Why is the Microbiome Important?

antibiotics anxiety autism bacteria carbohydrates celiac disease chronic disease dementia depression diabetes dysbiosis eczema elimination diet food additives food allergens gastrointestinal tract gut-brain axis immunity irritable bowel syndrome leaky gut mental disorders mental health mental illnesses metabolism microbiome nutrition obesity prebiotics probiotics rheumatoid arthritis supplements viruses Oct 28, 2023

An illustration of a man with green, rod-shaped bacteria in his stomach

You’ve probably heard that yogurt and kimchi are good for you. Or maybe you’ve had diarrhea while taking amoxicillin. But how do fermented foods benefit health, while antibiotics cause side effects? The answer has to do with your gut microbiome. In this article, we’ll explore:

What is the gut microbiome?
What are the microbiome’s functions?
What is dysbiosis?
What diseases are linked to dysbiosis?

Your microbiome is a complex network made of both helpful and harmful microbes. This internal ecosystem influences many aspects of your wellbeing. One of them is your risk of chronic disease. Keep reading to find out more.

What is the gut microbiome?

Your gastrointestinal (GI) tract has trillions of bacteria, viruses, fungi, archaea, and protists. Together, these microorganisms from over a thousand species make up your gut microbiome. They account for more than half of the cells in your body. Most of them live in your colon, where there is less acid and muscle movement than in your stomach and small intestine. These conditions make your colon a stable environment for microbes.^1,2

Your microbiome starts developing before birth. You’re exposed to your mother’s microbiome during pregnancy. Then you get covered in microbes while making your way out of her body. The exact species you come in contact with depends on how you were born (i.e., normal delivery vs. caesarean section). Your feeding habits (breast milk, formula milk, etc.) and medicine use shape your early microbiome too. So do your surroundings — for example, having siblings or pets.³

Bacteria dominate your microbiome. Most of them come from the phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Firmicutes include the genera Lactobacillus, Clostridium, Faecalibacterium, Ruminococcus, and Streptococcus. Meanwhile, Bacteroides and Prevotella fall under Bacteroidetes. Under Actinobacteria, the main genus is Bifidobacterium. Finally, Escherichia and Shigella are examples of Proteobacteria.⁴

In general, good bacteria include Lactobacillus and Bifidobacterium. In contrast, Clostridium perfringens and Shigella fall under bad ones. Other bacteria like Bacteroides don’t usually cause trouble. But they can be harmful when you have a weakened immune system.⁵

What are the microbiome’s functions?

The microbes in your gut play vital roles in metabolism, nutrition, and signaling. They also help with disease prevention and immunity.¹

Your gut bacteria break down complex carbs like starches and fibers. The best-known species for this job is Bacteroides thetaiotaomicron. Such bacterial action then leads to short-chain fatty acid (SCFA) production. SCFAs serve as a source of nutrients for your body.^1,6

Also, bacteria such as Clostridium scindens transform bile acids. By doing so, they aid in glucose and cholesterol metabolism.^1,7

Plus, some bacteria produce vitamins and amino acids. For example, Bifidobacterium and Lactobacillus make B vitamins. Escherichia and Bacteroides form Vitamin K. Bacteroides, along with Prevotella, synthesize amino acids.^8,9,10

Moreover, your gut and brain form a communication system called the gut-brain axis (GBA). This two-way network involves nerve, hormone, and immune signals. Through the GBA, your microbiome influences your brain development and function. For instance, Bifidobacterium and Lactobacillus impact your nerve cell formation and stress response.^11,12

Your microbiome stops disease-causing organisms from colonizing your gut as well. Specifically, your gut bacteria produce antimicrobial compounds like bacteriocins. Bacteriocin-producing bacteria include Lactobacillus and Streptococcus. What’s more, the cells in your gut wall have attachment sites for microorganisms. Foreign microbes must compete with huge numbers of gut bacteria for these sites. In effect, your microbiome prevents the invaders from thriving and making you sick.^1,13

Lastly, your gut lining serves as an interface between your immune system and outside environment. Your cells in this lining always interact with your gut microbes. As a result, your microbiome helps develop your immune response. For example, studies show that Clostridium can protect you from developing food allergies.^1,14

What is dysbiosis?

