR:INSTITUTE                     	Arkansas Children's Nutrition Center
PR:DEPARTMENT                    	Pediatrics
PR:LABORATORY                    	Metabolomics and Analytical Chemistry Core
PR:LAST_NAME                     	Lan
PR:FIRST_NAME                    	Renny
PR:ADDRESS                       	15 Children's Way
PR:EMAIL                         	slan@uams.edu
PR:PHONE                         	5013642813
#STUDY
ST:STUDY_TITLE                   	Associations Between Maternal Microbiome, Metabolome and Incidence of Low Birth
ST:STUDY_TITLE                   	Weight in Guatemalan Participants from the Women First Trial
ST:STUDY_SUMMARY                 	Low birth weight (babies born at less than 2,500 grams) affects approximately 15
ST:STUDY_SUMMARY                 	to 20 percent of global births annually and is associated with poor child
ST:STUDY_SUMMARY                 	development. The goal of this study was to examine relationships between
ST:STUDY_SUMMARY                 	maternal microbial taxa, fecal metabolites, and maternal anthropometry on
ST:STUDY_SUMMARY                 	incidence of LBW in resource-limited settings. This was a secondary analysis of
ST:STUDY_SUMMARY                 	the Women First trial conducted in a semi-rural region of Guatemala. Maternal
ST:STUDY_SUMMARY                 	weight was measured at 12 and 34 weeks (wk) of gestation. Infant anthropometry
ST:STUDY_SUMMARY                 	measures were collected within 48 h of delivery. Maternal fecal samples at 12
ST:STUDY_SUMMARY                 	and 34 wk were used for microbiome (16S rRNA gene amplicon sequencing) and
ST:STUDY_SUMMARY                 	metabolomics analysis (34 wk only). Linear mixed models using the MaAslin2
ST:STUDY_SUMMARY                 	package were utilized to assess changes in microbiome associated with LBW.
ST:STUDY_SUMMARY                 	Predictive models using gradient boosted machines (XGBoost) were developed using
ST:STUDY_SUMMARY                 	the H2o.ai engine. No differences in β-diversity were observed at either time
ST:STUDY_SUMMARY                 	point between mothers with LBW infants relative to normal weight (NW) infants.
ST:STUDY_SUMMARY                 	Simpson diversity at 12 and 34 wk was lower in mothers with LBW infants. Notable
ST:STUDY_SUMMARY                 	differences in genus-level abundance between LBW and NW mothers (p< 0.05) were
ST:STUDY_SUMMARY                 	observed at 12 weeks with increasing abundances of Barnesiella,
ST:STUDY_SUMMARY                 	Faecalibacterium, Sutterella, and Bacterioides. At 34 weeks, there were lower
ST:STUDY_SUMMARY                 	abundances of Magasphaera, Phascolarctobacterium, and Turicibacter and higher
ST:STUDY_SUMMARY                 	abundances of Bacteriodes, and Fusobacterium in mothers with LBW infants. Fecal
ST:STUDY_SUMMARY                 	metabolites related to bile acids, tryptophan metabolism and fatty acid related
ST:STUDY_SUMMARY                 	metabolites changed in mothers with LBW infants. Classification models to
ST:STUDY_SUMMARY                 	predict LBW based on maternal anthropometry and predicted microbial functions
ST:STUDY_SUMMARY                 	showed moderate performance. Collectively, the findings indicate that less
ST:STUDY_SUMMARY                 	beneficial gut microbes and circulating metabolites of the mother is associated
ST:STUDY_SUMMARY                 	with low birth weight infants compared to normal weight. Future research should
ST:STUDY_SUMMARY                 	target functional and predictive roles of the maternal gut microbiome in infant
ST:STUDY_SUMMARY                 	birth outcomes including birthweight.
