Fig. 3

The microbiome response in the gut to the probiotic engraftment in humans and mice. A The Aitchison distance between the samples in baseline and other time points both in the human and mouse model. The colored points represented the samples at different time points. We found that interindividual heterogeneity in the human gut microbiota is greatest among those in the gut microbiota of all host models. B The temporal dynamic of 19 intestinal species belonged to the genera Bacteroides and Bifidobacterium, which were commonly identified in both human and mouse models. The dynamics of the same species residing in both humans and mice were highly divergent, suggesting niche-specific adaptation strategies of resident gut microbes responding to probiotic invasion. C The ecological relationships between the Lp082 and resident intestinal microbes are visualized by the co-occurrence networks in the human and mouse model. The nodes in different colors respectively represent Lp082 (green), the probiotic positively correlated species (orange), the probiotic negatively correlated species (purple), and the species indirectly correlated with the probiotic (grey). The correlation strength between nodes (species) was calculated by the SpiecEasi based on the CLR-transformed microbial relative abundance. The thickness of an edge represents the correlation strength between two nodes. A dashed edge indicates a negative correlation while a solid edge indicates a positive correlation between microbial species