How to Restore Healthy Gut Flora

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What is the microbiome? From digestion to depression, healthy skin, and a strong immune system, our gut health – our gut microbiome – has a say in what goes on elsewhere in our bodies. So, why is the gut still considered by many people to be nothing but an organ? Although the extent to which our gut influences our health all over our bodies is slowly coming to light, some experts believe that this is just the tip of the iceberg.

Our gut is home to a hefty 100 trillion bacteria that influence our health and well-being – and even our mood. Our gut flora is important for digestion, protection against dangerous germs and toxins, and strengthening the immune system. Experts now link various diseases, allergies, and even depression to the fact that the gut flora is out of balance.

In Japan, people regard the gut as the center of physical and mental strength in our bodies. In this part of the world, however, our guts are often still considered a purely digestive organ – and are thus grossly underestimated. Flatulence, diarrhea, and constipation are taboo subjects, and digestive disorders represent roughly 10 percent of GPs’ workload – although it is believed that many people avoid making appointments with their doctor for such health issues. This suggests that gut health and digestive health do not appear high on the priority list for many patients across the United Kingdom.

So, it goes without saying that gut flora demands a lot more attention than we give it. Find out what exactly the microbiome is, the typical symptoms of bad gut health, how to restore healthy gut flora, and how to take the right probiotics!

What is the microbiome?

The microbiome, also known as gut flora or gut bacteria, is defined as a community of microorganisms – that is, bacteria, fungi, and viruses – that live in the human body. Our gut microbiome is, thus, the community of microorganisms that are located in our gut.

Up to 100 trillion different organisms, such as bacteria, viruses, and fungi, make up our gut microbiome. Most of the bacteria are located where the digestion process is almost over, in the intestinal mucosa of the colon. If digestion is impaired and the bacteria migrate from the large to the small intestine, this can lead to severe flatulence, abdominal pain, joint pain, nutrient deficiencies, and anemia. This still partly unexplored health issue is called bacterial overgrowth.

What is the microbiome important?

Bacteria are not always harmful. In fact, gut bacteria are essential for human survival. Among other things, the gut microbiome plays a very important role in the digestion of food. The good bacteria that make up our gut flora, which is vital for our body, have numerous other functions, for example:

  • They produce what is known as butyrate from our food, which has been shown to contribute to good gut health by promoting mechanisms to combat stress
  •  They produce a number of essential amino acids
  • They produce certain vitamins, such as vitamin K and water-soluble B vitamins

A study published in the journal Science revealed that the gut microbiome can block allergic reactions. Through its influence on our immune system, it can inhibit immune cells that are responsible for triggering allergies. This link could be an approach for new treatment options for allergy sufferers in the future.


You have a world of microorganisms living in your digestive system. This collection of microorganisms is your gut flora, also known as the gut microbiota—a complex ecosystem that consists of approximately 300 to 500 bacterial species. That’s nearly 10 times the number of cells in the human body.

Our knowledge of the interaction between gut health and overall health is still in its early stages. We do know that colonies of beneficial bacteria help you digest and absorb your food, fight off germs that make you sick and even make a large portion of your serotonin, which helps keep your moods level.

Science is continuing to discover ways that gut bacteria are directly linked to your health. We know that it’s normal to have balanced populations of beneficial gut bacteria and “bad” bacteria, and a healthy gut is able to keep the bad guys in check. But researchers are just now beginning to understand what happens when other factors—like antibiotics, diet, and stress—tilt the scales in the wrong direction.

Why is our gut so important?

Our intestines are constantly busy processing food and fighting off pathogens. The most important phase of digestion takes place in the small intestine. It digests our food until all the important nutrients, vitamins, and minerals have been absorbed. The rest of the food enters the large intestine, from which it is excreted.

But the gut has another function that has been underestimated for years: promoting a healthy immune system. The digestive tract constantly fends off pathogens such as bacteria, viruses, fungi, environmental toxins, and toxins.

The gut is also home to a nervous system that contains more neurons than the entire spinal cord. Scientists realized 100 years ago that bacteria in the gut constantly communicate with neurons in the brain. This is how our guts have gained recognition as our second brain. This is arguably how the phrase ‘gut feeling’ came into the picture, referring to intuitions triggered by a second brain.

How does your gut affect your immune system?

There are many complex connections between the microbiome and the immune system. A total of 70 to 80 percent of the cells of our immune system is located in the intestine. The microbiome thus plays an important role in protecting the body from pathogens and inflammation. To promote our body’s defense, information is constantly exchanged between the immune system and the good bacteria. These healthy bacteria include, above all, the genera of lactobacilli and bifidobacteria, which also make up a large part of our gut flora.

If there are fewer good bacteria and bad bacteria begin to dominate, inflammation can spread more easily, and pathogens can penetrate the body more easily. Such an imbalance (dysbiosis) of the gut microbiome can occur, for example, due to an unhealthy diet with a lot of saturated fats and sugar or after taking antibiotics.

