Does disease begin in the gut? Inflammation, diet & the gut

 by Liesa Huppertz
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We have learned already that chronic inflammation is the root cause for many diseases such as heart disease, inflammatory bowel disease, type 2 diabetes, rheumatoid arthritis or even obesity. Inflammation itself is nothing to worry about. It is our body’s defence mechanism against outside invaders. If the inflammatory response doesn’t stop when the pathogenic agent has been removed though, that’s when chronic inflammation occurs. When left unchecked, the immune system then turns from friend to foe and begins to attack healthy tissues. This process sets the stage for chronic diseases, like the ones mentioned above.

You’re probably wondering now, ‘why does inflammation become chronic’ or what’s causing your immune system to attack healthy cells. