Successional stages in infant gut microbiota maturation

• Published in: bioRxiv
• Main Authors: Beller, Leen, Ward Deboutte, Falony, Gwen, Sara Vieira Silva, Tito, Raul, Valles-Colomer, Mireia, Rymenans, Leen, Jansen, Daan, Lore Van Espen, Maria Ioanna Papadaki, Shi, Chenyan, Kwe Claude Yinda, Zeller, Mark, Faust, Karoline, Marc Van Ranst, Raes, Jeroen, Matthijnssens, Jelle
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 26.06.2021
• Subjects: Babies; Colonization; Dysbacteriosis; Infants; Intestinal microflora; Maturation; Microbiomes; Microbiota
• DOI: 10.1101/2021.06.25.450009

Background: 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 the infant gut microbiota development, our current understanding of the human gut colonization in early life remains limited. To gain more insights in the unique dynamics of this rapidly evolving ecosystem, we investigated the microbiota over the first year of life in eight densely sampled infants (total number of samples, n=303). To evaluate gut microbiota maturation transition towards an adult configuration, we compared the microbiome composition of the infants to the Flemish Gut Flora Project population (n=1,106). Results: We observed the infant gut microbiota to mature through three distinct, conserved stages of ecosystem development. Across these successional gut microbiota maturation stages, genus predominance 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 constellations, microbiome community typing against the background of the Flemish Gut Flora Project (FGFP) cohort clustered all infant samples within the (in adults) potentially dysbiotic Bact2 enterotype. Conclusion: We confirmed similarities between infant gut microbial colonization and adult dysbiosis. A profound knowledge about the primary gut colonization process in infants might provide crucial insights into how the secondary colonization of a dysbiotic adult gut can be redirected.