Bad Gut Bacteria Types – Risks & How To Get Rid Of Them

 by Dr. Steve Hruby, D.C.
Reviewed by Dr. Steve Hruby, D.C.

SuperHumans are the toughest, fittest, healthiest and happiest human beings on this planet. My mission is to help you realize your superhuman potential and learn how to live a long, happy and healthy life.

  Fact Checked
 by Rhealyn Tropia, RMT
Reviewed by Rhealyn Tropia, RMT

I’m a content organizer, fact-checker and super mom who ensures content is medically-reviewed, highly accurate, and engaging. My passion is organizing information and ensuring the facts are presented in a manner that is interesting and easy to understand.

bad gut bacteria types

How much impact do bad gut bacteria types have on our health?

Our digestive system is one of the most important organs of the body, producing multiple nutrients and enzymes to fuel vital bodily processes. Our gut bacteria also provide a number of essential functions, but only when they’re in balance.

A healthy colon should have trillions of gut bacteria which help breakdown food, synthesize vitamins and eliminate toxins but some are bad. A large number of people around the world do not have the right amount or right mixture of bacteria in their guts, which can be harmful to health.

What Is Gut Microbiome?

The gut microbiome is the term for the bacteria that lives inside your gastrointestinal tract. It’s important because it affects your immune system, digestion, and even mood.

The gut microbiome is made up of good and bad bacteria. When there are more good bacteria than bad, your body is healthy. But when there are more harmful bacteria than good ones (or vice versa), your health can suffer.

A healthy gut microbiome helps you absorb nutrients from food, aids in digestion and nutrient absorption, helps fight off infections by boosting your immune system, and keeps your mood stable.

How Are Microbiome Microorganisms Grouped?

There are thousands of genera and many more species of microbes that live in the human gut, and they all have a profound impact on our health. What is often referred to as the microbiome is the collective gene content of gut bacteria.

Some 3000 species have been identified so far, which puts it at about 10% of all described bacterial species. The vast majority of these live in the large intestine, but there are also small number in the stomach, mouth and urogenital tract.

Here is how these microorganisms are generally grouped:

Normal Flora

Regular flora are harmless bacteria that are normally present on skin, tongue as well as in the intestines, genital tract, and others. These resident microorganisms help to prevent infection by dangerous microbes and promote injury recovery.

taking care of skin

Potential Pathogens

Potential pathogens are worse than just bad. They actively infect and make the body seek out more of them. Once the infection has taken hold, it can be impossible to stop. The pathogenic infection will go on spreading and multiplying in a vicious cycle.

Unlike the symptomatic parasites that we usually call parasites, potential pathogens almost always attack other bacteria species in the gut flora, causing an ongoing war inside us that we’re also part of.

In fact this is what causes so many other symptoms – bloating, crampy pain, diarrhea , flatulence and constipation are all signs of microscopic battles going on inside us.

Pathogens (Bad Gut Bacteria)

Pathogenic bacteria are the type of microorganisms that can cause a variety of diseases which include dysentery, cholera, anthrax and botulism. Pathogenic bacteria are mostly acquired by eating contaminated food or drinking tainted water.

There are specific strains of pathogenic bacteria in the gut that can cause disease when transmitted to other parts of the body. Some people have more risk than others and this depends on factors such as age, genetics, exposure, lifestyle and environmental factors and health status.

Bad Gut Bacteria Types – Representative Examples:

  • Staphylococcus aureus

Staphylococcus is a bacteria that can cause skin infections, pneumonia, and food poisoning. Staphylococcus aureus (S. aureus) is the most common type of staph bacteria in the United States.

Staphylococcus bacteria produce a variety of toxins that can cause disease by damaging tissues and organs.

For example, S. aureus toxins damage the kidneys and cause kidney failure in patients with weakened immune systems, such as infants and elderly people. The toxins may also cause other types of health problems, including brain damage, meningitis and septic shock.

  • Clostridium perfringens

Clostridium perfringens is a type of bacteria that can make you sick if you eat food that is contaminated with it. It causes foodborne illness and is often found in meat, poultry, gravy, gravies, and sauces.