ST:INSTITUTE                     	Arkansas Children's Nutrition Center
ST:DEPARTMENT                    	Pediatrics
ST:LABORATORY                    	Metabolomics and Analytical Chemistry Core
ST:LAST_NAME                     	Lan
ST:FIRST_NAME                    	Renny
ST:ADDRESS                       	108 Holland Lane
ST:EMAIL                         	slan@uams.edu
ST:PHONE                         	9196073272
#SUBJECT
SU:SUBJECT_TYPE                  	Human
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
#FACTORS
#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           	626020B	F1	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_20B_F1_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_20B_F1_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	631970P	F10	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_70P_F10_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_70P_F10_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	673530J	F11	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm3	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_30J_F11_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_30J_F11_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	642110I	F12	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_10I_F12_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_10I_F12_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	626620A	F13	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_20A_F13_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_20A_F13_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	615680Q	F14	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_80Q_F14_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_80Q_F14_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	615950N	F15	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_50N_F15_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_50N_F15_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	615970H	F16	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_70H_F16_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_70H_F16_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	600950V	F17	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_50V_F17_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_50V_F17_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	662990J	F18	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm3	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_90J_F18_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_90J_F18_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	667770V	F19	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_70V_F19_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_70V_F19_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	663170T	F2	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_70T_F2_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_70T_F2_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	601280M	F20	Sample source:Feces | Low Birth Weight status status:no | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_80M_F20_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_80M_F20_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	606140D	F21	Sample source:Feces | Low Birth Weight status status:no | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_40D_F21_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_40D_F21_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	626540V	F22	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_40V_F22_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_40V_F22_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	600920H	F23	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_20H_F23_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_20H_F23_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	631930E	F24	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm3	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_30E_F24_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_30E_F24_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	600220M	F25	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_20M_F25_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_20M_F25_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	693680B	F26	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_80B_F26_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_80B_F26_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	616360G	F27	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm3	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_60G_F27_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_60G_F27_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	663040J	F28	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_40J_F28_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_40J_F28_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	616170L	F29	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_70L_F29_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_70L_F29_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	663010S	F3	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_10S_F3_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_10S_F3_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	641730G	F30	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm3	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_30G_F30_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_30G_F30_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	606170R	F31	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_70R_F31_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_70R_F31_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	610870N	F32	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_70N_F32_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_70N_F32_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	610440P	F33	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_40P_F33_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_40P_F33_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	672940S	F34	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_40S_F34_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_40S_F34_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	652160K	F35	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm3	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_60K_F35_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_60K_F35_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	653080D	F36	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_80D_F36_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_80D_F36_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	668010Q	F37	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_10Q_F37_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_10Q_F37_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	626840J	F38	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_40J_F38_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_40J_F38_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	663090R	F39	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm3	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_90R_F39_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_90R_F39_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	653880R	F4	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_80R_F4_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_80R_F4_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	636410F	F40	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm1	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_10F_F40_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_10F_F40_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	653760E	F5	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm3	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_60E_F5_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_60E_F5_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	663060D	F6	Sample source:Feces | Low Birth Weight status status:No | Treatment Arm:Arm3	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_60D_F6_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_60D_F6_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	606150A	F7	Sample source:Feces | Low Birth Weight status status:yes | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_50A_F7_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_50A_F7_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	663080U	F8	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_80U_F8_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_80U_F8_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	641950P	F9	Sample source:Feces | Low Birth Weight status status:Yes | Treatment Arm:Arm2	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_50P_F9_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_50P_F9_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	n/a	Process Blank	Sample source:Water | Low Birth Weight status status:n/a | Treatment Arm:n/a	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_Reagent_Blank_pos_02_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_Reagent_Blank_Neg_02_20220725.raw
SUBJECT_SAMPLE_FACTORS           	n/a	QC10	Sample source:Feces | Low Birth Weight status status:n/a | Treatment Arm:n/a	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_Pool_QC10_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_Pool_QC10_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	n/a	QC11	Sample source:Feces | Low Birth Weight status status:n/a | Treatment Arm:n/a	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_Pool_QC11_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_Pool_QC11_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	n/a	QC12	Sample source:Feces | Low Birth Weight status status:n/a | Treatment Arm:n/a	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_Pool_QC12_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_Pool_QC12_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	n/a	QC13	Sample source:Feces | Low Birth Weight status status:n/a | Treatment Arm:n/a	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_Pool_QC13_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_Pool_QC13_Neg_20220725.raw
SUBJECT_SAMPLE_FACTORS           	n/a	QC9	Sample source:Feces | Low Birth Weight status status:n/a | Treatment Arm:n/a	RAW_FILE_NAME(Raw data file name_Positive)=Laxmi_Pool_QC9_Pos_20220725.raw; RAW_FILE_NAME(Raw data file name_Negative)=Laxmi_Pool_QC9_Neg_20220725.raw
#COLLECTION
CO:COLLECTION_SUMMARY            	Fecal samples were collected at 34 weeks gestation (Arms 1, 2, and 3). Arm 1
CO:COLLECTION_SUMMARY            	received a daily small-quantity lipid-based micronutrient supplement (sqLNS)
CO:COLLECTION_SUMMARY            	starting at 3 months before conception and throughout pregnancy, Arm 2 received
CO:COLLECTION_SUMMARY            	daily sqLNS supplementation starting at 12 weeks of gestation and through the
CO:COLLECTION_SUMMARY            	remainder of pregnancy, and Arm 3 received only the local standard of care which
CO:COLLECTION_SUMMARY            	included iron and folate supplementation. Stool was collected into fecal bags
CO:COLLECTION_SUMMARY            	using a sterile scoop and placed into a Styrofoam container with ice or ice
CO:COLLECTION_SUMMARY            	packs. The research team picked up samples the day of stool passage, transferred
CO:COLLECTION_SUMMARY            	samples back to facility where they were aliquoted into storage tubes. Samples
CO:COLLECTION_SUMMARY            	were stored at -80° C until analyses.
