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The Effects of Too Much Bad Gut Bacteria On The Body and What You Can Do About Them
Updated on September 13, 2023
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The Effects of Too Much Bad Gut Bacteria On The Body and What You Can Do About Them
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You may not know it yet, but your gut has trillions of bacteria. They exist in a symbiotic relationship with your body, calling it their home.  

In a typical human gut environment, there is a balance of good and bad bacteria. Once this balance gets disrupted, health problems begin to occur. 

The Effects of Too Much Bad Gut Bacteria On The Body and What You Can Do About Them 2

Why Is There Bacteria In The Gut?

There is a negative perception surrounding gut bacteria. Some people think that all of them cause disease.

Yes, there are harmful ones. However, there are also friendly microbes that help you stay healthy.

Bacteria make up 90% of microorganisms found inside the human gut. They are introduced into the human body from birth to adulthood. 

The bacteria in your gut help you maintain good health by:

  • Aiding in digestion
  • Breaking down toxins
  • Supplying your body with energy
  • Protecting your gut
  • Producing vitamins
  • Strengthening the body’s immunity

The intestinal microbiota affects human health. Good gut balance is crucial for one’s health.

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What Are The Harmful Effects Of Bad Gut Bacteria On The Body?

An imbalance of bacteria in the gut directly affects your body organs and overall health. Here are some effects of having too much bad bacteria:


A particular type of bacteria produces a chemical that the liver converts into trimethylamine-N-oxide or TMAO. 

An increase in TMAO production causes the build-up of cholesterol in blood vessels, which may lead to heart disease.1


A rise in the production of TMAO is also associated with chronic kidney disease. It can also lead to the development of kidney stones.2


Harmful bacteria turn fiber into fatty acids. Your body may deposit them in the liver, and lead to the development of Metabolic Syndrome.3

When left untreated, metabolic syndrome can lead to:

  • Obesity
  • Heart disease
  • Type 2 diabetes


Your gut microbiomes can influence your immune system. Harmful gut bacteria can trigger inflammation. It’s linked to joint problems like rheumatoid arthritis and osteoarthritis.

Central Nervous System

The gut has many nerve endings that communicate directly with the brain. Doctors call it the gut-brain axis. Having too much harmful gut bacteria has been linked to:

  • Autism Spectrum Disorders
  • Anxiety
  • Depression

Digestive System

Poor gut health affects your overall health. It increases your risk for digestive problems, such as:

  • Ulcerative Colitis
  • Crohn’s Disease
  • Celiac Disease
  • Colon Cancer
  • Irritable Bowel Syndrome (IBS)

These symptoms are often accompanied by weight loss and abdominal pain. 

Immune System

Your gut microbiome helps regulate the balance of your immune system. An unhealthy gut increases systemic inflammation. It places you at risk of autoimmune diseases such as type 1 diabetes.4

Mental Health

Gut inflammation and dysbiosis are associated with poor mental health. This is because of the gut-brain axis. 

Anxiety and depression are just some mental health issues linked to poor gut health

How Do You Know If You Have More Bad Gut Bacteria?

Bacterial overgrowth causes an imbalance in the typical environment of the gut. When this happens, you’ll begin to notice tell-tale signs that you’d sometimes ignore, thinking they will pass.

The most common symptoms include:

  • Stomach discomfort
  • Bloating and gas
  • Diarrhea
  • Constipation
  • Heartburn
  • Constant fatigue
  • Persistent sleepiness
  • Poor concentration
  • Skin issues
  • Weight problems

Too much bad gut bacteria has also been linked to Crohn’s disease and Irritable Bowel Syndrome (IBS).

At-home microbiome test kits provide a comprehensive picture of your gut microbiota. 

Viome Gut Intelligence gives you information on the different microorganisms inside your gut. They offer food recommendations and personalized supplements to help maintain your gut health.

How Do You Restore Your Good Gut Health?

Here are several ways to improve your gut health.

Avoid unnecessary use of antibiotics

Doctors prescribe antibiotics to treat bacterial infections. But as we all know, too much of anything is bad for your health. 

Overusing antibiotics not only causes antibiotic resistance. Research has shown they can damage the gut microbiome. 

Antibiotics can decrease the number of good bacteria as they eliminate the bad ones. This affects the diversity of your gut microbiota.5

Have a healthy and balanced diet

The food you eat passes through the gastrointestinal tract and affects your gut flora. Healthy eating habits and the right dietary choices ensure your gut stays in good shape.

People who eat plenty of plant-based foods have a healthier gut microbiome. Studies show they have a more diverse gut microbiota compared to those who only eat meat.

A diet high in sugar and sweets causes an imbalance in your gut flora. It negatively affects the gut microbiome.

Health experts recommend avoiding certain foods like:

  • Red meat 
  • Fried food 
  • Artificial sugar 
  • Fructose-rich food 
  • Alcohol 
  • Processed foods 
  • Caffeine. 

Exercise more regularly

Regular exercise and physical activity can improve your health. It does so by helping you with:

  • Controlling your weight 
  • Improving your blood flow  
  • Positively impacting your heart health

At least 30 minutes of exercise each day can provide long-term health benefits. It can lead to better gut wellness. Research shows that regular exercise enriches the diversity of your gut flora.7

Get good quality sleep

When it comes to sleep, the time you spend sleeping is just as important as the quality of your sleep. Getting 8 hours of restless sleep won’t do any good. 