What causes bad gut bacteria?

The composition of our gut flora is different for every person and changes over the course of a lifetime. Over the last 20 years, researchers have been able to identify patterns by which a healthy gut can be recognized. Nevertheless, a large part of the functions performed by our microbiome is still unknown. What is known so far is that there are factors that continuously influence the composition of gut bacteria. These are age, gender and genetic predisposition – but above all, diet. You can influence which bacteria colonize your intestine yourself through your food choices.


Because gut bacteria play an important role in supplying essential nutrients, synthesizing vitamin K and a number of other processes, it can be problematic if you don’t have your gut health in check. What are some of the long-term ramifications?

Here are a few issues that can result from a damaged gut:

  • Inflammatory bowel disease
  • Poor sleep quality
  • Weakened immune system
  • Nutrient deficiencies


Here’s one of the hallmarks of a healthy gut: a thriving population of beneficial microbes and a diverse mix of them. These good guys support overall human health, but they also prevent the bad microbes from taking over—aka the harmful bacteria that can contribute to inflammation and changes to your weight.

What does that mean for you? Be mindful when you’re dealing with factors that can impact your healthy bacteria. Some factors, like age and getting sick, aren’t in our control. But you can take positive steps with other factors, like what you eat after taking antibiotics, the amount of sugar in your diet and how you manage stress. Below, we’ll expand on a few of these, plus general tips to restore gut flora. As always, maintain open communication with your healthcare provider.


You don’t have to sit around and just wait for your body to re-adjust. Read on to find out how to restore your gut flora so you bounce back and feel your best with a rockstar gut microbiome.


One way to rebalance gut flora is to eat polyphenol-rich foods. Polyphenols are organic compounds found in plants that have been shown to stimulate the growth of beneficial bacteria and inhibit the growth of pathogen bacteria. How can you get more in your diet? Bulletproof-friendly sources include dark chocolate, green tea, and coffee.


When a large portion of bacteria gets wiped out, they rebuild slowly. As with any population competing for resources, it’s a bit of a race to repopulate. While this is happening, you want to feed the good guys and starve the bad guys.

Cutting sugar will only take you so far. While you’re closing down the bar on the yeast party, why not serve the welcome guests whole foods? The gut microbes that help you digest and absorb your food love vegetables. Makes sense because they eat the portion of the veggies that humans do not break down and convert those portions into nutrients that you wouldn’t otherwise get.

Pile your plate with the whole foods that friendly microbes eat, and more of the good guys will colonize your gut. In particular, look for brightly colored vegetables (like dark leafy greens and vibrant cruciferous vegetables).


Losing sleep (or chronic low-quality sleep) can negatively change the ratio of bacteria in your gut, increasing the risk of insulin resistance, increased gut permeability, and even sugar cravings.


Another tip for how to balance gut bacteria: move around regularly. Exercise has been shown to determine changes in the composition of your gut microbiome, including stimulating the growth of beneficial bacteria that can regulate mucosal immunity.


You can also help restore gut flora by consuming dietary fiber. Research shows dietary fibers interact directly with gut microbes, leading to the production of metabolites like short-chain fatty acids.


Research shows that cigarette smoke toxicants disrupt the balance of intestinal microbiota. So, if you want to protect your gut (and overall health), steer clear of smoking.


Replacing sugar with artificial sweeteners isn’t any better—rodent studies indicate that saccharin, sucralose, and aspartame cause shifts in gut microbiota and contribute to intestinal dysbiosis or an imbalance of microorganisms.


Probiotics are your good gut bacteria—the ones that support healthy digestion, produce nutrients and get rid of toxins and pathogens, among other key roles. A diet rich in probiotics (like what you find in kefir, sauerkraut, kombucha, and kimchi) can help good microbes colonize your gut and keep the unfriendly ones at bay.

Probiotics are essential, but in order for good bacteria to thrive, they need to eat. That’s why you need prebiotics in your diet. Prebiotics are compounds that feed beneficial gut bacteria. Well-fed, friendly bacteria populate the gut lining, helping to nurture a healthy biome. This helps restore and maintain the integrity of your gut lining.

You can get prebiotics from chicory root, artichokes, leeks, whole grains, and foods that are high in resistant starch—a type of starch that resists digestion. It ferments your digestive tract and feeds the beneficial bacteria in your gut. Sources of resistant starch include unroasted cashews, raw green bananas, raw plantain flour, and raw potato starch. It can cause digestive distress in some people, so start slow and build up to a few tablespoons.

The bottom line

Restoring gut flora to optimal levels involves several factors, including your sugar consumption, the amount of prebiotic and probiotic foods in your diet, and your sleep quality. While antibiotics help wipe out bad bacteria, they wipe out good bacteria, too. Follow the steps outlined above to help bring balance back to your gut microbiome as soon as possible.


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