Fig. 2: High resolution community and intra-species population dynamics during gut colonization.

a Population of ~10⁸ E. coli cells with ~5 × 10⁵ unique chromosomal barcodes is introduced into mice with reduced microbiota by antibiotic pre-treatment (cohort 1). Fecal samples were collected over a 2-week period to track both community-level and intra-species dynamics. The leftmost panel shows the barcodes in the input (gavage) sample. The 1000 most frequent barcodes are uniquely colored, whereas the rest are shown in gray. Identical barcodes are colored consistently across mouse replicates and cohorts (see Supplementary Fig. 3a for Muller plot). b Dominant clonal clusters were identified by clustering barcodes that persisted for most of the 2-week period. Pairwise Pearson correlation of barcode frequency time series was used as the distance metric. These dominant clusters represent ~5–7% of total unique barcodes. The clusters are ranked by their average frequency (see Supplementary Fig. 6d). Roman numerals indicate distinct phases determined by DCM (Fig. 3). c Community dynamics by 16S rRNA profiling are analyzed at the level of the family. d Barcode frequency dynamics in germ-free (gf) mice colonized with the same E. coli population. The most frequent 1000 barcodes are colored uniquely, whereas the rest are shown in gray. Identical barcodes are colored similarly across mouse replicates and cohorts (see Supplementary Fig. 3b for the Muller plot). e. Dominant clonal clusters are determined by clustering of barcodes that persisted for most of the 2-week period (see Supplementary Fig. 6e). Phases are determined from DCM analysis of the gf cohort (Supplementary Fig. 7: DCM of gf cohort). f Community dynamics (16S rRNA profiling) are analyzed at the level of the family. E. coli did not successfully colonize the community, as shown by the CFU (Fig. 1e). There are not enough cells to perform high-resolution lineage-tracking with sufficient accuracy (Supplementary Fig. 4). g Community dynamics in mice with reduced microbiota, but non-gavage with E. coli, showing the recovery of bacterial community from the treatment of antibiotic cocktail. Colors correspond different bacterial families (legend box).