CO:SAMPLE_TYPE                   	Feces
#TREATMENT
TR:TREATMENT_SUMMARY             	This is a secondary analysis of the Women First: Preconception Maternal
TR:TREATMENT_SUMMARY             	Intervention Nutrition Trial (ClinicalTrials.gov ID: NCT01883193, (Hambidge et
TR:TREATMENT_SUMMARY             	al. 2019; DOI: 10.1093/ajcn/nqy228)). Only participants recruited from
TR:TREATMENT_SUMMARY             	Chimaltenango, Guatemala were included in the study. The full study details can
TR:TREATMENT_SUMMARY             	be found in previous publications (Hambidge et al 2019, DOI:
TR:TREATMENT_SUMMARY             	10.1093/ajcn/nqy228, Tang et al, 2022, DOI: 10.3389/fmicb.2022.823757). Briefly,
TR:TREATMENT_SUMMARY             	participants were randomized into three different treatment arms: Arm 1 received
TR:TREATMENT_SUMMARY             	a daily small-quantity lipid-based micronutrient supplement (sqLNS) starting at
TR:TREATMENT_SUMMARY             	≥ 3 months before conception and throughout pregnancy, Arm 2 received daily
TR:TREATMENT_SUMMARY             	sqLNS supplementation starting at 12 weeks of gestation and through the
TR:TREATMENT_SUMMARY             	remainder of pregnancy, and Arm 3 received only the local standard of care which
TR:TREATMENT_SUMMARY             	typically included iron and folate supplementation (Figure 1A). All participants
TR:TREATMENT_SUMMARY             	recruited for this study were between 16-35 years old, parity 0-5, and planned
TR:TREATMENT_SUMMARY             	to conceive during the following 18 months. Written informed consent was
TR:TREATMENT_SUMMARY             	obtained from all the participants. Study protocol was approved by Institutional
TR:TREATMENT_SUMMARY             	Review Board at the University of Colorado and Comité de Ética de la
TR:TREATMENT_SUMMARY             	Universidad Francisco Marroquín.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Approximately 100 mg of wet stool samples at 34 weeks LBW and NW group, were
SP:SAMPLEPREP_SUMMARY            	extracted and subjected to untargeted metabolomics analyses using liquid
SP:SAMPLEPREP_SUMMARY            	chromatography/mass spectrometry (LC-MS) at the Metabolomics and Analytical
SP:SAMPLEPREP_SUMMARY            	Chemistry Core at Arkansas Children’s Nutrition Center. Briefly, 500 µL of
SP:SAMPLEPREP_SUMMARY            	LC-MS grade 50% of MeOH in water and 1 ml of Acetonitrile was added to the
SP:SAMPLEPREP_SUMMARY            	stool. The mixture was quantitatively transferred to screw cap tube containing
SP:SAMPLEPREP_SUMMARY            	200 µl of 1.44 mm beads, 100 µL of 0.5 mm beads and 3 beads of 2.8 mm beads.
SP:SAMPLEPREP_SUMMARY            	Samples were homogenized with a Precellys 24 two cycles, 30 secs each at 5300
SP:SAMPLEPREP_SUMMARY            	rpm. . The mixture was vortexed for 10 min at 4 °C on a ThermoMixer (Eppendorf
SP:SAMPLEPREP_SUMMARY            	Inc., Enfield, CT) and then centrifuged at 4,347x g at 4 °C for 10 min
SP:SAMPLEPREP_SUMMARY            	(Centrifuge 5910 Ri, Eppendorf Inc., Enfield, CT). 700 µL of the supernatant
SP:SAMPLEPREP_SUMMARY            	was aliquoted and subsequently dried by using a vacuum concentrator (SpeedVac
SP:SAMPLEPREP_SUMMARY            	SPD210, Thermo Fisher Scientific Waltham, MA). Extracts were then reconstituted
SP:SAMPLEPREP_SUMMARY            	in 250μL of 5% methanol spiked with 1000 ng mL-1 sulfadimethoxine (SDMO) for
SP:SAMPLEPREP_SUMMARY            	immediate instrumental analysis. Pooled quality control (QC) samples were
SP:SAMPLEPREP_SUMMARY            	prepared by pooling equal volumes of each sample extract (50 µl).
