The development of the infant gut microbiome is described in two papers published in this week’s Nature. The findings provide insights into the associations between the microbiome, infant development, and the potential impact of type 1 diabetes.
The gut microbiome changes over time, but the transition from infancy to childhood is not well-understood. Research suggests that the microbiome may be associated with different disease pathologies, including type 1 diabetes. The Environmental Determinants of Diabetes in the Young (TEDDY) study is investigating this relationship and has generated one of the largest datasets on the infant microbiome to date, spanning samples from six clinical centres in the United States, Sweden, Germany and Finland.
Joseph Petrosino and colleagues used gene sequencing to analyse 12,500 stool samples from 903 children in the TEDDY study, collected monthly from children aged 3 to 46 months old. Microbiome composition and diversity changed over time in three distinct phases: the developmental phase (3-14 months), transitional phase (15-30 months) and stable phase (31 months onward). During the developmental stage, breastfeeding was associated with higher levels of Bifidobacterium bacteria, whereas microbiome diversity increased after weaning as the infants consumed a greater variety of foods. Vaginal birth was associated with a temporary increase in Bacteroides bacteria, which in turn was associated with increased gut diversity and maturation (regardless of birth mode). Siblings, exposure to pets, and geographical location were also factors in differences between microbiome profiles.
In a separate paper, Curtis Huttenhower and colleagues analysed nearly 11,000 stool samples from 783 infants in the TEDDY study to characterize the early gut microbiome in children progressing to type 1 diabetes. They report that the microbiomes of infants without type 1 diabetes harbour more genes related to fermentation and short-chain fatty-acid synthesis that, in combination with previous evidence, are associated with a protective effect.
The authors highlight that the infants sampled (mostly non-Hispanic white and at high risk of type 1 diabetes) may not represent other populations. Together, these two studies characterize the infant gut microbiome and will provide a valuable resource to researchers.