Once you’ve eaten contaminated food, Clostridium perfringens multiplies in your intestines. It produces toxins that cause diarrhea and abdominal cramps within 8 to 24 hours of eating the contaminated food.

The symptoms may last up to 10 days. The illness is not serious and most people recover without treatment. But severe cases can require hospitalization or intravenous antibiotics.

  • Escherichia coli

E.coli is a bacteria that normally lives in the gut of animals, including humans. It’s known as an “enteric” bacteria because it lives in the intestines.

Escherichia coli

People can get infected with E.coli by eating or drinking food or water contaminated with feces. For example, if you touch something that has been contaminated with feces and then eat without washing your hands first, you could get sick.

The symptoms of E.coli infection include diarrhea, which may be bloody, fever and abdominal cramps.

Most cases of E.coli infection are mild and resolve within a week without treatment, but some people develop complications that require hospitalization and intravenous fluids to treat dehydration caused by severe diarrhea or vomiting and nausea caused by the illness itself.

The Risk Of Unbalanced Bad Gut Bacteria – 3 Conditions


Dysbiosis is a condition that occurs when the bacteria in your gut (or microbiome) are out of balance, and there are too many bad bacteria in your body.

This can cause a range of issues, including weight gain, inflammation, bloating and gas, diarrhea or constipation, food allergies, skin problems like acne or eczema, and more.

General Imbalance

A general imbalance of gut bacteria is when there are more bad bacteria than good bacteria in the digestive tract. The body relies on good bacteria to produce enzymes, absorb nutrients, and keep pathogens at bay.

When bad bacteria outnumber good bacteria, these functions can no longer be carried out. This can lead to a number of health problems, including bloating, gas, abdominal pain, diarrhea or constipation (or both), cramps and bloating after eating specific foods.

“Small Intestine Bacterial Overgrowth” (SIBO)

Small Intestine Bacterial Overgrowth or SIBO is the presence of an excessive number of harmful bacteria in your small intestine. This can cause symptoms such as bloating, gas, abdominal pain and diarrhea.

The condition is often misdiagnosed as Irritable Bowel Syndrome (IBS) because they share similar symptoms, but SIBO can be much more serious than IBS.

The bacteria involved in SIBO are usually the same ones that live in your large intestine, but they have migrated to your small intestine where they should not be present.

In addition to causing digestive problems, SIBO can also lead to a variety of other health issues including weight loss resistance, headaches and brain fog. The following are other indicators of SIBO:

  • Bloating

Bloating is an indicator of small intestine bacterial overgrowth or SIBO, which is caused by the proliferation of bacteria in your small intestine. The bacteria release gas as they’re digested, which leads to bloating and discomfort in your abdomen.

The most common strain of bacteria associated with SIBO is called H. pylori. This strain can cause stomach ulcers and other gastrointestinal issues, so it’s important to get rid of it before you start experiencing symptoms like bloating and discomfort in your abdomen.

  • Constipation

In this case, the bacteria that normally reside in the large intestine (colon) can move into the small intestine and cause constipation. This is because they feed on carbohydrates, which are not digested in the colon.

The most common symptoms of SIBO include chronic diarrhea, abdominal pain and bloating, excess gas and frequent belching, as well as constipation. These symptoms often go hand-in-hand with irritable bowel syndrome (IBS) and other digestive disorders such as inflammatory bowel disease (IBD).

  • Diarrhea

SIBO is a condition in which bacteria in the small intestine proliferate to an extent that they cause problems. In some cases, it can lead to diarrhea, which is often accompanied by abdominal discomfort and bloating. If you have chronic diarrhea, it’s important to get tested for SIBO so you can get the right treatment.

  • Excessive Gas

This condition occurs when there is an imbalance of good and bad gut bacteria in the small intestine. Gas can be caused by an overgrowth of harmful bacteria that produce methane, hydrogen and carbon dioxide. The excess gas leads to abdominal bloating and pain.

  • Abdominal pain

SIBO is caused by the overgrowth of bacteria in the small intestine. The majority of this bacteria is normally found in the colon, but it can migrate up into the small intestine when someone has leaky gut syndrome.