SP:SAMPLEPREP_PROTOCOL_ID        	Meghan_et_al_Sample_Preparation_Chromatography_and_Mass_Spectrometry_conditions.pdf
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	An Orbitrap Exploris 480 mass spectrometer (ThermoFisher Scientific, Waltham,
CH:CHROMATOGRAPHY_SUMMARY        	MA) interfaced with the Vanquish UHPLC system and fitted with high flow and low
CH:CHROMATOGRAPHY_SUMMARY        	flow heat-electrospray ionization (HESI) probes was used for instrumental
CH:CHROMATOGRAPHY_SUMMARY        	analysis. A flow rate of 0.3 mL min–1 was employed to carry out
CH:CHROMATOGRAPHY_SUMMARY        	chromatographic separations using an Acquity Premier CSH C18 1.7 μm × 2.1 ×
CH:CHROMATOGRAPHY_SUMMARY        	100 mm Column (Waters, USA). Water (A) and acetonitrile (B), both acidified with
CH:CHROMATOGRAPHY_SUMMARY        	0.1% formic acid, made up the mobile phase system. The LC gradient was set to 0
CH:CHROMATOGRAPHY_SUMMARY        	min, 0% B; 2 min, 40% B; 8 min, 98% B; 10 min, 98% B; 10.5 min, 0% B; 15 min, 0%
CH:CHROMATOGRAPHY_SUMMARY        	B. Throughout the analysis, a 40 °C column temperature and a 5.0 μL injection
CH:CHROMATOGRAPHY_SUMMARY        	volume were employed.
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Thermo Vanquish
CH:COLUMN_NAME                   	Acquity Premier CSH C18 (100 x 2.1 mm, 1.7 um)
CH:SOLVENT_A                     	100% water; 0.1% formic acid
CH:SOLVENT_B                     	100% acetonitrile; 0.1% formic acid
CH:FLOW_GRADIENT                 	The LC gradient was set to 0 min, 0% B; 2 min, 40% B; 8 min, 98% B; 10 min, 98%
CH:FLOW_GRADIENT                 	B; 10.5 min, 0% B; 15 min, 0% B.
CH:FLOW_RATE                     	0.3 mL/min
CH:COLUMN_TEMPERATURE            	40 °C
CH:METHODS_FILENAME              	Meghan_et_al_Sample_Preparation_Chromatography_and_Mass_Spectrometry_conditions.pdf
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
AN:ANALYSIS_PROTOCOL_FILE        	Meghan_et_al_Sample_Preparation_Chromatography_and_Mass_Spectrometry_conditions.pdf
#MS
MS:INSTRUMENT_NAME               	Thermo Orbitrap Exploris 480
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	The samples were analysed in both positive and negative ionization mode. The
MS:MS_COMMENTS                   	electrospray ionization voltage was kept at 3.5 kV in the negative mode. Sheath
MS:MS_COMMENTS                   	gas was set to 35, auxiliary gas was set at 10, and sweep gas was set to 1
MS:MS_COMMENTS                   	arbitrary unit (Arb). The ion transfer tube temperature (ITT) was set at 350°C
MS:MS_COMMENTS                   	and the vaporizer temperature was set at 350°C. The scan parameters for the
MS:MS_COMMENTS                   	mass spectrometer included 6 s chromatogram peak width and a 15-min duration
MS:MS_COMMENTS                   	time in DDA mode. Full MS1 used the Orbitrap mass analyzer with a resolution of
MS:MS_COMMENTS                   	180,000, scan range (m/z) of 60–900 in positive mode and 58-870 in negative
MS:MS_COMMENTS                   	mode, maximum injection time (MIT) of 100, automatic gain control (AGC) target
MS:MS_COMMENTS                   	of 5e5, 1 microscan, and RF lens set to 70. MS/MS analysis was performed on the
MS:MS_COMMENTS                   	pooled QC samples using six rounds of iterative DDA (ThermoFisher AcquireX) at a
MS:MS_COMMENTS                   	resolution of 30,000 FWH using a stepped HCD collision energies of 20, 40, and
MS:MS_COMMENTS                   	60 V. Other MS/MS parameters included: MIT of 50 ms, microscan set to 1, AGC set
MS:MS_COMMENTS                   	to 1e6, and a scan range of 60–900 in positive mode and 58-870 in negative
MS:MS_COMMENTS                   	mode. The top 5 abundant precursors within an isolation window of 2 m/z were
MS:MS_COMMENTS                   	chosen for MS/MS analysis. Xcalibur v4.4.16.14 (ThermoFisher Scientific,
MS:MS_COMMENTS                   	Waltham, MA) was used for instrument control and data acquisition.
MS:MS_RESULTS_FILE               	ST003508_AN005762_Results.txt	UNITS:Peak area	Has m/z:Yes	Has RT:Yes	RT units:Minutes
#END