How To Restore Healthy Gut Flora: A Simple Guide

A healthy gut can benefit our overall wellness in so many ways. This post is a guide for how to restore your healthy gut flora.

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What Is the Gut Microbiome?

Good health is made in the gut. Tapping into good gut health comes down to getting to know your personal, unique gut microbiome. Located in your large intestine, your microbiome is a collection of microbes that actually functions like a vital organ.

gut microbiome

Think of your digestive system as a unique ecosystem. It needs the right balance for everything to flourish, thrive and stave off ruin. Like a lush ecosystem, your microbiome is home to diverse bacteria. It's also very vulnerable to outside influences.

You have more than 1,000 species of bacteria living in your gut microbiome right now. Each one has a unique role in maintaining balance. Most are keeping you healthy. “Bad” ones that have been allowed to grow due to lifestyle, dietary and genetic factors could be causing disease.

Every single person has a completely unique microbiome. A microbiome is like a snowflake, fingerprint or DNA sequence in that way. Some factors that influence gut microbiome include:

  • Age.
  • Gender.
  • Geography.
  • Diet.
  • Lifestyle.
  • Stress.
  • Genetics.
  • Health conditions.
  • Medications.

Your gut microbiome begins to diversify after birth every time you're exposed to different microbial species. In fact, microbiome diversity is considered essential for health, vitality and disease prevention. The state of your gut microbiome impacts:

  • Your immune system.
  • Brain health and function.
  • Absorption of nutrients.
  • Your central nervous system.
  • Digestion of fiber. This one is important for preventing weight gain, diabetes, heart disease and some cancers.
  • Heart health and cholesterol levels.

Your gut microbiome also plays a role in overall digestive health. Issues like inflammatory bowel disease (IBD) and leaky gut syndrome are linked to microbiome imbalances. Many people who experience bloating and cramping are actually experiencing gas and chemicals being released by microbes that are not in check. The good news is that there's a lot we can do to turn an unhealthy gut microbiome around. Consider it “ecosystem rehab.”

Good Bacteria for Gut Health

Most people associate the word “bacteria” with sickness and disease. The truth is that maintaining the right amount of good bacteria is essential for survival. You can't live without the good bacteria in your gut. You also can't live if the “bad” bacteria types overrun your gut.

good bacteria gut health

Your gut microbiome is home to trillions and trillions of bacteria cells. When you're born, those bacteria cells are actually hard at work training your immune system every time you come into contact with something new. The bacteria cells continue to work throughout your life. In fact, your bacteria cells are actually producing key substances to protect your gut lining as you read this! They are also at war with “bad” bacteria cells.

The good news is that your body sends cues right away when bad bacteria cells are overrunning your gut microbiome. The bad news is that most people aren't taught to recognize those cues. In fact, the prevailing thought is to simply “reduce” discomfort by taking antacids, avoiding certain foods or using pain relievers. None of these solutions actually solve the root problem.

Ideally, your gut will have the right amount of microbial diversity for everything to keep swimming along. However, you may experience something called dysbiosis when your gut is out of balance. Common signs include

  • Digestive issues.
  • Bloating.
  • Cramping.
  • Pain and inflammation.
  • Dysfunction in the gut lining.
  • Brain fog.
  • Mood issues.

Studies actually link dysbiosis with IBD and Crohn's disease. It's also possible that many digestive and autoimmune conditions are actually tied to an out-of-whack gut microbiome. Unfortunately, many people suffer for years with body-wide symptoms that originate in the gut without ever getting proper advice for restoring balance.

Immune Health and Gut Bacteria

The gut is “central command” for the immune system. When there's a takeover of bad bacteria, a person's immune system can be compromised. This leads to disease, infection and chronic illness. The gut microbiome communicates directly with the cells in the immune system to help identify harmful microorganism that come into contact with the body.

gut bacteria immune health

Unfortunately, an imbalanced microbiome is like a communication system with cut, frayed wires. This is where many people get into trouble with autoimmune disorders. An imbalanced gut microbiome can direct the immune system to attack healthy cells that it has mistaken for foreign invaders.

The ideal is just the opposite of this. A balanced microbiome communicates smoothly with the gut to leave healthy tissue alone, go after actual threats and maintain a strong response to pathogens without disruptions. In fact, the secret to a perfectly synced microbiome is that you're completely unaware that any work is being done at all!

Do Antibiotics Damage Your Gut Health?

