Gut Flora Meaning | Symptoms | Diet


In This Article, we will cover the detailed information about Gut Flora Meaning, Symptoms, Causes, Diet, Treatment, etc.

Gut Flora Definition

A human body is inhabited by huge numbers of various micro-organisms. The largest colonies of microbes live in our digestive system.

Some of the gut flora functions include:

  • Fermentation of non-digestible carbohydrates. Producing short-chain fatty acids.
  • Vitamin synthesis
  • Development and control of the immune system is the main function of Gut Flora.
  • Protection against pathogens

A healthy adult carries 1,5-2 kg off bacteria in the gut and should have hundreds of different species of micro-organisms. (1) Gut Flora composition varies greatly between individuals, but certain species should be predominating and be able to “control” others.

Gut Flora can be divided into three groups

Essential flora
The most important group and the most numerous in a healthy individual. Some of the main members include Bifidobacteria, Lactobacteria, Propionobacteria, physiological strains of E.Coli, Peptostreptococci and Enterococci.

Opportunistic flora
A large group of various microbes, the numbers and combinations can be quite individual. These are Bacteroids, Peptococci, Staphylococci, Streptococci, Bacilli, Clostridia, yeasts, Enterobacteria(Proteus, Clebsielli, Citrobacteria, etc.), Fusobacterium, Eubacteria, Catenobacteria, and many others.

Transitional flora
These are various microbes which we daily come in contact with from f.ex food and drinks. Usually non-fermenting gram-negative bacilli from the environment.

When the gut is well protected by essential flora and controlled amounts of opportunistic flora, this group of microbes usually goes through our digestive tract without doing any harm.

Gut Flora in Health and Disease

A damaged gut flora and/or leaky gut compromises the immune system and can cause havoc on the entire body. Pretty much every disease or health problem can be tracked back to the gut.

gut flora disease

Conventional medicine often fails to acknowledge this root cause, and the symptoms are treated locally with pills and creams that do nothing to improve the underlying problem.

There’s a lot of research on the importance of a healthy gut, but there’s still a lot of research left to be done in linking a dysfunctional gut flora and leaky gut to different diseases.


  • Acne
  • Psoriasis
  • Dermatitis
  • Eczema
  • Itching skin


Gastrointestinal tract

  • Food intolerance
  • Irritable bowel syndrome
  • Inflammatory Bowel Disease
  • Bad breath
  • Rectal itch
  • White coated tongue and thrush


“Gut Flora Mental Heath Disorders

  • Gut Flora and depression
  • Gut Fora and Autism


Other ailments

  • Arthritis
  • Chronic Liver Disease
  • Pancreatic disease
  • Polycystic Ovary Syndrome
  • Vitamin and mineral deficiencies
  • Sugar cravings
  • A general feeling that something is wrong

Gut Flora Test

If you have one or more of the listed symptoms you probably have some degree of gut issues. If you don’t have any of the listed symptoms you might still have some minor gut flora problems.

However, more severe gut flora problems usually mean several of the listed symptoms. If you’re still unsure if you have any gut issues you can do some testing

Gut dysbiosis and Candida

  • Stool analysis.
    This will give you an indication of parasites, good bacteria, harmful bacteria and yeast in the digestive system.
    However, stool analysis only shows what microbes might be in the lumen of the gut. It gives no information on the most important habitats in the gut – the ones that live on the gut wall, the mural bacteria. However, low numbers of essential flora in stools indicate that there’s a gut dysbiosis.
  • Blood test for food intolerance (Not the same as food allergy).
    As mentioned food intolerances are strongly linked to gut flora problems. If you test positive for food intolerances you definitely have some degree of gut flora problems.
  • Candida Albicans blood test
    This test reveals if you have unusually high amounts of antibodies against Candida.

Leaky gut/Increased intestinal permeability

  • The Lactulose and Mannitol Test. This test measures the ability of two sugar molecules, Lactulose and mannitol, to permeate the intestinal lining. The patients fast overnight and then drinks a mixture of lactulose and mannitol. The patient then collects urine for the next 6 hours.

