Supplementary Figures

Supplementary Figure 1.

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Supplementary Figure 2.

The effect of antibiotics on the relative abundance of Clostridium cluster XIVa. 2a) The

abundance of Clostridium cluster XIVa is significantly lower (LME: p=0.02) in samples that

have been collected after antibiotics intake (n=13, average time between antibiotics and

sampling 7 weeks) than in samples without antibiotics(n=70). Samples more than 1.5

times above the upper quartile or below the lower quartile are denoted by circles. 2b) In

the follow-up samples in average 25 weeks after the cessation of antibiotic usage the

abundance difference is not significant when compared to the baseline or the first sample

after antibiotic course (LME p=ns). Data shown from 6 subjects from whom all 3 samples

were available.

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Supplementary Figure 3.

The relative abundance of bifidobacteria. Differences between the age categories of

children are not significant (dashed line describes LME fit, p=ns), but all are significantly

higher than in adults (p<0.05 in all comparisons, Wilcoxon rank-sum test). Samples more

than 1.5 times above the upper quartile (3rd quartile) are denoted by circles.

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Supplementary Figure 4.

The relative abundance of phylum-level groups. In children, the increased relative

abundance was only observed in Clostridium clusters IV (d, LME, p=0.053) and XI (e,

LME, p=0.003), whereas no change was observed in the other phylum-level groups.

Statistical significances between age categories in children and adults were assessed by

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Wilcoxon rank-sum test and Benjamini-Hochberg p-value correction. Samples more than

1.5 times above the upper quartile (3rd quartile) are denoted by circles.

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Supplementary Figure 5.

The relative abundance of Akkermansia spp. in different age categories. The relative

abundance of Akkermansia spp. does not change during 1-5 years of age (LME: p=ns),

and is at similar level as compared to adults. Samples more than 1.5 times above the

upper quartile (3rd quartile) are denoted by circles.

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Supplementary Figure 6.

The stability of two main sub-groups of Bacteroidetes: Bacteroides (panel a) and

Prevotella spp. (panel b). The stability is assessed by Pearson correlation between

consecutive time points from oligo-level data. Each point plotted represents the older age

in the pair compared. The time interval between the first plotted time point and the

baseline sample is four months. Samples from the same individual are connected by solid

lines. The development of stability is estimated by linear mixed effects model, and

indicated by the dashed line. The profile similarities of Bacteroides spp. (p=0.03) increase

from 1 to 5 years, while no change is observed in Prevotella spp. (p=ns).

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Supplementary Figure 7.

The inter-individual similarity of microbiota in different age categories. In each age

category, the similarities are calculated by Pearson correlation between individuals.

Children in 3-4Y category have higher inter-individual similarity as compared to the other

age categories (p<0.05, Wilcoxon rank-sum test).

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Supplementary Figure 8.

The relative abundance of core microbiota in different age categories. No significant

difference between the age categories was observed (p=0.08, Kruskal-Wallis test).

Samples less than 1.5 times below the lower quartile (1st quartile) are denoted by circles.

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Supplementary Figure 9.

The relative abundance of butyrate-producing bacteria in different age categories. The

relative abundance of butyrate-producing bacteria increases significantly from 1 to 5 years

(LME: p=0.02), but is not significantly different from adults, mostly due to large variation in

the adult cohort. Samples less than 1.5 times below the lower quartile (1st quartile) are

denoted by circles.

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