What is the gut microbiome?
A biome is a distinct ecosystem characterized by its environment and its inhabitants. Your gut — inside your intestines — is in fact a miniature biome, populated by trillions of microscopic organisms. These microorganisms include over a thousand species of bacteria, as well as viruses, fungi and parasites.
Your gut microbiome is unique to you. Infants inherit their first gut microbes during vaginal delivery or breastfeeding (chestfeeding). Later, your diet and other environmental exposures introduce new microbes to your biome. Some of these exposures can also harm and diminish your gut microbiota.
Why is the gut microbiome important?
Most of the microorganisms in our guts have a symbiotic relationship with us, their hosts. That means we both benefit from the relationship. We provide them with food and shelter, and they provide important services for our bodies. These helpful microbes also help to keep potentially harmful ones in check.
You can think of your gut microbiome as a diverse native garden that you rely on for nutritious foods and medicines. When your garden is healthy and thriving, you thrive, too. But if the soil is depleted or polluted, or if pests or weeds are overrunning the helpful plants, it can upset your whole ecosystem.
Function
What does your gut microbiome do?
Your gut microbiome interacts with many of your body systems and assists with many body functions. It plays such an active role in your body that some healthcare providers have described it as being almost like an organ itself. Some of these interactions we’re still learning about, while others are well known.
Digestive system
Bacteria in your gut help break down certain complex carbohydrates and dietary fibers that you can’t break down on your own. They produce short-chain fatty acids — an important nutrient — as byproducts. They also provide the enzymes necessary to synthesize certain vitamins, including B1, B9, B12 and K.
These might seem like small nutrients, but micronutrient deficiencies can have a big impact on your health. (See: vitamin B12 deficiency, folate deficiency and vitamin K deficiency.) Short-chain fatty acids, in particular, feed the cells in your gut lining and help to keep your overall gut environment healthy.
Gut bacteria also help to metabolize bile in your intestines. Your liver sends bile to your small intestine to help you digest fats.
When that’s done, bacteria and their enzymes help to break it down so that the bile acids can be reabsorbed and recycled by your liver. This is called enterohepatic circulation.
If this process stopped working, your body would be unable to recycle bile acids and your liver wouldn’t have enough to produce new bile. Your digestive system wouldn’t get the bile it needs to digest and absorb fats. And leftover cholesterol, one of the components of bile, would build up in your blood.
Immune system
Beneficial microbes in your gut help to train your immune system to tell them apart from the unhelpful, pathogenic types. Your gut is your largest immune system organ, containing up to 80% of your body’s immune cells. These cells help to clear out the many pathogens that pass through it every day.
Helpful gut microbes also compete directly with unhelpful types for real estate and nutrients, preventing them from taking up too much territory. Some of the chronic bacterial infections that can affect your GI tract, including C. difficile and H. pylori, are directly related to having a diminished gut microbiome.
Short-chain fatty acids, the byproducts of helpful gut bacteria, have important benefits for your immune system. They help maintain your gut barrier, keeping the bacteria and bacterial toxins inside from escaping into your bloodstream. They also have anti-inflammatory properties for your gut.
Inflammation is a function of your immune system, but it can malfunction, becoming hyper-reactive. Chronic inflammation is a feature of autoimmune disease and may have a role in many other diseases, including cancer. Short-chain fatty acids appear to suppress these types of inflammatory reactions.
Nervous system
Gut microbes can affect your nervous system through the gut-brain axis — the network of nerves, neurons and neurotransmitters that runs through your GI tract. Certain bacteria actually produce or stimulate the production of neurotransmitters (like serotonin) that send chemical signals to your brain.
Bacterial products may also affect your nervous system. Short-chain fatty acids appear to have positive effects, while bacterial toxins might damage nerves. Researchers continue to investigate how your gut microbiome might be involved in various neurological, behavioral, nerve pain and mood disorders.
Endocrine system
Gut microbes and their products also interact with endocrine cells in your gut lining. These cells (enteroendocrine cells) make your gut the largest endocrine system organ in your body. They secrete hormones that regulate aspects of your metabolism, including blood sugar, hunger and satiety.
Researchers continue to explore how your gut microbiome might be involved in metabolic syndrome (obesity, insulin resistance and Type 2 diabetes) and excess fat storage in your liver. These conditions have some relationship with certain gut microbiota, although exactly what it is isn’t clear yet.
Anatomy
Where is your gut microbiome?
Your “gut” roughly refers to your gastrointestinal (GI) tract. Most people use it to mean your intestines. You have some gut microbiota in your stomach and small intestine, but most of them are in your large intestine (colon). They float around inside or attach to the mucous lining on the inner walls (mucosa).
The types of gut bacteria that live in your colon are different from the types that live elsewhere. They’re mostly anaerobic bacteria that require a low-oxygen environment to survive. The higher oxygen, faster movement and strong digestive juices in your upper GI tract prevent them from colonizing there.
Anaerobic gut bacteria perform important functions within your colon that only they can. They help break down indigestible fibers in your digestive tract and produce essential nutrients that you can’t get otherwise. By the same token, these organisms are only helpful to you within their natural microbiome.
If these bacteria stray beyond your colon, they can be harmful. Colon bacteria that manage to creep up and settle in your small intestine can interfere with digestive processes there. Colon bacteria that invade your colon wall, or that escape through a wound in your colon wall, can cause an infection in your body.