Gut Flora Imbalance Causes

The factors listed below can create gut issues in one or more of the following ways and becomes the cause of the Imbalance of Gut Flora:

  • Cause decreased amounts of essential flora. Members of the opportunistic flora get a chance to overgrow
  • Cause reduced resistance or promote an overgrowth of certain micro-organisms
  • Cause a “simplified” gut flora with missing species and improper digestion
  • Cause increased intestinal permeability

Gut Flora Complex Side Effects

When some of the mentioned causes disrupt the composition of the Gut Flora Health the following can happen:

Mild-moderate cases
If you are “healthy”, but have some symptoms of food intolerance, mild skin problems, etc you probably have mild-moderate gut problems. This often includes:

  • Missing strains of gut bacteria and/or unhealthy gut flora composition
  • Mild Leaky gut/increased intestinal permeability

Mild/moderate cases will most of the time be resolved by going on The Gut Diet. Huge emphasis on beneficial bacteria and prebiotics.

Moderate-severe cases
If you have several symptoms linked to gut flora problems you probably have a moderate-severe case involving:

  • Gut Dysbiosis
  • Leaky Gut

Moderate-severe cases can sometimes be treated with The Gut Diet.

However, in many cases, you have to use Gut Dysbiosis and Leaky Gut treatment.

Gut Flora Dysbiosis

Gut Flora Dysbiosis means that there has been a change to the natural balance of micro-organisms in the gut.

gut flora dysbiosis

We get reduced numbers of essential flora, and members of the opportunistic flora get a chance to overgrow.

Common microorganisms to overgrow include Candida Albicans, Bacteroids, Clostridia spp, Proteus family, Streptococci and Staphylococci.

Candida is naturally occurring in the gut, but if the yeast gets a chance to grow out of control it can wreak havoc on the body. When there’s a disturbance to the gut flora there’s reduced resistance to Candida colonization.

Opportunistic flora produces toxic substances, and in a healthy person, these can be beneficial in the right amounts. However, when members of the opportunistic flora overgrow we get an excess of these substances.

Leaky gut/increased intestinal permeability

If the intestinal barrier is working properly it allows properly digested fats, carbohydrates, and proteins to pass into the bloodstream. Other minerals, amino acids and more get to pass through the intestinal cells.

The intestinal barrier is the main interface between the immune system and the external environment. It has been estimated that around 80-85% of our immunity is located in the gut wall.

“The dialogue between host and bacteria at the mucosal interface seems to play a part in the development of a competent immune system”

Gut flora in health provides a major source of energy for the cells which are lining the digestive tract, and a damaged gut flora leads to a malnourished gut wall.

Our digestive tract is coated with a bacterial layer providing a natural barrier against invaders, undigested food, toxins, and parasites.

If our healthy gut flora is damaged our digestive tract is open to invasion by anything that comes along: a virus from vaccination or the environments, fungi such as Candida Albicans, various bacteria and parasites and toxic substances.

“Certain opportunists, when not controlled by good bacteria, get access to the gut wall and damage its integrity making it leaky. Its cells attach themselves to the gut lining literally putting “roots” through it and making it leaky”

If the intestinal lining gets damaged unwanted molecules get to pass through into the bloodstream. If the intestinal lining gets further damaged undigested food particles, bacteria and more can pass.

This is foreign to the immune system and it triggers an antibody reaction. In the end, we get inflammation throughout the body!

Some unwanted food molecules have the ability to breach the intestinal lining even in a healthy gut. F.ex some anti-nutrients in grains can get access to the bloodstream. Regular consumption will lead to a state of chronic inflammation.

Gut Flora Diet 


The Gut Diet strongly resembles the Paleo Diet. Simply because modern foods pose a lot of problems in the digestive tract.

gut flora diet

Food intolerances should be avoided until you have started to incorporate new strains of bacteria into your gut. Then you should slowly introduce problem foods.

