Additional file 1 of In utero human intestine contains maternally derived bacterial metabolites
Creators: name: Wang, Wenjia
name: Gu, Weihong
name: Schweitzer, Ron
name: Koren, Omry
name: Khatib, Soliman
name: Tseng, George
name: Konnikova, Liza
Publisher: name: figshare
Year: 2025
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Supplementary Material 1: Supplementary Figure S1. t-distributed stochastic neighbor embedding (t-SNE) plot using all metabolites. The samples are color-coded by different tissue sites, with different letter shapes according to their source subjects. Those subjects that only have one sample are labelled as “Others”. Supplementary Figure S2. Distribution of gestational agein samples (A) The density curves of gestational age for samples within each of the four groups. (B) Boxplots of gestational age for each group where each black dot represents a sample. The median sample age shown on the top is 22.5 weeks for decidua, 18.5 weeks for GI, 21 weeks for meconium and 22 weeks for PV group respectively. The pairwise difference among the four groups is not significant (i.e., all adjusted P-value &gt; 0.05) by one-factor ANOVA and post-hoc analysis. Supplementary Figure S3. Correlation between tissue groups of microbial metabolites, xenobiotics, and fetal metabolites. Correlation between tissue groups of microbial metabolites, xenobiotics, and fetal metabolites. Boxplots visualizing the correlations between GI and decidua samples and between GI and meconium samples from the subjects at gestational age of 23 weeks, based on 41 microbial metabolites, 47 xenobiotics, and 8 fetal-derived metabolites respectively from Supplementary Table S5. Red asterisk points represent the pairwise correlations between tissue samples from subject No. 16. Supplementary Figure S4. Metabolites validation. Boxplots in the first row show the abundance difference between tissue groups for the eight metabolites in the main data set, while the second and third rows present the difference in validation data sets for the corresponding metabolites. Supplementary Figure S5. Markers for cell type annotation. Dot plot of the marker genes for the annotation of fetal epithelial cells (A) and of fetal immune cells (B). Color represents normalized mean expression of marker genes in each cell type, and size indicates the proportion of cells expressing marker genes. Supplementary tables: Table S1. Sample demographics. Demographic information for all samples used. N/A, not available; SI, small intestine; LI, large intestine; SI Mec, small intestine meconium; LI Mec, large intestine meconium; F, female; M, male. Supplementary Table S2. List of the detectable metabolites and their abbreviations. Supplementary Table S3. Difference of metabolite abundance in pairwise comparisons between GI and the other tissue groups. Supplementary Table S4. Enriched pathways in pairwise comparisons between GI and the other tissue groups. Supplementary Table S5. List of microbial metabolites, xenobiotics, and fetal-derived metabolites used in the analysis. * indicates the microbial metabolites reported by (30) (Supplementary Tables S8, S9), and † indicates the identified microbial metabolites based on (32, 33). Supplementary Table S6. Correlation coefficients and significance levels (p value and q value) of gestational age for each bile acid by ANOVA analysis with adjustment of gestational age. Supplementary Table S7. Correlation coefficients between the abundance of individual metabolites and the gestational age within each tissue group. Except for the bile acids and SCFA in Table 2[1], showing all the other nine bile acids and two SCFAs. The columns are the correlation coefficient within each tissue group separately. The q value for the correlation coefficient shows in parathesis *P &lt; 0.05, **P &lt; 0.01, ***P &lt; 0.001. Supplementary Table S8. Comprehensive information of all metabolites detected in the samples. The table contain all the metabolites detected in the samples with information about MW, RT values, and if the metabolites detected based on MS2 or just by MS1 scan, MzCloud best much, as well as alternative options for the metabolite's names especially those that identified just by MS1. Supplementary Table S9. Information on metabolites discussed in the manuscript. Identification information of discussed metabolites including microbial metabolites (secondary bile acid, SCFA, aromatic lactic acids, and others), xenobiotics, fetal-derived metabolites, primary bile acids, aromatic amino acids, top 20 abundant metabolites in GI tract in Fig. 1B, and DE metabolites labelled on volcano plots of Fig. 1 C-E CE: This citation is not found in floats.Please check if it is citation or not and proceed further