Settlers of our inner surface - factors shaping the gut microbiota from birth to toddlerhood

Abstract

During the first 3 years of life, the microbial ecosystem within the human gut undergoes a process that is unlike what happens in this ecosystem at any other time of our life. This period in time is considered a highly important developmental window, where the gut microbiota is much less resilient and much more responsive to external and environmental factors than seen in the adult gut. While advanced bioinformatics and clinical correlation studies have received extensive focus within studies of the human microbiome, basic microbial growth physiology has attracted much less attention, although it plays a pivotal role to understand the developing gut microbiota during early life. In this review, we will thus take a microbial ecology perspective on the analysis of factors that influence the temporal development of the infant gut microbiota. Such factors include sources of microbes that seed the intestinal environment, physico-chemical (abiotic) conditions influencing microbial growth and the availability of nutrients needed by the intestinal microbes.

Keywords: abiotic factors; breastfeeding; competition; infant gut microbiota; nutrients.

Figure 1.

Influence of selected factors on the developing microbiota. In the first period after birth, the bacterial load in the intestine is low, meaning that many ecological niches are free for the seeded bacteria to explore. The high inter-individual (beta) diversity at this stage is probably reflecting a high influence from the many different sources of seeding to the gut at this stage. When the complexity of diet increases, so does the complexity (alpha diversity) of the bacterial community, and eventually the impact of original seeding sources is no longer detectable. The increasing hostility of the gut environment, characterized by reduced oxygen availability and reduced pH and later by scarceness bacterial of nutrients subject to competition, selects for a community that is optimized for coping with this, thereby reducing the beta diversity, and increasing the impact of competition. (The figure was created in BioRender).