Gut Microbiome


Invisible to the eye, our bodies are covered in rich ecosystems inhabited by trillions of microscopic organisms, which collectively make up the human microbiome. Of these, studies increasingly show one of the most consequential microbiomes lies inside the digestive tract.

This 30-foot-long tube—which includes the large and small intestines—is filled to the brim with about as many (if not more) microorganisms as there are cells in the human body (almost 40 trillion). The exact makeup of the gut microbe population varies from gut to gut, but they generally all have yeast, protists, bacteria, viruses, and archaea.

It’s currently believed that the gut microbiome comes from bacterial colonization that slowly covers the body, inside and out, after birth. 

When a baby becomes a toddler, their gut microbiome has stabilized into what it’s likely to resemble as an adult (take a deep dive here).

What affects it?

In the early stages of the gut microbiome’s development—so, in the early stages of child development—nutrition plays a crucial role in setting the stage for the gut’s ecosystem for the rest of a person’s life. Later in life, it’s possible to influence gut microbe composition through nutrition, medication, and social and environmental changes. 

The microbes inhabiting the gut are influenced by available resources, which is why diet is a strong indicator of gut microbe diversity.

Vegetables, fruits, whole grains, and legumes are associated with anti-inflammatory bacteria in the gut microbiome, while high animal protein and artificial sugar intake are associated with inflammatory pathobionts or microbiota that can cause disease.

What does it do?

Mounting evidence suggests the gut microbiome has tendrils of influence that extend far beyond the digestive tract. 

These microbiota help regulate the immune system, release precursors to neurotransmitters that can cross the blood-brain barrier, and produce vitamins, enzymes, and hormones.

The population of the gut microbiome is a fluid balancing act. If one type of microbe starts to outpace others or is left behind, the entire system can fall into a state known as dysbiosis

The disruption of the gut microbiota ecosystem can lead to immunity issues and is associated with chronic diseases, including asthma, Type 2 diabetes, and depression.

Gut microbiota’s exact range of influence is still under study, but findings have opened new avenues of treatment, such as by addressing the gut-brain axis, for mental and physical health conditions.

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A 3D render of six petri dishes labeled "coral," "bird," "stick insect," "human," "bat," and "shrimp." The stick insect and the shrimp have nearly empty dishes, while the coral and human dishes overflow with various microbes.
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Researchers have discovered that some animals, ranging from ants and caterpillars to birds and bats, have no stabilized gut microbiota population if any at all. This finding upends scientific expectations of the gut microbiome, which is so critical to health that some researchers consider creatures "the sum of their microbial parts." Subverting the human-centric understanding of the gut microbiome has highlighted the spectrum of possible microbe symbiosis.

Paper cutouts of bacteria and viruses float in a petri dish.
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An imbalance of gut microorganisms may influence the likelihood of addiction and addictive behaviors. Some of the molecules produced by the gut microbiome impact the body's production of hormones and neurotransmitters, meaning a less-than-healthy microbiome could make for worse withdrawal symptoms. A "leaky gut" could inspire brain inflammation that promotes addiction via increased activity in regions associated with threats, reward, and impulse control.

Digital 3D render of fuzzy Y-shaped bacteria.
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The digestive tract is a bustling city for the trillions of microorganisms that live and work there. Packed together like micro-apartment renters, the gut microbiome is home to bacteria, viruses, fungi, and more. Parts of the digestive tract are more hospitable than others, such as the stomach, whose conditions allow bacteria that can aid digestion or cause strep to flourish but is too acidic to host much else.

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Exercise causes diet-independent changes in the gut microbiome's composition and functions. Cardiovascular exercise, like running or aerobics, boosts the gut microbiome's population of beneficial bacteria. Exercise overall decreases the likelihood of developing a "leaky gut," a condition characterized by a porous gut lining that allows bacteria to leak into the bloodstream and cause inflammation. However, excessive exercise, exercise-induced stress, and subpar recovery contribute to dysbiosis and worsened immunity.

Man in t-shirt leans against a wall and looks down forlornly.
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According to research in mice, changes in the gut microbiome affect how anxiety, personality, and mood disorders manifest. Growing research suggests this holds true for other mammals, including humans. How so? The specifics aren't yet clear, but the process may involve the enteric nervous system, a collection of hundreds of millions of neurons throughout the gut that pass messages up the vagus nerve and into the brain.

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The trillions of bacteria populating the gut microbiome are "squashed together like sardines in a can," engaging in horizontal gene transfer at rates unseen elsewhere. This means the bacteria lend or share their genes even when they are not the same species, contributing to processes including antibiotic resistance and nutrition uptake. Better understanding of the microbiome may reveal methods of behavioral and chemical engineering to improve health outcomes.

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