Meet the Gut Microbiome

Human beings live alongside enormous communities of microorganisms. Many inhabit the gastrointestinal tract, where they form a complex and changing biological ecosystem.

Researchers study these microbial communities because they interact with digestion, metabolism, the intestinal barrier and immune system and produce substances that can participate in communication throughout the body.

To understand gut-brain research, it helps first to understand the microorganisms themselves.

Microbiota and Microbiome

The words microbiota and microbiome are closely related, although they are not always used in exactly the same way.

Microbiota generally refers to the community of microorganisms living within a particular environment. These microorganisms can include:

• bacteria
• fungi
• viruses
• archaea
• protozoa

Microbiome can refer to the collective genetic material of these microorganisms and is also commonly used more broadly when discussing the microbial ecosystem and its biological activity.

The gastrointestinal tract is one of the body's major microbial habitats.

A Dynamic Ecosystem

The gut microbiome is not identical from person to person. Microbial communities develop and change across the lifespan. Early development, diet, environment, medications and many other biological and lifestyle factors can influence microbial composition.

As children grow and diets change, their microbial communities continue to develop. Even in adulthood, the microbiome is not completely static.

This is one reason microbiome research is complex: there is no single microbial profile shared by every person.

What Do Gut Microorganisms Do?

Gut microorganisms participate in many biological processes. Researchers study their involvement in:

Digestion and Fermentation

Some microorganisms help process dietary substances that human digestive enzymes do not completely break down.

Microbial Metabolites

Microbial activity produces numerous metabolic products, including short-chain fatty acids and other compounds.

The Intestinal Environment

Microbial communities interact with the mucus layer and intestinal epithelium that help form the gut barrier.

Immune Function

The gastrointestinal tract contains extensive immune activity. Gut microorganisms and the immune system continuously interact.

Nutrient Metabolism

Microorganisms can participate in the synthesis or metabolism of certain nutrients and biologically active compounds.

These functions demonstrate why researchers increasingly view the gut microbiome as part of a larger biological ecosystem rather than simply a collection of bacteria.

Not All Microbes Are the Same

It can be tempting to divide microorganisms into simple categories such as “good bacteria” and “bad bacteria.” The biology is more complicated.

Some microorganisms commonly coexist with humans without causing disease. Others may become problematic under particular circumstances.

The effects of a microbial community can depend on factors including:

• which organisms are present
• their relative abundance
• their biological activity
• the surrounding intestinal environment
• interactions with other microorganisms
• interactions with the host

For this reason, researchers often study the microbial community as an ecosystem.

What Can Shape the Microbiome?

Researchers investigate many influences on microbial communities, including:

• diet and nutrition
• age and development
• environmental exposures
• medications, including antibiotics
• illness
• geography
• lifestyle
• individual biology

These influences can interact. Observing that a factor changes the microbiome does not automatically mean that the factor causes a particular developmental or health condition.

Every Microbiome Is Different

One important lesson from microbiome research is individual variation. People can have substantially different microbial communities. Those communities can also change over time.

This makes it difficult to define one universal microbial composition that represents an “ideal” microbiome for every person.

Researchers therefore examine not only which microorganisms are present, but also what they are doing and how their activity interacts with the host.

Why Scientists Study the Microbiome

Scientists study the gut microbiome because microbial activity intersects with many areas of biology. These include:

• gastrointestinal function
• metabolism
• immune-system activity
• intestinal barrier function
• production of microbial metabolites
• gut-brain communication

These relationships have led researchers to investigate the microbiome in many areas of human health and disease. Neurodevelopment is one of those areas.