Antibiotics are known as gut “disruptors.” That's because antibiotics are tasked with killing bad bacteria. However, these drugs don't have the intelligence to decipher between good bacteria and bad bacteria. As a result, they often kill off both. In fact, antibiotics often kill off more of your good bacteria because your bacteria cells have been activated to go to work on tackling an infection when you're prescribed an antibiotic. This makes a person more susceptible to harmful bacteria like salmonella, C.diff and E.coli. Even people who don't have severe reactions can experience the “subtle” effects of having an unbalanced gut microbiome that can impact their health for years if nothing is done.

gut health and antibiotics

Common Side Effects of Antibiotics

It's no surprise that many people experience digestive issues when taking antibiotics. Changes in digestion are telltale signs that too much good bacteria is being killed off. Common side effects of antibiotics include:

  • Diarrhea.
  • Constipation.
  • Yeast infections.
  • Gas.
  • Vomiting.
  • Nausea.

Unfortunately, many people are led to believe that these are “normal” side effects of taking antibiotics. While they may be common, these side effects aren't normal. It's so important to be proactive about restoring gut health right away when completing a course of antibiotics!

The Best Ways to Restore Gut Health

There are many different ways to boost gut health. This should really be viewed as a whole-body, integrated plan that looks beyond just “masking” bloating and discomfort. First, a gut-friendly diet should be prioritized.

restore your gut health

Eating a balanced diet rich in naturally high-fiber foods like vegetables and grains can be great for naturally restoring gut health. Your bacteria cells actually feed on fiber and nutrients from natural plants. Focus on things like leafy greens to feed good bacteria the feast needed for restoration!

We also know that foods that are natural probiotics are amazing for gut health. Probiotics actually live naturally in your body. However, using probiotic foods can help you to get the amount needed to get good bacteria back to where it needs to be. Yogurt, kombucha and sauerkraut are the most common probiotic foods.

Some people just aren't able to “eat their way” back to a balanced gut microbiome because the damage is simply too severe. This is where probiotic supplements can make a huge difference. Many effective probiotic supplements contain bacteria and yeast strains like Bifidobacterium, Lactobacillus, Lactococcus and Saccharomyces that march in like soldiers to combat bad bacteria.

How Long Does It Take to Repopulate Good Gut Bacteria?

The answer is different for everyone. Keep in mind that your unique, snowflake-like gut microbiome doesn't look like any other gut microbiome in the world. The right solution depends on just how overrun with bad bacteria your gut microbiome is when you begin taking actions to reverse the damage. Repopulation times can also be impacted by the overall state of your health, the quality of your diet, your stress levels, your age, your exercise levels and any medications that you're currently taking. Ready for the good news? The gut microbiome is generally very responsive to positive changes!

repopulate good bacteria gut health

How to Restore Healthy Gut Flora

There's no shortcut to a healthy gut. First, prioritize a healthy, balanced diet that's paired with exercise. Studies show that exercise modifies the gut microbiota with positive health effects. If you're prescribed antibiotics, consider taking probiotics both during and after your course of treatment. Second, become aware of your actual health of your gut microbiome. There are several ways to do this:

  • Visit your doctor – medical professionals can help you choose a particular probiotic (like ONNIT total gut health, for example) or prescribe medication in case you need it
  • Take an at-home gut health test – some companies offer probiotics and other diet plans based on your test results, so they are as close to personalized as possible (Viome and Ombre are great, affordable options)
  • Talk to a registered dietitian – RD's can help you plan a specific diet so you know exactly what you're eating / putting in your body (usually this is where the problem starts when it comes to gut health)

Lastly, execute on the game plan. Whether you go with a gut test, talk to your MD, or strategically plan a healthier diet, it's up to you to follow through and hold yourself accountable.

restoring healthy gut flora

Probiotics for Antibiotic Side Effects

What can you expect when you're taking probiotics while doing a round of antibiotics? You might not feel anything different if you're proactive about taking probiotics when starting antibiotics. Probiotics can combat common antibiotic side effects like diarrhea, infections and digestive symptoms. However, patience is important. Studies shows that it can actually take six months for the gut to recover from the damage done by antibiotic use. It's even possible that your gut will never fully return to its original state.

Damaged Gut Health: Long-Term Effects

We don't fully know the extent of the damage that's done by having a damaged or compromised gut. However, we do know that an unbalanced gut microbiome is connected with chronic inflammation, a compromised immune system and poor digestion. There's plenty of research linking an imbalanced gut microbiome with serious conditions like diabetes, heart disease, certain cancers, Parkinson’s disease and Alzheimer’s disease.

long term gut health effects


Use your brain when it comes to your gut! Maintaining a balanced microbiome is essential for whole-body health. Start with a gut-friendly diet full of high-fiber vegetables and leafy greens. Feeding your gut the specific bacteria types needed for perfect balance using probiotics can also help to ensure that all of the gaps left by diet and lifestyle are filled in for stronger fortification against bad bacteria.

Photo of author

Courtney D'Angelo, MS, RD

Courtney D'Angelo, MS, RD, earned her masters degree in Nutrition and Foods from the University of Georgia. She's a Registered Dietitian at Morrison Healthcare and has a strong passion in helping people improve their wellness!

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