Temporal Development of the Gut Microbiome in Early Childhood - The TEDDY Study
TEDDY study infant gut microbiome analyses by Baylor College of Medicine
This repository contains code for the transition model showing the progression of samples through each DMM cluster, which are presented in Figure 1 and Extended Data Figure 2 of the "Temporal Development of the Gut Microbiome in Early Childhood - The TEDDY Study" by Stewart et al. (citation to be included).
The gut microbiome undergoes substantial development from birth into childhood and is believed to have significant consequences for long-term health, including the development of persistant islet autoimmunity (IA) and Type 1 Diabetes (T1D). In a multi-geographical population of 903 infants at-risk for T1D who developed IA and/or T1D by months 46 of age and their matched controls, we sought to characterize the gut microbiome from 3 to 46 months of life and determine the key covariates influencing its development. The study included two datasets, 1) 16S rRNA gene sequencing of >12,000 stool samples and 2) metagenomic sequencing of 10,867 stool samples.