A general rule is that foods that can be found in nature and eaten directly without processing can be part of the Gut Flora Foods.

This, of course, excludes known toxic plants, berries, etc. Good Gut Flora health starts in the gut and diet should reflect this.

This diet is not recommended if you:

Have moderate-severe gastrointestinal problems and/or gut dysbiosis (Candida overgrowth?). The Gut Diet will in most cases not be enough to help you, and you should look at the Gut dysbiosis and Leaky Gut treatment

This diet is recommended if you:

  • Haven’t got any health problems, but want to keep your gut and health in the best possible condition.
  • Have health problems like food intolerances, skin problems or other common symptoms

Main goals include:

  • Avoid foods linked to increased intestinal permeability
  • Avoid foods linked to gut dysbiosis
  • Reduce inflammation
  • Eat plenty of foods meant for human consumption.
  • Develop a healthy gut flora by coming in contact with new bacteria and feeding the gut flora

Feed the Gut Flora

Prebiotics should be included in your diet either by eating foods containing prebiotics or through supplements. Prebiotics are a soluble fiber that stimulates the growth of beneficial bacteria in the digestive tract.

Gastrointestinal problems are common for the first couple of days on a diet with an increased amount of prebiotics. It takes time for the gut flora to adjust.

  • Inulin and Oligofructose
  • Pectin

Beneficial Bacteria

You should have several sources of bacteria in your diet. Healthy gut flora is vital for optimal health, and we need hundreds of different species for proper digestion.

Few bacteria cause Gut Flora disease, and there are several different ways to come in contact with new species.

  • Fermented foods
  • Gut Flora and Probiotics
  • Avoid excessive hygiene
  • Eat foods with some soil clinging to it
  • Stay in contact with healthy people and pets


No restrictions

  • Meat, fish and fowl
  • Eggs
  • Vegetables
  • Fruits and berries
  • Mushrooms
  • Certain oils
  • Fermented foods

In moderation

  • Fermented dairy
  • Spices and herbs
  • Alcohol
  • Nuts and seeds
  • Nightshades

Avoid or eat in small quantities

  • Sugar
  • Grains
  • Legumes
  • Certain types of dairy
  • Vegetable oils

Gut Flora Treatment

Treatment is divided into three parts:

1. Antimicrobials

  • Information
  • Herxheimer or die-off reaction
  • Antimicrobial supplements and foods you’ll be using



The better you stick to the diet the faster you’ll get better. The diet will be very strict in the beginning, but gradually ease up as you’re getting better.

gut flora diet

As the treatment progresses you’ll gradually introduce some of the Gut Flora foods you’ve avoided. In the end, you’ll hopefully be able to digest pretty much everything. People with gut dysbiosis have damaged enterocytes.

The enterocytes don’t have to do much work in absorbing fats and that’s why people with digestive disorders usually tolerate fats well. That’s one of the reasons why fat will be your main source of energy.

Basic diet

  • Meat, fish, fowl and eggs
  • Low-carb vegetables
  • Certain Oils
  • Certain fruits
  • Certain dairy
  •  Salt

Avoid in the beginning and slowly introduce

  • Fermented dairy
  • Nuts and nut oils
  • Carbohydrate sources
  • Yeast containing foods
  • Your food intolerances

Avoid or eat in small quantities

  • Sugar
  • Grains
  • Certain types of dairy
  • Legumes

3. Gut Flora Probiotics and prebiotics

After we’ve reduced or removed the numbers of overgrowing microbes it’s important to rebuild a healthy gut flora.

gut flora probiotics

A healthy gut flora with a lot of essential flora is the best defense against Gut Dysbiosis.

A healthy gut has hundreds of different strains of bacteria. Best Gut Flora Probiotic supplements only contain some of the needed strains of bacteria and can for that reason only be part of the solution.

  • Stage 1: Fermented dairy
  • Stage 2: Probiotics
  • Stage 3: Prebiotics
  • Stage 4: Fermented foods
  • Stage 5: Other sources of bacteria

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