Fig. 3: Variation across samples is highly impacted by the dominant Bifidobacterium species.

A Principal Coordinate Analysis (PCoA) of infant gut microbiome samples using Bray-Curtis dissimilarity. Points are color-coded based on the dominant Bifidobacterium species in each sample, and non-Bifidobacterium dominated samples are colored in gray. Samples without a dominant species (>30% relative abundance) are labeled as “No dominant” (yellow). The size of each point represents the relative abundance of the dominant bacteria in that sample. Ellipses encompass four groups identified using k-means clustering. Each group represents a primary dominant species (indicated by the ellipse color): BL. infantis (blue), BL. longum (green), B. breve (red), and “Mixed” (gray). B Changes in group assignment observed in consecutive samples from the same infant (colors as in A). C Microbial diversity of samples within each group (measured by the Shannon index; colors as in A; two sided t-test, n = 80 samples from 21 infants, ***p ≤ 0.001, ****p ≤ 0.0001). Box boundaries are the 25th and 75th percentiles, and the median is highlighted. Whiskers represent 1.5 * IQR and points past them are outliers. D Relative abundance of BL. infantis (x-axis) versus the relative abundance of B. breve (y-axis) in each sample, indicating the mutual exclusiveness of the two species.