Fig. 2: Functional and phenotype characteristics differ between persistent colonizing and transient colonizing species.

Radar plots showing the fraction of biological functions or pathways enriched in either (A) core metabolism, virulence, or mobile genetic elements (MGEs) or (B) accessory metabolism, tested by linear mixed-effects models (adjusted p-value < 10⁻³). Persistent colonizing species (PCS) were enriched in core metabolism whilst transient colonizing species (TCS) were enriched in accessory metabolism (e.g., BTEX contaminants). We estimated physiological properties of PCS and TCS by growth rate estimations using GRiD scores (C–F) and genome-scale metabolic modeling (G, H). We estimated GRiD scores of PCS and TCS from (C) individuals with microbiomes highly enriched in PCS species and (D) individuals with microbiomes highly enriched in TCS and observed higher GRiD scores for PCS. In additional experiments investigating bioreactor fermentation of human faecal samples, we observed higher GRiD scores for (E) PCS after 24 h, compared to original faecal samples, whereas (F) TCS GRiD scores remained unchanged at 24 h. We also predicted (G) the growth rates and (H) their variance for PCS and TCS using the representative genome-scale metabolic models and found higher growth rates and less growth variances of PCS. For boxplots, Q1, median, and Q3 quantiles of given boxes were denoted, together with outliers shown as dots.