When this happens, the bacteria starts feeding on sugars and carbohydrates that are not digested properly, which leads to fermentation and gas production. This gas can cause abdominal pain in addition to other symptoms such as bloating, constipation/diarrhea, nausea and vomiting.

  • Flatulence

The bacteria that cause flatulence in your gut are known as methanogens. These types of bacteria produce methane as a byproduct of their metabolism, which can result in bloating and excessive gas production.

Diseases Caused By Bad Gut Bacteria


  • Allergic Diseases

Allergic diseases have become one of the most widespread health problems in the world. According to studies, 30% of the population suffers from at least one allergy, while 10% are allergic to more than one substance.

The most common allergies are food allergies and dust mite allergies. The reason for this is that these substances often enter our body through inhalation or ingestion.

One of the main causes of allergic reactions is a bacterial infection in the digestive tract.

This type of infection is called Helicobacter pylori (H. pylori) and is considered to be one of the leading causes of stomach ulcers and gastritis. H. pylori can also cause other symptoms such as esophageal reflux disease, which negatively affect your health in a number of ways. In fact, it even causes cancer.

  • Autoimmunity

Autoimmunity is when your immune system mistakenly attacks your own body, resulting in chronic inflammation and disease.

man with stomach pain

Bad gut bacteria can cause this because they release toxins that damage the lining of the digestive tract and make it more permeable. This allows larger food particles to enter the bloodstream, which can trigger an immune response.

  • Cancer (Gastrointestinal)

Bad bacteria in your gut can lead to cancer by damaging the cells that line the intestines. In particular, they can cause inflammation, which can make it easier for cancer-causing chemicals to enter those cells and cause damage. This is a well-known risk factor for colorectal cancer.

  • Ankylosing Spondylitis

Ankylosing spondylitis is a type of arthritis that mainly affects the spine, but can also affect other parts of the body. It causes inflammation and stiffness of the joints, especially in the lower back, hips and shoulders. The condition most commonly affects men between 20 and 40 years old.

It’s not clear exactly what causes ankylosing spondylitis, but researchers believe it’s due to a combination of factors such as genes, infections and bad gut bacteria.

Bad gut bacteria can contribute to this condition by causing inflammation in the digestive tract which then travels into other parts of your body including your joints.

  • Inflammatory Bowel Diseases

Inflammatory Bowel Diseases (IBD) is a condition that affects the gastrointestinal tract. It’s characterized by chronic inflammation of the intestines, which can cause abdominal pain, severe diarrhea, and even life-threatening complications.

The exact causes of IBD are still unknown, but it is thought that bad gut bacteria may play a role in its development. The most common types of bad gut bacteria include Clostridium difficile, Salmonella, Helicobacter pylori and E. coli.

  • Lupus

Lupus is an autoimmune disease, which means that it occurs when your immune system turns against your own tissues. In the case of lupus, the immune system attacks the skin and joints, causing inflammation that can lead to severe pain, swelling and tissue damage.

The exact cause of lupus is also unknown, but it’s thought to be a combination of genetics and environmental factors. One of these factors is bad gut bacteria. There are different types of bad bacteria in our bodies, some of which are good (probiotics) while others are bad (pathogens).

Exposure to pathogenic bacteria can increase your risk for developing lupus by activating your immune system against healthy tissue in your body.

  • Obesity

Obesity is a condition in which excessive amounts of body fat has accumulated to the extent that it may have a negative effect on health. It is most commonly caused by a combination of excessive food intake, lack of physical activity, and genetic susceptibility.

Bad gut bacteria are responsible for obesity. They make you gain weight by producing excess fat and blocking the absorption of nutrients from foods. As a result, you feel hungry even after eating a lot and gain weight rapidly.

  • Multiple Sclerosis

Multiple sclerosis is a disease in which your immune system attacks your body’s own cells, causing inflammation throughout your nervous system. Symptoms of MS include blurred vision, difficulty walking, muscle weakness or spasms, numbness or tingling in hands or feet and trouble thinking clearly.

Experts believe that certain types of bad gut bacteria may contribute to the development of MS because they increase inflammation throughout the body. This can lead to inflammation in the brain and spinal cord which could trigger an MS flare-up.

