Development of gut microbiota during the first 2 years of life

Abstract

Although development of microbiota in childhood has been linked to chronic immune-related conditions, early childhood determinants of microbiota development have not been fully elucidated. We used 16S rRNA sequencing to analyse faecal and saliva samples from 83 children at four time-points during their first 2 years of life and from their mothers. Our findings confirm that gut microbiota in infants have low diversity and highlight that some properties are shared with the oral microbiota, although inter-individual differences are present. A considerable convergence in gut microbiota composition was noted across the first 2 years of life, towards a more diverse adult-like microbiota. Mode of delivery accounted for some of the inter-individual variation in early childhood, but with a pronounced attenuation over time. Our study extends previous research with further characterization of the major shift in gut microbiota composition during the first 2 years of life.

Figure 1

Flow chart of the study population. The cohort consists of pregnant women who lived in Stockholm, Sweden enrolled in the LifeGene study. After obtaining parental consent, the children were included in the prospective cohort (n = 93). A red cross indicates that questionnaires or saliva samples were not administrated. Light green questionnaire symbol indicates that the answers were not used in the current study. Number of samples with at least 12,588 reads reported in black font. Number of samples sequenced are reported in grey font. The figure is made by Andreas Dahlin at Visualize your Science.

Figure 2

Principal coordinate analysis plot (Bray–Curtis distances) illustrating the children and their mother’s overall composition of the gut and oral microbiota at different time points, from birth (neonatal sample) of the child to 24 months and from mothers at 26–28 weeks of gestation and 6 months after delivery. W gestational week and m month.

Figure 3

Comparison of microbiota composition based on Bray–Curtis distances. The shorter the distance between any pair of comparisons indicate greater similarity between microbial communities collected at those times. W gestational week and m month. Symbols represent means and error bars 95% confidence intervals. (a) Comparisons of gut microbiota at different sampling times, where distances between different sampling points within the same child/mother (self), and distances between unrelated children (non-self) and between unrelated mothers (non-self) are denoted. (b) Comparisons between gut and oral microbiota, and between children and their mothers and unrelated mothers. The distance between child and mother is based on the maternal sample at gestational week 26–28.

Figure 4

Bacterial phyla present in at least 75% of the faecal samples. a Stacked bar charts of the relative distribution of phyla detected in the gut at different time points. (b) Model-based predictions of relative abundance of phyla in the gut of children plotted against age. Lines indicate mean values (solid) and 95% confidence intervals (dashed). The y-axis shows the relative abundance in proportion. The predictions are shown from the 10th to the 90th percentile of age. W gestational week and m month.

Figure 5

Model-based predictions of relative abundance in bacterial phyla and specific operational taxonomic units (OTUs) in the gut microbiota by mode of delivery plotted against age. Lines indicate mean values (solid) and 95% confidence intervals (dashed), adjusted for potential confounders (see Table 1). P reflect for the interaction between mode of delivery and child age. All continuous adjustment variables are fixed at their median value and all categorical adjustment variables are fixed at their most common category.