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Additional file 3. Attirition analyses.

Additional file 2. STROBE checklist.

Figure S2. Gene count distribution in Dutch children. Black indicates all individuals, n = 281; red indicates lean children (BMI z-score

Figure S1. Compositional and functional comparison between Dutch children and adults. Relative abundance of major phyla in Dutch children (a) and adults (b). (c) Relative abundance of COG (clusters of orthologous groups) categories across each sample in Dutch children and adults. (PDF 298 kb)

Figure S4. Comparison of gut microbial functional potentials between enterotypes. (a) Differentially enrichment of KEGG modules between enterotypes. Dashed lines indicate a reporter score of 1.96, corresponding to 95% confidence in a normal distribution. (b) Heatmap showing that the relative abundance profiles of 8 selected KOs involved in key functions of metabolic pathways for carbohydrate metabolism (K00845, K01051 and K00873) and amino acid biosynthesis (K01738, K00928, K00058, K00651and K00765) distinguishes E3 from E1 and E2. (PDF 358 kb)

Figure S6. Correlations between continuous phenotypic parameters. (a) Spearman’s rank correlations between continuous phenotypic parameters in the entire cohort (n = 281). (b) Spearman’s correlations between continuous phenotypic parameters in E1 (n = 143). (c) Spearman’s rank correlations between continuous phenotypic parameters in E2 (n = 74). (d) Spearman’s rank correlations between continuous phenotypic parameters in E3 (n = 64). The “*” indicates significant correlation with adjusted P

Figure S8. Evaluation of enterotying protocols for Dutch children. (a-c) Evaluation of optimal cluster number by using the DMM protocol (a), the PAM-JSD protocol (b) and the PAM-BC protocol (c). The optimal number of clusters was calculated using Laplace approximation for the DMM protocol (a) and the Calinskiâ Harabasz index for the PAM-based protocols (b-c). Cluster stability using the DMM (d), the PAM-JSD (e) and the PAM-BC protocols (f). The X axis indicates resampling number and the Y axis indicates the consistency of resampling relative to the original result based on 281 samples. (PDF 221 kb)

Figure S5. Correlations between continuous phenotypic parameters and species profile in the entire cohort. (a) Spearman’s rank correlations between early events, pre-school lifestyle and species profile (n = 281). (b) Spearman’s rank correlations between blood parameters and species profiles (n = 281). P values were adjusted for each parameter. The “*” indicates significant correlation with adjusted P

Figure S4. Comparison of gut microbial functional potentials between enterotypes. (a) Differentially enrichment of KEGG modules between enterotypes. Dashed lines indicate a reporter score of 1.96, corresponding to 95% confidence in a normal distribution. (b) Heatmap showing that the relative abundance profiles of 8 selected KOs involved in key functions of metabolic pathways for carbohydrate metabolism (K00845, K01051 and K00873) and amino acid biosynthesis (K01738, K00928, K00058, K00651and K00765) distinguishes E3 from E1 and E2. (PDF 358 kb)

Figure S7. Correlations between Streptococcus species profile and selected phenotypic parameters in enterotypes. Heatmap showing the Spearman’s rank correlations between Streptococcus species and selected phenotypic parameters including free fatty acids levels and the intake of total carbohydrate, total fat, dietary fiber, and plant-based protein. P values were adjusted for each parameter. The “*” indicates significant correlation with adjusted P 0.05. FFA, free fatty acids. (PDF 197 kb)

Figure S5. Correlations between continuous phenotypic parameters and species profile in the entire cohort. (a) Spearman’s rank correlations between early events, pre-school lifestyle and species profile (n = 281). (b) Spearman’s rank correlations between blood parameters and species profiles (n = 281). P values were adjusted for each parameter. The “*” indicates significant correlation with adjusted P

Figure S6. Correlations between continuous phenotypic parameters. (a) Spearman’s rank correlations between continuous phenotypic parameters in the entire cohort (n = 281). (b) Spearman’s correlations between continuous phenotypic parameters in E1 (n = 143). (c) Spearman’s rank correlations between continuous phenotypic parameters in E2 (n = 74). (d) Spearman’s rank correlations between continuous phenotypic parameters in E3 (n = 64). The “*” indicates significant correlation with adjusted P

Figure S3. Comparison of gut microbial compositional and functional structure between enterotypes. (a-c) Comparison of gene count, gene-based Shannon diversity and reads mapping ratio to the taxonomic annotated genes between enterotypes. (d-f) Comparison of gene count, KO-based Shannon diversity and reads mapping ratio to the KO annotated genes between enterotypes. Dunn’s post hoc test, *, P

