Fig. 6

The variable bifidogenic effect observed in vivo was reproduced in vitro in the organoid platform as shown by a 16S rRNA amplicon sequencing and b high-throughput qPCR. c Shannon diversity and species richness within microbiota-colonized organoids declined over time. d Unweighted UniFrac PCoA plots revealed differences between old and young microbiota upon colonization in organoids, which converged to a single grouping over 72 h. e Taxonomy plots of microbiota-colonized organoids showed changes over time in communities derived from both old and young animals