Microbial diversity within samples (alpha diversity) as measured by the Shannon index—which incorporates both microbial richness and evenness—showed highly significant differences across the four study time points ( p = 0.0002) when all dose groups were combined.
While these changes fell just short of significance, the findings are consistent with the in vitro experiments and prior work supporting that infant microbiota convert HMOs to SCFAs 46 .
The microbes enriched after HMO treatment included 13 members of the Bacteroides genus, which collectively showed a trend towards depletion on day 7 but clear expansion compared to baseline on day 14 (Fig. 3 B–C).