Additional file 1 of The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels
Creators: name: Anzà, Simone
name: Schneider, Dominik
name: Daniel, Rolf
name: Heistermann, Michael
name: Sangmaneedet, Somboon
name: Ostner, Julia
name: Schülke, Oliver
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Ecology
subject: Developmental Biology

description: Additional file 1. Amplification of 16S rRNA genes and sequencing: full procedure. Supplementary Table 1. Full models 1a-1c explaining the offspring’s gut bacteria alpha diversity (from richness estimators). Significant P values of explanatory variables are in bold. R2 indicates the conditional coefficient of determination. All covariates are logn-transformed and then z-transformed (mean = 0, SD = 1) to meet model requirements and increase model interpretability. (1) coded with “female” as the reference category, (2) coded with “infant” as the reference category, (3) coded with “lean” as the reference category, (4) coded with the group “MOT” as the reference category. Supplementary Table 2. Full model 1d-1e explaining the offspring’s gut bacteria alpha diversity (from richness-evenness estimators). Significant P values of explanatory variables are in bold. R2 indicates the conditional coefficient of determination. All covariates are logn-transformed and then z-transformed (mean = 0, SD = 1) to meet model requirements and increase model interpretability. (1) coded with “female” as the reference category, (2) coded with “infant” as the reference category, (3) coded with “lean” as the reference category, (4) coded with the group “MOT” as the reference category. Supplementary Table 3. Reduced models 1a-1c explaining the offspring’s gut bacteria alpha diversity (from richness estimators). Significant P values of explanatory variables are in bold. The model was tested via model comparison with null models: Model 1a: χ2 = 72.85, df = 11, p &lt; 0.001; Model 1b: χ2 = 91.98, df = 11, p &lt; 0.001; Model 1c: χ2 = 66.38, df = 11, p &lt; 0.001. R2 indicates conditional coefficient of determination. All covariates are logn-transformed and then z-transformed (mean = 0, SD = 1) to meet model requirements and increase model interpretability. (1) coded with “female” as the reference category, (2) coded with “infant” as the reference category, (3) coded with “lean” as the reference category, (4) coded with the group “MOT” as the reference category. Supplementary Table 4. Reduced model 1d and 1e explaining the offspring’s gut bacteria alpha diversity (from richness-evenness estimators). Significant P values of explanatory variables are in bold. The model was tested via model comparison with null models: Model 1d: χ2 = 29.26, df = 15, p = 0.015; Model 1e: χ2 = 20.08, df = 11, p = 0.044. R2 indicates the conditional coefficient of determination. All covariates represent average values log-transformed and then z-transformed. All covariates are logn-transformed and then z-transformed (mean = 0, SD = 1) to meet model requirements and increase model interpretability. (1) coded with “female” as the reference category, (2) coded with “infant” as the reference category, (3) coded with “lean” as the reference category, (4) coded with the group “MOT” as the reference category. Supplementary Table 5. Full linear models explaining the Firmicutes to Bacteroidota ratio of offspring’s gut bacteria during the lean (Full-Model L) and the rich season (Full-Model R). (1) indicates that the predictor has been logn-transformed and then z-transformed with mean = 0 and SD = 1 to meet model requirements and to increase model interpretability; (2) indicates that the predictor has been z-transformed with mean = 0 and SD = 1; (3) coded with the group “MOT” as the reference category; (3) coded with “female” as the reference category. Supplementary Table 6. Effect of Early-preGC in interaction with age on gut bacterial composition during the rich season. Infants are excluded from the analyses. UN = unclassified at the genus level. Supplementary Figure 1. Predicted functional pathways significantly affected by the prenatal maternal GCs and offspring age (Late-PreGC*Age). KOs are grouped at level 3 of KEGG database. Only significantly affected pathways are plotted (BH adjusted p-values). Colored bars indicate the effect of an increase in 1SD of Late-preGC (SD = 67.0 ng/g) estimated at the mean value of age (mean = 4.7 years), and at the mean value of all the other predictors. Red and black lines indicate the effect estimated at the mean plus1SD (red = 7.1 years) and at the mean minus1SD (black = 2.3) of age. When the bar is not plotted, the effect of the same increase in maternal GCs at the mean age is 0. Taxa showing the black head (estimates at 2.3 years) further from 0 than the red head (estimates at 7.1 years) show an effect that is reduced with age. Supplementary Figure 2. Predicted functional pathways significantly affected by the postnatal maternal GCs and offspring age (PostGC*Age). KOs are grouped at level 3 of KEGG database. Only significantly affected pathways are plotted (BH adjusted p-values). Colored bars indicate the effect of an increase in 1SD of PostGC (SD = 52.7 ng/g) estimated at the mean value of age (mean = 4.7 years), and at the mean value of all the other predictors. Red and black lines indicate the effect estimated at the mean plus1SD (red = 7.1 years) and at the mean minus1SD (black = 2.3) of age. When the bar is not plotted, the effect of the same increase in maternal GCs at the mean age is 0. Taxa showing the black head (estimates at 2.3 years) further from 0 than the red head (estimates at 7.1 years) show an effect that is reduced with age. Supplementary Figure 3. Predicted functional pathways significantly affected by the offspring GCs and offspring age (OffspringGC*Age). KOs are grouped at level 3 of KEGG database. Only significantly affected pathways are plotted (BH adjusted p-values). Colored bars indicate the effect of an increase in 1SD of OffspringGC (SD = 130.1 ng/g) estimated at the mean value of age (mean = 4.7 years), and at the mean value of all the other predictors. Red and black lines indicate the effect estimated at the mean plus1SD (red = 7.1 years) and at the mean minus1SD (black = 2.3) of age. When the bar is not plotted, the effect of the same increase in maternal GCs at the mean age is 0. Taxa showing the black head (estimates at 2.3 years) further from 0 than the red head (estimates at 7.1 years) show an effect that is reduced with age.