Successional Stages in Infant Gut Microbiota Maturation

Disturbances in the primary colonization of the infant gut can result in life-long consequences and have been associated with a range of host conditions. Although early-life factors have been shown to affect infant gut microbiota develop-ment, our current understanding of human gut colonization in early life remains limited. To gain more insights into the unique dynamics of this rapidly evolving ecosystem, we investigated the microbiota over the first year of life in eight densely sampled infants (n = 303 total samples). To evaluate the gut microbiota maturation transition toward an adult configuration, we compared the microbiome composition of the infants to that of the Flemish Gut Flora Project (FGFP) population (n = 1,106). We observed the infant gut microbiota to mature through three distinct, conserved stages of ecosystem develop-ment. Across these successional gut microbiota maturation stages, the genus predomi-nance was observed to shift from Escherichia over Bifidobacterium to Bacteroides. Both disease and antibiotic treatment were observed to be associated occasionally with gut microbiota maturation stage regression, a transient setback in microbiota maturation dynamics. Although the studied microbiota trajectories evolved to more adult-like con-stellations, microbiome community typing against the background of the FGFP cohort clustered all infant samples within the (in adults) potentially dysbiotic Bacteroides 2 (Bact2) enterotype. We confirmed the similarities between infant gut microbial coloniza-tion and adult dysbiosis. Profound knowledge about the primary gut colonization pro-cess in infants might provide crucial insights into how the secondary colonization of a dysbiotic adult gut can be redirected. IMPORTANCE After birth, microbial colonization of the infant intestinal tract is important for health later in life. However, this initial process is highly dynamic and influ-enced by many factors. Studying this process in detail requires a dense longitudinal sampling effort. In the current study, the bacterial microbiota of .300 stool samples was analyzed from 8 healthy infants, suggesting that the infant gut microbial popu-lation matures along a path involving distinct microbial constellations and that the timing of these transitions is infant specific and can temporarily retrace upon exter-nal events. We also showed that the infant microbial populations show similarities to suboptimal bacterial populations in the guts of adults. These insights are crucial for a better understanding of the dynamics and characteristics of a healthy gut micro-bial population in both infants and adults and might allow the identification of intervention targets in cases of microbial disturbances or disease.

Automated summary

The study tracked the microbial colonization in the gut of 8 infants over the first year of life, revealing three distinct stages of development and potential setbacks associated with disease or antibiotic treatment. While the infant gut microbiota evolved towards an adult-like composition, it clustered within a potentially dysbiotic enterotype similar to that of adults.