Fig. 2. Specific day care is a significant contributor to gut microbial composition in early childhood.

a Binary Jaccard distance was calculated between pairs of age-matched children (born within up to 1 month apart). Distances are shown for age-matched children pairs participating in the same day care (orange) or a different day care facility (blue), showing that from the second sampling onward, age-matched pairs from the same day care share more of their microbiome in comparison to pairs from different day care facilities. P-values for differences between same and different day care pairs were calculated using a two-sided Mann–Whitney test. b PERMANOVA shows that inter-individual variation explains most (44%) of the variation when using longitudinal sampling, followed by age (11%), day care class (6%), and day care facility (4%) (left most column). The effect of day care facility and class is further noted when examining each sampling point separately, where the variation explained by day care class increases to 12% in the fourth and fifth sampling point. Stars show statistical significance (*P ≤ 0.01). Variance is estimated for each feature independently, while accounting for age, gender, and subject when needed (see Methods section). Total n is shown in brackets. c Age against relative abundance of 4 ASVs significantly associated with day care class in the maaslin2 analysis (see Methods section). Barnesiellaceae appeared in 4 of the 7 children in day care C class 2, and in none of the other children. Longicatena also appeared in 4 of the 7 children in day care C class 2, and in none of the other children (not the same 4 children as Barnesiellaceae). Veillonella appeared in 12 of the 14 children in day care C class 1, and in additional 2 children from day care B class 1. Lastly, Ruminococcus appeared in 4 of the 12 children in day care B class 1, and in 4 of the 6 children in day care B class 2, and in none of the other day cares. d A cohort figure showing all children from specific day care classes over age, similar to Fig. 1a. Samples positive to Veillonella (ASV1147, Supplementary Data Source) are marked in a black circle. Source data are provided as a Source Data file.