Microba Research Discovery Report

Methods:

P lmer study group effect (sqrt): Differentially abundant functions were identified by linear mixed effect regression without confounders. Random effects: Participant (intercept). Fixed effects: Fibre_Intake, Treatment, Fibre_Intake vs Treatment. Effect tested: Fibre_Intake.

P lmer study group effect (clr): Differentially abundant functions were identified by linear mixed effect regression without confounders. Random effects: Participant (intercept). Fixed effects: Fibre_Intake, Treatment, Fibre_Intake vs Treatment. Effect tested: Fibre_Intake.

P lmer time effect (sqrt): Differentially abundant functions were identified by linear mixed effect regression without confounders. Random effects: Participant (intercept). Fixed effects: Fibre_Intake, Treatment, Fibre_Intake vs Treatment. Effect tested: Treatment.

P lmer time effect (clr): Differentially abundant functions were identified by linear mixed effect regression without confounders. Random effects: Participant (intercept). Fixed effects: Fibre_Intake, Treatment, Fibre_Intake vs Treatment. Effect tested: Treatment.

P lmer treatment effect (interaction) (sqrt): Differentially abundant functions were identified by linear mixed effect regression without confounders. Random effects: Participant (intercept). Fixed effects: Fibre_Intake, Treatment, Fibre_Intake vs Treatment. Effect tested: Fibre_Intake vs Treatment.

P lmer treatment effect (interaction) (clr): Differentially abundant functions were identified by linear mixed effect regression without confounders. Random effects: Participant (intercept). Fixed effects: Fibre_Intake, Treatment, Fibre_Intake vs Treatment. Effect tested: Fibre_Intake vs Treatment.

Glossary:

clr: Centered log-ratio transformation. P Welch's ANOVA (sqrt): Welch's ANOVA p-values (Anova was run on sqrt transformed abundances). It is an alternative to the classic ANOVA and can be used even if the samples have unequal variances and/or unequal sample sizes. P Welch's t-test (sqrt): Welch's T-test p-values (run on sqrt transformed abundances). It is an alternative to the classic Student's t-test and is more reliable if the data violates the assumption of homogeneity of variances and/or if the study conditions have unequal sample sizes. P Welch's ANOVA (clr): Welch's ANOVA p-values (Anova was run on clr transformed abundances). It is an alternative to the classic ANOVA and can be used even if the samples have unequal variances and/or unequal sample sizes. P Welch's t-test (clr): Welch's T-test p-values (run on clr transformed abundances). It is an alternative to the classic Student's t-test and is more reliable if the data violates the assumption of homogeneity of variances and/or if the study conditions have unequal sample sizes. P lmer XXX (clr): P-value of Linear Mixed-Effects Regression on clr transformed abundances, testing significance of XXX effect. Varying intercepts per subjects are used to control for repeated measures. Pbonf: Bonferroni corrected p-value. FDR: False Discovery Rate q-value. Mean Pos: Mean abundance in positive samples. Positive samples: The number and percentage of samples in which each function has been detected. Positive XXX: The number and percentage of positive samples in study group XXX. Positive_XXX_percent: Percentage of positive samples in study group XXX. P Welch's t-test (Aldex2): Expected P value of Welch’s t-test computed by Aldex2. FDR Welch's t-test (Aldex2): Expected Benjamini-Hochberg corrected P value for Welch’s t-test. P Wilcoxon rank test (Aldex2): Expected P value of Wilcoxon rank test computed by Aldex2. FDR Wilcoxon rank test (Aldex2): Expected Benjamini-Hochberg corrected P value of Wilcoxon test. P Kruskal-Wallace test (Aldex2): Expected P value of Kruskal-Wallace test. FDR Kruskal-Wallace test (Aldex2): Expected Benjamini-Hochberg corrected P value of Kruskal-Wallace test. P GLM test (Aldex2): Expected P value of generalized linear model. FDR GLM test (Aldex2): Expected Benjamini-Hochberg corrected P value of generalized linear model.