Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children

Abstract

The colonization pattern of intestinal microbiota during childhood may impact health later in life, but children older than 1 year are poorly studied. We followed healthy children aged 1-4 years (n=28) for up to 12 months, during which a synbiotic intervention and occasional antibiotics intake occurred, and compared them with adults from the same region. Microbiota was quantified with the HITChip phylogenetic microarray and analyzed with linear mixed effects model and other statistical approaches. Synbiotic administration increased the stability of Actinobacteria and antibiotics decreased Clostridium cluster XIVa abundance. Bacterial diversity did not increase in 1- to 5-year-old children and remained significantly lower than in adults. Actinobacteria, Bacilli and Clostridium cluster IV retained child-like abundances, whereas some other groups were converting to adult-like profiles. Microbiota stability increased, with Bacteroidetes being the main contributor. The common core of microbiota in children increased with age from 18 to 25 highly abundant genus-level taxa, including several butyrate-producing organisms, and developed toward an adult-like composition. In conclusion, intestinal microbiota is not established before 5 years of age and diversity, core microbiota and different taxa are still developing toward adult-type configuration. Discordant development patterns of bacterial phyla may reflect physiological development steps in children.

Figure 1

The effect of age on (a) diversity, (b) richness and (c) evenness of microbiota. No significant change is observed for diversity, richness or evenness during 1–5 years. Left panel: solid line indicates repeated sampling from the same individual. Dashed line indicates regression fit with LME line (P=NS). Right panel: diversity, richness and evenness plotted in age categories. Samples 1.5 times more than the upper quartile (third quartile) or less than the lower quartile (first quartile) are denoted by circles. Microbial community is significantly less diverse (panel a) and rich (b) in all age categories in children than in adults, whereas being less even (c) in the ‘1–2 Y' and ‘4–5 Y' age categories than in adults. Significances were estimated by Wilcoxon rank-sum test, with Benjamini–Hochberg P-value correction.

Figure 2

Stability of total microbiota in children of 1 to 5 years old. Stability is assessed as the similarity (Pearson correlation) of microbiota profiles between consecutive time points. Each point plotted represents the older age in the pair compared. The time interval between the first plotted time point and the baseline sample point is 4 months. The microbiota stability is increasing significantly with age (LME: P=0.03, slope=0.006 per month). The model fit is indicated by the dashed line.

Figure 3

Relative abundance of Actinobacteria and Clostridium cluster III in different age categories. Between 1 and 5 years, the relative abundances of Actinobacteria (a) do not change (LME: P=NS), whereas the relative abundance of Clostridium cluster III (b) increases significantly (LME: P=0.03). The relative abundances of Actinobacteria (a) in all age categories in children are significantly higher than that of adults, whereas significant differences of Clostridium cluster III (b) between children and adults are observed in the first two age categories: ‘1–2 Y' (P=0.0008) and ‘2–3 Y' (P=0.003). Samples 1.5 times more than the upper quartile (third quartile) or less than the lower quartile (first quartile) are denoted by circles.

Figure 4

The stability of phylum-level groups in 1- to 5-year old children. The boxplot shows the distribution of profile similarities (Pearson correlation of oligo-level profiles between consecutive time points) of genus-like taxa with each phylum. The groups with average similarity <0.6 (indicated with the lower horizontal dashed line) are considered as low stability groups, whereas groups with average similarity >0.8 are considered as highly stable (indicated by the upper horizontal dashed line). The groups with similarities between 0.6 and 0.8 are considered moderately stable. Samples 1.5 times more than the upper quartile (third quartile) or less than the lower quartile (first quartile) are denoted by circles.

Figure 5

The development of stability of phylum-level groups in 1- to 5-year-old children. The stability is assessed by similarity of profiles (Pearson correlation) between consecutive time points from oligo-level data. Each plotted point represents the older age in the pair compared. The time interval from the first plotted time point to the baseline sample point is 4 months. Samples from the same individual are connected by solid lines. The development of stability is estimated by LME, and indicated by the dashed line. The stability of Bacteroidetes increases significantly (c, LME: P=0.04), whereas Clostridium cluster XI shows increasing trend (g, LME: P=0.08) and the stabilities of other phylum-level groups remain at similar levels at 1 to 5 years of age (a, b, d, e, f, h and i, LME: P=NS).

Figure 6

The development of core microbiota^#. The asterisk (*) indicates typical infant taxa that are diminished in the adult core. The taxa of butyrate-producing bacteria are underlined. ^# For the core microbiota estimation, see text for details.