Additional file 1: Table S1. of Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort

Metadata collected from the Infantmet cohort. Blank space in the metadata table indicates that information on that particular factor was not received for that infant (or mother). Table S2. Preterm infant details and clinical metadata, including gestational age and antibiotic exposure(s). Table S3. Complete list of all oligonucleotides used for PCR amplification. Table S4. The influence of birth mode and getational age on the infant gut microbiota from week 1 to 24 of life. Results of pairwise PerMANOVA tests on Spearman distance matrix between birth modes at given time points, after adjustment for batch effects. p value adjustment was performed using Benjamini-Hochberg. Table S5. Reporting classes of metabolites annotated in urine. Table S6. 2S MS2 and MS3 spectra of annotated biomarkers. Detailed breakdown of the classification of the biomarkers used for metabolomics analysis. Table S7. Prolonged breastfeeding influences FT-CS but not FT-SVD infants’ gut microbiota. PerMANOVA p value results comparing the microbiota of infants breastfed for different durations, after adjusting for potential batch effect. Where birth modes were combined, p values were obtained after adjusting for birth modes. Table S8. Genera found to be significantly different at week 24 between infants that were breastfed for less than, or greater than 4 months. In red (positive log2 fold change) indicates genera that are higher in infants that were breastfed for longer, whereas in green are genera that are lower in infants that were breastfed for longer. Table S9. Pairwise comparisons of Spearman distances between groups of infants at due dates, grouped by the number of weeks early that they were born. PerMANOVA was used on Spearman distance matrix between all samples of the group pairs being tested, and multiple testing. Table S10. Genera found to be differentially abundant, or trending toward significance, between birth modes at week 1. L2FC: Log2 fold change; p.adj: adjusted p value; sig.: significance level. Positive L2FC (in blue) indicates that the genus is higher in the first birth mode of the pair listed, whereas a negative p value (in orange) indicates that the genus is lower in the first birth mode listed. Table S11. Genera found to be differentially abundant, or trending toward significance, between birth modes at week 4. L2FC: Log2 fold change; p.adj: adjusted p value; sig.: significance level. Positive L2FC (in blue) indicates that the genus is higher in the first birth mode of the pair listed, whereas a negative p value (in orange) indicates that the genus is lower in the first birth mode listed. Table S12. Genera found to be differentially abundant, or trending toward significance, between birth modes at week 8. L2FC: Log2 fold change; p.adj: adjusted p value; sig.: significance level. Positive L2FC (in blue) indicates that the genus is higher in the first birth mode of the pair listed, whereas a negative p value (in orange) indicates that the genus is lower in the first birth mode listed. Table S13. Genera found to be differentially abundant, or trending toward significance, between birth modes at week 24. L2FC: Log2 fold change; p.adj: adjusted p value; sig.: significance level. Positive L2FC (in blue) indicates that the genus is higher in the first birth mode of the pair listed, whereas a negative p value (in orange) indicates that the genus is lower in the first birth mode listed. Table S14. Genera found to be differentially abundant, or trending toward significance, between time points for FT-CS. L2FC: Log2 fold change; p.adj: adjusted p value; sig.: significance level. Positive L2FC (in blue) indicates that the genus is higher at the earlier of the two compared time points, whereas a negative p value (in orange) indicates that the genus is lower in the first of the two time points. Table S15. Genera found to be differentially abundant, or trending toward significance, between time points for PT-CS. L2FC: Log2 fold change; p.adj: adjusted p value; sig.: significance level. Positive L2FC (in blue) indicates that the genus is higher at the earlier of the two compared time points, whereas a negative p value (in orange) indicates that the genus is lower in the first of the two time points. Table S16. Genera found to be differentially abundant, or trending toward significance, between time points for FT-SVD. L2FC: Log2 fold change; p.adj: adjusted p value; sig.: significance level. Positive L2FC (in blue) indicates that the genus is higher at the earlier of the two compared time points, whereas a negative p value (in orange) indicates that the genus is lower in the first of the two time points. Table S17. Genera found to be significantly different, or trending toward different, between time points for PT-SVD. L2FC: Log2 fold change; p.adj: adjusted p value; sig.: significance level. Positive L2FC (in blue) indicates that the genus is higher at the earlier of the two compared time points, whereas a negative p value (in orange) indicates that the genus is lower in the first of the two time points. Table S18. Significant negative correlations of abundances of genera pairs. Correlations were tested with Pearson correlation. The false discovery rate was adjusted for with Benjamini-Hochberg adjustment. (XLSX 188 kb)