In the largest clinical microbiome study in infants reported to date, a team led by researchers at Baylor College of Medicine explored the sequence of microbial colonization in the infant gut through age 4 and found distinct stages of development in the microbiome that were associated with early life exposures. Published in the journal Nature, their report and an accompanying report led by the Broad Institute are the result of extensive analysis of data collected from a cohort of participants involved in the TEDDY diabetes study.
The TEDDY study (The Environmental Determinants of Diabetes in the Young) study has been collecting data for 10 years with the goal of understanding what triggers type 1 diabetes in children at increased genetic risk for the disease. Researchers at six clinical centers in the U.S., Sweden, Finland, and Germany, as well as the Data Coordinating Center at the University of South Florida, have gathered monthly stool samples and data from more than 8,600 children who are genetically susceptible to type 1 diabetes. From this cohort, researchers at Baylor College of Medicine sequenced and analyzed 12,005 stool samples that were collected from 903 children between three and 46 months of age to further understand what the microbiome looks like early in life.
“We know that the first few years of life are important for microbiome establishment. You are born with very few microbes, and microbial communities assemble on and in your body through those first years of your life,” said Dr. Joseph Petrosino, director of the Alkek Center for Metagenomics and Microbiome Research and professor and interim chair of molecular virology and microbiology at Baylor. “In this study, we took a closer look in this amazing cohort at the establishment of the microbiome over the first few years of life and the early life exposures associated with that sequence of events.”
In collaboration with the Human Genome Sequencing Center at Baylor, state-of-the-art sequencing of both RNA and DNA was applied to uncover the complete genetic makeup of all microbes. Upon analysis of these data, Petrosino and his team determined that the developing gut microbiome undergoes three distinct phases of microbiome progression:
- Developmental phase (3 to 14 months of age)
- Transitional phase (15 to 30 months of age)
- Stable phase (31 to 46 months of age)
“This information is useful for any future microbiome studies looking at an infant cohort for scientific discovery and potential intervention purposes. The idea that we can stratify the development phases in this manner may give researchers additional resolution to reveal differences that could potentially be disease-associated,” Petrosino said.