Structure and function of the healthy pre-adolescent pediatric gut microbiome - PubMed (original) (raw)

doi: 10.1186/s40168-015-0101-x.

Kevin Riehle 3 4, Ruth Ann Luna 5 6, Erica M Weidler 7 8 9, Michelle Rubio-Gonzales 5 6, Toni-Ann Mistretta 5 6, Sabeen Raza 5 6, Harsha V Doddapaneni 10, Ginger A Metcalf 10, Donna M Muzny 10, Richard A Gibbs 10, Joseph F Petrosino 11 10 12, Robert J Shulman 7 8 9, James Versalovic 5 6

Affiliations

Structure and function of the healthy pre-adolescent pediatric gut microbiome

Emily B Hollister et al. Microbiome. 2015.

Abstract

Background: The gut microbiome influences myriad host functions, including nutrient acquisition, immune modulation, brain development, and behavior. Although human gut microbiota are recognized to change as we age, information regarding the structure and function of the gut microbiome during childhood is limited. Using 16S rRNA gene and shotgun metagenomic sequencing, we characterized the structure, function, and variation of the healthy pediatric gut microbiome in a cohort of school-aged, pre-adolescent children (ages 7-12 years). We compared the healthy pediatric gut microbiome with that of healthy adults previously recruited from the same region (Houston, TX, USA).

Results: Although healthy children and adults harbored similar numbers of taxa and functional genes, their composition and functional potential differed significantly. Children were enriched in Bifidobacterium spp., Faecalibacterium spp., and members of the Lachnospiraceae, while adults harbored greater abundances of Bacteroides spp. From a functional perspective, significant differences were detected with respect to the relative abundances of genes involved in vitamin synthesis, amino acid degradation, oxidative phosphorylation, and triggering mucosal inflammation. Children's gut communities were enriched in functions which may support ongoing development, while adult communities were enriched in functions associated with inflammation, obesity, and increased risk of adiposity.

Conclusions: Previous studies suggest that the human gut microbiome is relatively stable and adult-like after the first 1 to 3 years of life. Our results suggest that the healthy pediatric gut microbiome harbors compositional and functional qualities that differ from those of healthy adults and that the gut microbiome may undergo a more prolonged development than previously suspected.

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Figures

Fig. 1

Fig. 1

Distribution of taxa in healthy child and adult GI communities. a Variation in bacterial relative abundances at the phylum level via 16S rRNA gene sequencing (n = 37 children, 43 adults). Mean genus-level relative abundances as detected by b 16S sequencing (n = 37 children, 43 adults) and c shotgun metagenomic profiling (n = 22 children, 22 adults)

Fig. 2

Fig. 2

PCoA of adult and child fecal communities. Plots are based on Bray-Curtis dissimilarities of a 16S-based OTUs (n = 37 children, 43 adults) and b species detected via WGS (n = 22 children, 22 adults). The percent variation captured by each axis is indicated in parenthesis. Adonis test results related to age group are also presented. c Bray-Curtis dissimilarity within and between healthy children and adults, as a function of 16S-based OTUs or WGS-based species. **q < 0.01 by two-tailed Student’s _t_-test with 1000 permutations and Bonferroni multiple testing correction

Fig. 3

Fig. 3

a The abundances of genes involved in vitamin B12 metabolism differed significantly between children and adults. Enrichment of KO groups (White’s non-parametric _t_-test, q < 0.10) is indicated by color (green: children; blue: adults). b Child and adult metagenomic profiles could be differentiated from one another at the pathway level. KEGG pathways with the greatest Random Forests importance scores are highlighted here

Fig. 4

Fig. 4

Differences in KEGG pathway profiles contribute to the differentiation of children and adults. a PCoA of KEGG pathway profiles from healthy children and adults (n = 22 children, 22 adults; Bray-Curtis dissimilarity). The percent variation captured by each axis is indicated in parenthesis, and an Adonis test of age group is presented. b KEGG pathways associated with anti-inflammatory properties were significantly enriched or trended toward enrichment in children. c KEGG pathways associated with pro-inflammatory processes, adiposity, and aging were significantly enriched in adults (White’s non-parametric _t_-test)

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