  • Psoriatic arthritis

Psoriatic arthritis is a chronic inflammatory disease that occurs when the immune system attacks healthy cells and tissues in the body. It is a type of autoimmune disorder. The most common symptoms include joint pain, stiffness, swelling, and fatigue.

Bad gut bacteria contributes to this condition by contributing to inflammation in the body. Inflammation is the key driver of many diseases, including psoriatic arthritis. This can lead to joint pain and stiffness.


  • Anxiety

Bad gut bacteria types such as E. Coli and Salmonella can cause anxiety in some people because they produce toxins that can enter the bloodstream and then travel to the brain. These toxins can cause the brain to release neurochemical messengers like dopamine and serotonin, which trigger feelings of anxiety.

These feelings may occur when you’re stressed out or anxious about something specific—for example, a job interview or an upcoming exam—but they could also happen without any clear reason at all. In fact, some people are more prone than others to developing anxiety disorders due to poor gut health.

  • Parkinson’s disease

Parkinson’s disease is a chronic and progressive neurological condition that affects the motor system. It is caused by the loss of dopamine producing brain cells which results in tremors, stiffness and difficulty with movement.

Parkinson’s disease is a complex illness where multiple factors contribute to its development including genetics, environment and lifestyle choices. Bad gut bacteria has been identified as one of these factors.

Studies have shown that people with Parkinson’s disease have higher levels of certain types of bacteria such as Clostridium species (C. difficile) in their intestines compared to healthy controls.

These bacteria produce toxins that can damage cells in the intestines and colon resulting in inflammation which may make it easier for other toxins produced by bad gut bacteria to get into the bloodstream.

These toxins are known to damage dopamine producing brain cells which may explain why we see an increase in Parkinson’s disease risk among people with compromised intestinal health or who have taken antibiotics which kill good gut flora.

  • Crohn’s Disease

Crohn’s disease causes inflammation in the digestive tract. It can be either a mild or severe condition and can affect any part of the gastrointestinal tract, from the mouth to the anus.

woman with severe stomach pain

The condition is characterized by symptoms such as diarrhea, rectal bleeding, abdominal pain, fever, weight loss, joint pain and skin rashes. These symptoms are caused by inflammation of the mucosal lining of your intestines. In more severe cases, a person may develop fistulas or strictures (scarring inside your intestines).

  • Scleroderma

Scleroderma is a condition that causes the skin to become more rigid and harden. It can also affect internal organs, including the lungs and digestive system. The exact cause of scleroderma is unknown, but research has found that it’s associated with bacteria in the gut.

Bad bacteria in your gut can contribute to scleroderma by causing inflammation and triggering an immune response.

The immune system then starts attacking healthy tissue, which causes its own chronic inflammation. This leads to scarring and hardening of the skin, as well as other organs like the lungs or skin.

  • Fibromyalgia

Fibromyalgia is a chronic pain condition that affects millions of people, and it’s often misunderstood. Symptoms include widespread pain, fatigue, and mood changes. It is believed that an imbalance in the brain’s neurotransmitters may contribute to the development of fibromyalgia, but the exact cause is unknown.

One thing scientists have discovered that contributes to the development of fibromyalgia: bad gut bacteria. When your gut is full of “bad” bacteria, it can cause inflammation in your body.

This inflammation can affect your nervous system and lead to symptoms like pain and fatigue, as well as other conditions like depression and anxiety.

  • Irritable Bowel Syndrome (IBS)

Irritable Bowel Syndrome (IBS) symptoms include bloating, abdominal pain, and change in bowel habits. The cause of IBS is unknown, but there are many theories including food intolerance and irritable bowel syndrome symptoms being caused by a virus.

Bad gut bacteria can contribute to IBS symptoms by releasing toxins into the body which can cause inflammation.

Food intolerances to certain foods such as gluten, lactose, or fructose can also trigger IBS symptoms. Bad gut bacteria can also change the way your body responds to foods which could lead to an increase in food intolerances for you.

  • Restless Leg Syndrome

Restless leg syndrome has been linked with a number of health conditions including diabetes and cardiovascular disease, but there is no clear evidence that any of these conditions are actually caused by restless leg syndrome itself.