In a study, researchers found that sleep disruptions negatively affect gut health. They can change the composition of your gut microbiome.8

Researchers linked good quality sleep to improvements in human gut health, cognition, and mood.

Manage Stress

Did you ever notice how your digestive tract reacts when you feel anxious? “Butterflies in the stomach” is often associated with stress, anxiety, and poor mental health.

Studies reveal that various stressors can negatively affect the balance of bacteria in the gut. In humans, the stressors may be:

  • Psychological stress 
  • Environmental stress 
  • Deprivation of sleep 
  • Disruption of the body’s internal clock 

Stress management is essential for a healthy immune system and overall health. Some stress management techniques include:

  • Deep breathing exercises
  • Meditation
  • Progressive muscle relaxation

Eat more prebiotics and probiotic foods

Maintaining the balance of bacteria is vital to ensuring a healthy gut. You should encourage the friendly bacteria to continue growing and the bad ones to stop multiplying. 

To do this, you must feed the good gut bacteria with the food they like — prebiotics. You may add living microbes directly into the GI tract through probiotics. 

Prebiotics and probiotics are essential to good gut health. You can get them from foods and dietary supplements.

What Are The Common Types of Beneficial Bacteria That You Need?

There are several strains of yeast and bacteria in your gut environment. Each has a specific role, and they work together as a collective.

It's also important to understand that we keep the beneficial bacteria at the right levels. Here are the bacteria that promote a healthy gut:


Lactobacillus strain produces the enzyme lactase. It helps in the breakdown of lactose in dairy products. If you don’t have enough of this strain, you may experience poor reactions to dairy.

Lactobacillus helps maintain the acidity level in the bowel. It is vital in the absorption of key minerals, such as:

  • Calcium
  • Magnesium
  • Copper
  • Iron

Research also shows that Lactobacillus may be a treatment for vaginal and urinary tract infections.9


Bifidobacteria is the primary bacteria found in babies and children up to 7 years of age. It stays in the lining of the large intestine wall and benefits your body by:

  • Protecting the gut lining
  • Maintaining the acidity level of bowel
  • Restricting the growth of nitrate-producing microbes
  • Producing B vitamins and vitamin K
  • Regulate your bowel movement

Bifidobacteria and Lactobacillus strains help in fermenting carbohydrates. The process releases short-chain fatty acids, or SCFA.

SCFA are nutrients that make the cells in the GI tract lining healthy. They help support a well-functioning digestive system.

What Are the Best Foods for Healthy Gut Bacteria?

Your digestive health depends on what you feed your gut microbiome bacteria. Certain foods are known to make the gut healthy.

Some of the most recommended gut-healthy foods are listed below. Dietary changes can help improve your gut health significantly.


Almonds contain 12.5 grams of fiber per 100 grams. They have high fiber content and prebiotic characteristics. They promote good bacterial growth while preventing bad bacteria from thriving.


Bananas provide the gut with a kind of fiber known as inulin. Inulin promotes the growth of beneficial bacteria.


There are many kinds of cheese, but not all are excellent probiotic sources. The good ones for the bacteria in your gut are:

  • Cottage
  • Cheddar
  • Mozzarella
  • Gouda cheese

Fermented foods 

Fermented foods are natural sources of probiotics. They have live and active cultures, such as yeast and bacteria.

Some examples of fermented foods are:

  • Kefir
  • Kimchi
  • Kombucha
  • Miso
  • Natto
  • Pickles
  • Sauerkraut
  • Tempeh
  • Yogurt


Garlic is an herb known for its taste and prebiotic properties. It helps ensure a healthy gut by promoting the growth of good bacteria. 

It also prevents bad bacteria from taking over the digestive system.

Green leafy vegetables

Green leafy vegetables contain a special kind of carbohydrates that supplies good bacteria with food. Plus, veggies are also high in fiber which helps with digestion.


Legumes have prebiotic properties that help restore your GI tract to good health. Soybeans, baked beans, and red kidney beans are excellent examples. 


Polyphenols are compounds found in dark-colored foods like green tea. They help maintain the balance of bacteria in the gut.

They fight off pathogenic bacteria and encourage the growth of good bacteria in your gut. Polyphenols are also good at easing the symptoms of peptic ulcers and inflammatory bowel disease. 

Good Gut Health for Overall Health and Wellness

Your overall health and wellness depend on various systems working together efficiently. Each of your organs is dependent on one another. If one fails, a chain of reactions happens.

People with poor gut health experience frequent bloating, excess gas, and chronic fatigue. And they are more prone to developing diseases, such as:

  • Irritable bowel syndrome
  • Inflammatory bowel diseases (Crohn’s disease)
  • Type 1 diabetes
  • Heart disease
  • Many more

A healthy gut contributes to a healthy you. So pay attention to what you eat — and avoid what you shouldn’t eat. A few healthy changes have positive effects that will go a long way.

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Updated on September 13, 2023
Cristine Santander
Cristine Santander
Content Contributor
Cristine Santander is a content writer for KnowYourDNA. She has a B.S. in Psychology and enjoys writing about health and wellness.
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