The community of microbes living in the human gut is not present at birth in its mature form. It is assembled over the first years of life, in a process of colonization and development. Researchers increasingly regard early life as a particularly important window for the microbiome—a formative period that may have lasting influence.

Starting Close to Empty

A developing baby is, in microbial terms, beginning largely from scratch. The rich, complex gut microbiome of an adult does not exist yet.

From the time of birth onward, the infant gut is colonized—populated by microbes from the surrounding environment. Over the following months and years, this community grows, diversifies, and gradually develops toward the more complex, stable microbiome characteristic of later childhood and adulthood.

This assembly is not instantaneous. It is a gradual succession, with the microbial community shifting in composition as the child grows and the diet changes.

A Period of Co-Development

What makes early life such an interesting window is timing. The microbiome is being assembled during exactly the same period that the infant's own body is undergoing crucial development—including the development of the immune system.

This creates an opportunity for co-development. The maturing immune system and the developing microbiome grow up alongside one another, and they appear to influence each other. The microbiome may play a role in helping to "educate" and calibrate the developing immune system, teaching it, in a sense, to distinguish appropriately between friend and threat.

Because this co-development happens during a formative window, researchers hypothesize that the early-life microbiome may have influences that extend well beyond infancy.

Influences on Microbiome Development

Many factors influence how the early-life microbiome develops, including the circumstances of birth, early feeding, the surrounding environment, and the introduction of solid foods. The transition to a varied solid diet, in particular, is a major step in the microbiome's maturation, as new foods feed new microbes and the community diversifies.

A Note of Scientific Humility

This is an exciting and fast-moving area of science, and it is important to discuss it with appropriate humility.

It is well supported that the microbiome is assembled in early life, that this coincides with immune development, and that the two interact. It is plausible and actively researched that early-life microbial development has lasting significance.

But the field is still young. The precise long-term consequences, and exactly how much any single early-life factor matters, are not fully settled. Early-life health is also, properly, a matter for pediatric and medical guidance. This article describes a genuine and important area of research—not a set of definitive instructions.

A Foundational Window

The microbiome of early life is best understood as a foundation being laid. During a formative window, a complex microbial community is assembled, in step with the development of the body's own systems. Understanding this window is one of the most compelling frontiers in the science of gut health and developmental biology—a reminder that the partnership between humans and their microbes begins, and begins shaping us, very early indeed.