However, having bad gut bacteria may contribute to restless leg syndrome symptoms because these organisms produce toxins called lipopolysaccharides (LPS).

These toxins can cause inflammation throughout the body and release neurotransmitters like dopamine into the bloodstream. This increased amount of dopamine causes uneasiness in your legs that makes them feel like they must move around constantly.

  • Multiple Sclerosis

There are many theories as to what causes MS, but it’s thought that there may be a link between gut bacteria and this condition.

disbaled woman on a wheelchair

It’s known that an imbalance in gut bacteria can lead to autoimmune conditions like multiple sclerosis, but how does this happen?

Research shows that when there is an imbalance between good and bad bacteria in your gut, the immune system can become confused and start attacking healthy tissue as if it were harmful.

  • Non-alcoholic fatty liver disease

Non-alcoholic fatty liver disease or (NAFLD)occurs when fat stores up in the liver, which results in inflammation and scarring.

In most cases, it’s not caused by excess alcohol consumption, but rather by obesity and other lifestyle factors. It can lead to serious complications such as cirrhosis, or severe scarring of the liver.

Poor diet and lack of exercise are two major risk factors for NAFLD. These conditions can lead to higher levels of circulating fats in the blood, which then accumulate in the liver where they may cause damage or inflammation. The bacteria within your intestinal tract also affect how much fat your body absorbs from food.

Testing Your Gut For Imbalanced Bacteria – What You Need To Know 

Testing for bad bacteria in your gut is pretty simple. You can do this at home, but the best way is to see a healthcare professional. They have the equipment and knowledge that you might not have access to. Here are two popular tests that determine whether you have a bacteria imbalance in your gut:


This test measures the amount of hydrogen and methane gas in your breath after eating. If there is a higher level of hydrogen and methane in your breath than normal, it means that some of the bacteria in your small intestine have taken up residence there and are causing problems with digestion.

Stool Test

A stool test is the most accurate way to determine bacterial imbalance. A stool test is administered by a doctor or other health care provider, and involves collecting one or two samples of your stool in a container that is provided by the doctor. The sample is then sent to a laboratory for analysis.

The lab will analyze the sample for certain bacteria and parasites that are present, as well as how much of each type there is.

The lab will also look at how many beneficial bacteria are present and how much of them there are. Based on these results, you can determine if your gut bacteria are out of balance, or if you are suffering from an infection or disease.

While these two tests are more accurate and comprehensive, you can also do your own assessment at home prior to consulting a medical professional by taking this leaky gut test online.

It is important to remember that whatever the result of the online assessment, you should proceed with consulting your doctor and do the clinical test to verify.

5 Ways To Get Rid of Bad Bacteria in the Gut 

We’ve established that bad bacteria practically exist everywhere. They can be found in your gut, on your skin and even in your mouth.

And while you may be thinking that getting rid of them is easy, the truth is that it can be very daunting. I’ve put together this list of 5 simple ways to get rid of bad bacteria in the gut and help you achieve a healthy digestive system.

#1 – Lifestyle Changes

If you’re looking to get rid of bad bacteria in your gut, there are lifestyle changes you can make that will help prevent it from happening again:

reading book
  • Stress reduction is one way to keep bad bacteria away because stress causes you to eat more processed foods which often contain harmful ingredients such as sugar and salt.
  • A leaky gut diet consists of eating foods that help repair your intestinal lining so that harmful toxins don’t seep out into your bloodstream where they can cause inflammation throughout your body leading to weight gain due to increased inflammation which causes more cortisol production, which is the stress hormone.
  • Sleep deprivation increases cortisol levels which causes weight gain because cortisol tells your body that it needs more fuel than it actually does so when you don’t get enough sleep (or at least 6 hours per night), you end up eating more calories than usual without realizing it until later on.

#2 – Prebiotics and Probiotics

The bacteria in your gut are not all bad, but there are some that can cause problems. Prebiotics and Probiotics help to prevent bad bacteria from taking over and causing digestive issues.

Prebiotics are food for good bacteria, while probiotics are live cultures of the good bacteria. Both of these can be found in yogurt, kimchi, kefir and other fermented foods. If you don’t want to eat these foods every day, you can use a supplement that contains both prebiotics and probiotics.

