Fig. 1

Taxonomic classification of metagenomic reads for EVC001-fed infants and controls. a Relative abundance of the top bacterial genera identified between the two groups of infants. b Relative abundance of bacterial species belonging to the Bifidobacterium genus identified among groups. c Hierarchical clustering based on a strain-level analysis of Bifidobacterium longum subspecies. Gene family profiles of a subgroup of reference genomes were selected from a global (n = 38) strain analysis. Each column represents the presence or absence of genes in a sample or a reference genome with respect to the total pangenome. All samples from EVC001-fed infants clustered together with B. longum subsp. infantis ATCC 15697 (B. infantis), whereas the samples from infants in the control group clustered separately with other B. longum subspecies (e.g., B. suis, B. longum DJ01A, and B. longum NCC2705). Functional analysis of gene families confirmed that the EVC001 samples were dominated by B. infantis due to the presence of unique genes (e.g., Blon_2348 in B. infantis), while genes present only in B. longum subsp. longum (e.g., araD; araA), were abundant in the communities from control infants. P-values were computed for each gene via Fisher’s exact test according to group