Figure S7. Correlations between Streptococcus species profile and selected phenotypic parameters in enterotypes. Heatmap showing the Spearman’s rank correlations between Streptococcus species and selected phenotypic parameters including free fatty acids levels and the intake of total carbohydrate, total fat, dietary fiber, and plant-based protein. P values were adjusted for each parameter. The “*” indicates significant correlation with adjusted P 0.05. FFA, free fatty acids. (PDF 197 kb)

Figure S8. Evaluation of enterotying protocols for Dutch children. (a-c) Evaluation of optimal cluster number by using the DMM protocol (a), the PAM-JSD protocol (b) and the PAM-BC protocol (c). The optimal number of clusters was calculated using Laplace approximation for the DMM protocol (a) and the Calinskiâ Harabasz index for the PAM-based protocols (b-c). Cluster stability using the DMM (d), the PAM-JSD (e) and the PAM-BC protocols (f). The X axis indicates resampling number and the Y axis indicates the consistency of resampling relative to the original result based on 281 samples. (PDF 221 kb)

Figure S3. Comparison of gut microbial compositional and functional structure between enterotypes. (a-c) Comparison of gene count, gene-based Shannon diversity and reads mapping ratio to the taxonomic annotated genes between enterotypes. (d-f) Comparison of gene count, KO-based Shannon diversity and reads mapping ratio to the KO annotated genes between enterotypes. Dunn’s post hoc test, *, P

Figure S1. Flow chart of participating cohorts and individuals. Table S1. Cohort-specific methods of data collection for maternal anthropometrics and gestational age. Table S2. Box-Cox t model specifications for each maternal pre-pregnancy body mass index group. Table S3. Gestational weight measurements per participating cohort and maternal pre-pregnancy body mass index group. Figure S2. Sample size according to gestational age for each maternal pre-pregnancy body mass index group. Figure S3. Predicted z scores for the average weight gain according to gestational age for each maternal pre-pregnancy body mass index group. Table S4. Week-specific Box-Cox t model parameters and selected percentiles of gestational weight gain for maternal pre-pregnancy underweight. Table S5. Week-specific Box-Cox t model parameters and selected percentiles of gestational weight gain for maternal pre-pregnancy normal weight. Table S6. Week-specific Box-Cox t model parameters and selected percentiles of gestational weight gain for maternal pre-pregnancy overweight. Table S7. Week-specific Box-Cox t model parameters and selected percentiles of gestational weight gain for maternal pre-pregnancy obesity grade 1. Table S8. Week-specific Box-Cox t model parameters and selected percentiles of gestational weight gain for maternal pre-pregnancy obesity grade 2. Table S9. Week-specific Box-Cox t model parameters and selected percentiles of gestational weight gain for maternal pre-pregnancy obesity grade 3. Table S10. Local institutional ethical review boards per cohort. (DOCX 631 kb)

Figure S1. Flow chart of participating cohorts and individuals. Table S1. Cohort-specific methods of data collection for maternal anthropometrics and gestational age. Table S2. Box-Cox t model specifications for each maternal pre-pregnancy body mass index group. Table S3. Gestational weight measurements per participating cohort and maternal pre-pregnancy body mass index group. Figure S2. Sample size according to gestational age for each maternal pre-pregnancy body mass index group. Figure S3. Predicted z scores for the average weight gain according to gestational age for each maternal pre-pregnancy body mass index group. Table S4. Week-specific Box-Cox t model parameters and selected percentiles of gestational weight gain for maternal pre-pregnancy underweight. Table S5. Week-specific Box-Cox t model parameters and selected percentiles of gestational weight gain for maternal pre-pregnancy normal weight. Table S6. Week-specific Box-Cox t model parameters and selected percentiles of gestational weight gain for maternal pre-pregnancy overweight. Table S7. Week-specific Box-Cox t model parameters and selected percentiles of gestational weight gain for maternal pre-pregnancy obesity grade 1. Table S8. Week-specific Box-Cox t model parameters and selected percentiles of gestational weight gain for maternal pre-pregnancy obesity grade 2. Table S9. Week-specific Box-Cox t model parameters and selected percentiles of gestational weight gain for maternal pre-pregnancy obesity grade 3. Table S10. Local institutional ethical review boards per cohort. (DOCX 631 kb)