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Klaassens et al. Microbiome Res Rep 2024;3:38 https://dx.doi.org/10.20517/mrr.2024.13 Page 13 of 19

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Figure 5. Probiotic strain abundances in the SHIME model. (A) High inter-individual differences in relative abundance of Bb; (B)
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Relative abundance of Lf. From samples after 48 h in the ex vivo SHIME model for each infant fecal inoculum. Blank: No probiotics; iPF:
intact protein formula; GOS: galactooligosaccharides; eHF: extensively hydrolyzed formula; Bb: B. breve DSMZ 32583; Lf: L. fermentum
CECT 5716; Lf + Bb: both probiotics added; VD: fecal inoculum derived from vaginally delivered infant; CS: fecal inoculum derived from
cesarean-delivered infant; SHIME: Simulator of the Human Intestinal Microbial Ecosystem.

strain-dependent effects (e.g., acetate production) were still found in vitro and ex vivo, and therefore even in
complex ecosystems, but independent of the formula matrix.

Nevertheless, high inter-individual differences in the donor microbiota composition and probiotic
abundance were observed in the complex ecosystem and could be demonstrated at the strain level.