Table 3.

Significant shifts in microbiota relative abundances on the genera level after prebiotic intervention, according to 16S-rRNA sequencing and linear mixed effects modelling after FDR-correction for multiple comparisons

	Interaction effect time (follow-up)×intervention (prebiotic)		ANOVA null model comparison
Increased abundance	b	t	P value	padj
Anaerostipes	0.73	3.01	0.003	0.017
Bifidobacterium	9.82	10.42	<0.001	<0.001
Collinsella	2.66	4.96	<0.001	<0.001
Holdemanella	0.37	3.13	0.002	0.011
Lachnospiraceae FCS020 group	0.21	3.31	0.001	0.006
Lacticaseibacillus	0.10	2.05	<0.001	0.002
Lactiplantibacillus	0.03	2.82	<0.001	<0.001
Lactobacillus*	2.08	2.65	0.008	0.045
Ligilactobacillus	0.28	2.67	0.008	0.045
Limosilactobacillus	0.28	5.10	<0.001	<0.001
Decreased abundance
Desulfovibrio	0.20	3.41	0.001	0.006
Eggerthella	0.33	3.46	0.001	0.006
Eubacterium brachy group	0.11	3.18	0.002	0.011
Eubacterium eligens group	0.21	2.76	0.006	0.033
Roseburia	1.10	3.86	<0.001	0.001
Ruminococcus gauvreauii group	0.69	3.86	<0.001	0.001
Shuttleworthia	0.08	2.78	0.006	0.033
Subdoligranulum	1.30	2.82	0.005	0.028

Linear mixed effects modelling outcome compared to null model and model of interest as follows (ANOVA model comparison with p<0.05): with the Formula: bacterial_genus_of_interest−time point×intervention+time point+intervention+(1+(intervention+time point)|subject). All models run on n_obs =204 in n_subj=58 and listed in alphabetical order of genera of interest.

*Statistics refer to models without random slopes due to non-convergence.

ANOVA, analysis of variance; FDR, false-discovery rate.