Bacteroides abundance drives birth mode dependent infant gut microbiota developmental trajectories

Abstract

Background and aims: Birth mode and other early life factors affect a newborn's microbial colonization with potential long-term health effects. Individual variations in early life gut microbiota development, especially their effects on the functional repertoire of microbiota, are still poorly characterized. This study aims to provide new insights into the gut microbiome developmental trajectories during the first year of life.

Methods: Our study comprised 78 term infants sampled at 3 weeks, 3 months, 6 months, and 12 months (n = 280 total samples), and their mothers were sampled in late pregnancy (n = 50). Fecal DNA was subjected to shotgun metagenomic sequencing. Infant samples were studied for taxonomic and functional maturation, and maternal microbiota was used as a reference. Hierarchical clustering on taxonomic profiles was used to identify the main microbiota developmental trajectories in the infants, and their associations with perinatal and postnatal factors were assessed.

Results: In line with previous studies, infant microbiota composition showed increased alpha diversity and decreased beta diversity by age, converging toward an adult-like profile. However, we did not observe an increase in functional alpha diversity, which was stable and comparable with the mother samples throughout all the sampling points. Using a de novo clustering approach, two main infant microbiota clusters driven by Bacteroidaceae and Clostridiaceae emerged at each time point. The clusters were associated with birth mode and their functions differed mainly in terms of biosynthetic and carbohydrate degradation pathways, some of which consistently differed between the clusters for all the time points. The longitudinal analysis indicated three main microbiota developmental trajectories, with the majority of the infants retaining their characteristic cluster until 1 year. As many as 40% of vaginally delivered infants were grouped with infants delivered by C-section due to their clear and persistent depletion in Bacteroides. Intrapartum antibiotics, any perinatal or postnatal factors, maternal microbiota composition, or other maternal factors did not explain the depletion in Bacteroides in the subset of vaginally born infants.

Conclusion: Our study provides an enhanced understanding of the compositional and functional early life gut microbiota trajectories, opening avenues for investigating elusive causes that influence non-typical microbiota development.

Keywords: Bacteroides; cesarean section; functional maturation; hierarchical clustering; infant gut microbiota; shotgun metagenomics; vaginal delivery.

Figure 1

Taxonomic and functional maturation of infant microbiota during the first year of life. (A) PCoA on genus level taxonomic profiles. Taxonomic profiles were aggregated at the genus level. The beta diversity Bray-Curtis distance was computed between sample pairs and plotted as a PCoA. (B) Taxonomic alpha diversity and richness. Taxonomic profiles were aggregated at the species level. The Shannon alpha-diversity index and the Chao1 richness index were computed for each sample. (C) PCoA on KO functional profiles. The KO profiles were normalized as count per million reads. The beta diversity Bray-Curtis distance was computed between each sample pair and plotted as a PCoA. (D) Functional alpha diversity and richness. The KO profiles were normalized as previously described. The Shannon alpha-diversity index and the Chao1 richness index were computed for each sample. The comparisons between groups were conducted by unpaired Wilcoxon test.

Figure 2

Infant gut microbiota clusters, representative bacterial families, and enriched functions related to carbohydrate metabolism. At each sampling time point (3 weeks, 3 months, 6 months, and 1 year), the infants' samples were clustered by hierarchical clustering on taxonomic profiles aggregated at the family level using the Aitchison distance (Column 1). The color blocks below the dendrograms represent the clusters identified using the silhouette maximization method (Column 2). The average relative abundance of the families in each cluster was represented in the associated bar plots. Families with detection and prevalence below 10% were grouped into the “Other” category (Column 3). Bar plot showing the coefficients of differentially abundant carbohydrate metabolism-related pathways (MaAsLin2, linear model, q < 0.1) in the two identified clusters. Negative coefficients indicate association to cluster 1.

Figure 3

Three major microbiota development trajectories identified. (A) Alluvial plot showing the evolution of infants' microbiota trajectories through the first year of life, grouped according to the microbiota clusters identified at each time point. Groups of infants are colored according to the type of their trajectories. (B) Average relative abundance of bacterial families for infants within the same trajectory. Families with below 10% of relative abundance and prevalence are summed and grouped as “Other.” (C) The proportion of infants born by CS and VD infants with or without IAP in each trajectory.

Figure 4

Depletion of genus Bacteroides in a subset of VD infants. (A) PCA biplot based on family-level taxonomic profiles for VD infants at 3 weeks of age. Taxonomic profiles obtained for the 3-week samples were aggregated at the family level, and low abundance taxa were excluded before computing an Aitchinson distance between samples. Samples in the PCA biplot are colored as per the groups based on relative abundance of Bacteroides genus. Bacterial families contributing most to the observed variation were plotted as arrows on the biplot. (B) Average microbiota composition for infants grouped by the abundance of Bacteroides at 3 weeks. Taxonomic profiles are aggregated at the family level, and families with below 10% of relative abundance and prevalence are summed and grouped as “Other.” (C) Alluvial plot showing the evolution over the first year of life of infants according to the relative abundance of Bacteroides. A cutoff of 1% relative abundance of Bacteroides was chosen to group the samples, and the infants are colored by the relative abundance of Bacteroides at 3 weeks. (D) The taxonomic richness of the Bacteroides species (Chao1 index) in the infants and their respective mothers according to Bacteroides relative abundance at 3 weeks.