It’s not possible to get rid of all of the “bad” microbes in your gut. Instead, maintaining a balance between the good and bad species allows your microbiome to perform its functions well.⁴

When you lose good microbes and grow too many bad ones, an imbalance occurs. The species in your gut also become less diverse. This altered state is called dysbiosis.¹⁵

Your tendency for dysbiosis partly depends on your genes. Having inflammation or an infection can lead to this condition too.¹⁵

Environmental factors can trigger dysbiosis as well, with diet among the top culprits. In particular, high sugar and low fiber intake makes Proteobacteria thrive. At the same time, it decreases Bacteroidetes. Food preservatives like emulsifiers, colorants, and artificial sweeteners also cause Proteobacteria overgrowth. This imbalance, in turn, disrupts your gut barrier and promotes inflammation.^15,16,17

The use of some drugs, especially antibiotics, also causes dysbiosis. For example, amoxicillin increases Escherichia and Shigella. At the same time, the drug decreases Bacteroides, Bifidobacterium, and Lactobacillus. Such disruption of the microbiome can result in diarrhea and other side effects. If the imbalance is not corrected, these symptoms can persist long after the course of antibiotics is completed.^15,18,19

What diseases are linked to dysbiosis?

Dysbiosis is associated with various chronic conditions, including GI and metabolic disorders. Dysbiosis is also tied to autoimmune, mental, and developmental problems.

Examples of GI issues are irritable bowel syndrome (IBS) and celiac disease. IBS is linked to low Bifidobacterium and Faecalibacterium, but high Ruminococcus and Clostridium. Meanwhile, celiac disease patients seem to have reduced Lactobacillus and Bifidobacterium, but increased Bacteroides and Escherichia coli (E. coli).^4,20

Obesity, a metabolic disorder, is associated with fewer Bacteroidetes and more Firmicutes. On the other hand, high ratios of Bacteroidetes to Firmicutes and Bacteroides to Prevotella mark type-2 diabetes.⁴

Rheumatoid arthritis, an autoimmune condition, is linked to reduced Faecalibacterium and increased Prevotella copri. In comparison, atopic eczema is marked by low Bifidobacteria and Bacteroidetes, but high Clostridium difficile and E. coli.²⁰

As for mental illnesses, depression is tied to high Prevotella. A low Firmicutes to Bacteroidetes ratio has been found in people with anxiety. Dementia is associated with a lot of Escherichia and Streptococcus, but few Actinobacteria and Bacteroides. Autism is linked to low Bifidobacterium and Firmicutes, but high Clostridium and Bacteroidetes. This developmental condition is also marked by an overgrowth of the fungal species Candida albicans.^4,21,22

Conclusion

Your microbiome performs crucial functions, from breaking down food to preventing disease. For sure, you’ll benefit from a gut with a healthy microbe composition. And your diet is key to achieving this condition.

Prebiotics can help you have a balanced and diverse makeup of microbes. These fiber-rich foods include garlic, onion, asparagus, and barley.²³

Probiotics, which contain live bacteria, have a similar effect. They allow good species to flourish in your gut. Examples of probiotic foods are yogurt, kimchi, and sauerkraut. Probiotic supplements can help too. These medicines vary in the microbe strains they contain. Your choice of supplement depends on the condition you’re dealing with. For instance, supplements with both Bifidobacterium and Lactobacillus help relieve IBS-related pain. Meanwhile, Saccharomyces boulardii supplements can reduce symptoms of autism in children.^24,25

The exact composition of microbes in your gut differs from everyone else’s.⁴ That’s why your microbiome will thrive the most on a diet customized to it. And when your microbiome is at its best, all aspects of your health will reap rewards. You can better manage any chronic condition you have. You can feel more energized for work and personal stuff. You can improve your focus too. Ready to maximize your performance and enhance the quality of your life? Click here to start.

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