EBI metagenomics

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Project overview (SRP002437)

Developing infant gut microbiome

Last updated: 18-Feb-2014

Description

The colonization process of the infant gut microbiome has been called chaotic, but this view could reflect insufficient documentation of the factors affecting the microbiome. We performed a 2.5-year case study of the assembly of the human infant gut microbiome to relate life events to microbiome composition and function. Sixty fecal samples were collected from a healthy infant along with a diary of diet and health status. Analysis of >300,000 16S rRNA genes indicated that the phylogenetic diversity of the microbiome increased gradually over time and that changes in community composition conformed to a smooth temporal gradient. In contrast, major taxonomic groups showed abrupt shifts in abundance corresponding to changes in diet or health. Community assembly was nonrandom: we observed discrete steps of bacterial succession punctuated by life events. Furthermore, analysis of ~500,000 DNA metagenomic reads from 12 fecal samples revealed that the earliest microbiome was enriched in genes facilitating lactate utilization, and that functional genes involved in plant polysaccharide metabolism were present prior to the introduction of solid food, priming the infant gut for an adult diet. However, ingestion of table foods caused a sustained increase in the abundance of Bacteroidetes, elevated fecal short chain fatty acid levels, enrichment of genes associated with carbohydrate utilization, vitamin biosynthesis and xenobiotic degradation, and a more stable community composition, all of which are characteristic of the adult microbiome. This study revealed that seemingly chaotic shifts in the microbiome could be attributed to life events.

Experimental factor: time

Contact details

Institute:
Cornell University
Name:
Ruth E. Ley
Email:
not available

Associated samples

Sample name Sample ID Collection date Source
838 day old Infant gut microbiome SRS086437 - Host associated
835 day old Infant gut microbiome SRS086436 - Host associated
831 day old Infant gut microbiome SRS086435 - Host associated
745 day old Infant gut microbiome SRS086434 - Host associated
623 day old Infant gut microbiome SRS086433 - Host associated
100 day old Infant gut microbiome SRS086444 - Host associated
3 day old Infant gut microbiome SRS086439 - Host associated
98 day old Infant gut microbiome SRS086443 - Host associated
92 day old Infant gut microbiome SRS086442 - Host associated
85 day old Infant gut microbiome SRS086441 - Host associated
6 day old Infant gut microbiome SRS086448 - Host associated
454 day old Infant gut microbiome SRS086447 - Host associated
441 day old Infant gut microbiome SRS086446 - Host associated
432 day old Infant gut microbiome SRS086440 - Host associated
413 day old Infant gut microbiome SRS086449 - Host associated
118 day old Infant gut microbiome SRS086445 - Host associated
371 day old Infant gut microbiome SRS086438 - Host associated

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