#3 – Antimicrobial Herbs and Nutrients

It’s important to take measures to prevent bad bacteria from growing in your gut by taking antimicrobial herbs and nutrients.

These include:

  • Garlic has been shown to help kill off bad bacteria in the gut. It also helps with digestion and boosts immunity.
  • Sage is believed to be antibacterial, antifungal, anti-inflammatory and antiviral. It can help treat stomach problems such as heartburn or bloating caused by excess gas.
  • Oregano is another herb that has been shown to fight off harmful bacteria in the digestive tract while also boosting immunity and improving digestion.
  • Turmeric contains curcumin which has been shown to kill off bad bacteria without harming good ones like lactobacillus acidophilus which is known for helping break down food into nutrients so they can be absorbed properly into your bloodstream where they belong.

#4 – Prescribed Pharmaceutical Antibiotics

Some people have good bacteria in their gut that keeps the bad bacteria under control, but if you take prescribed pharmaceutical antibiotics to prevent bad bacteria in your gut, you may find that these drugs disrupt your natural balance of good and bad bacteria.


This can lead to serious health problems because it disrupts your body’s ability to fight off infections and diseases.

To prevent this from happening, it’s important for you to talk with your doctor about how long you should take prescription antibiotics for before stopping them completely. Your doctor will also be able to advise you on any other treatments available for treating certain conditions.

#5 – Optima Healthy Gut Solution

If you’re experiencing any of the symptoms of bad bacteria in your gut, it’s important to take steps to minimize the risk.

A good first step is to incorporate an L-glutamine supplement into your diet. Products like Optima Healthy Gut Solution has a unique formula, what is packed with L-glutamine – an amino acid that stimulates the growth of good bacteria in your gut.

How Do I Know if I Have Bad Bacteria in My Gut?

There are different types of bad bacteria in the gut that could be present, but the most common symptoms are:

  • Gas and bloating
  • Bloating after eating
  • Diarrhea or constipation
  • Intestinal cramps and pain
  • Nausea and vomiting

What Is a Type of Harmful Bacteria Found in the Human Gut?

There are many types of harmful bacteria that can be found in the human gut. One type is Clostridium difficile (C. diff), a species of bacteria that can cause diarrhea and even death when it spreads to other parts of the body.

Another type is E. coli, which can cause food poisoning when it gets into your system through contaminated food or water.

Other types of harmful bacteria include Salmonella and Campylobacter, which can cause diarrhea and fever.

What Types of Bacteria Are in the Gut?

There are a number of different types of bacteria that can live in your gut.

holding stomach

There are two main types:

The first are called good bacteria, which are more commonly known as probiotics. These are the bacteria that help you digest food and keep your body healthy by fighting off infection-causing bad bacteria.

The second type is called bad or pathogenic bacteria. They can cause digestive problems and infections if they grow out of control in your system. Some common examples include Salmonella, E-Coli and Clostridium difficile (C-diff).

How Do I Get Rid of Bad Bacteria in My Gut?

There are several ways to get rid of bad bacteria in your gut.

The first is to eat a diet that consists of lots of fruits and vegetables, but no artificial sweeteners, processed foods or sugars. You should also avoid alcohol and other recreational drugs, as well as caffeine.

In addition to your diet, you should increase your intake of probiotics. These are live bacteria that can be found in certain foods such as yogurt or miso soup, as well as supplements like kimchi or sauerkraut juice. You should also consider taking a probiotic supplement if you don’t like the taste of these foods.

Finally, you should consider taking antibiotics if necessary. This will kill off the bad bacteria while leaving the good ones intact so they can repopulate your gut with healthy flora again once treatment is complete.


In a nutshell, gut microbiome is really important for your overall health. When it comes to the composition of gut bacteria, it’s better to have more strains of good bacteria than bad ones.

That’s not to say that having one type of bacteria is impossible, but in a healthy gut (without any infections), there’s a certain balance that should be achieved between the various strains.

I hope that you’ve enjoyed learning about the most common types of gut bacteria and their function in your body. They can make all the difference when it comes to your general well-being, so don’t neglect making sure that yours is healthy.

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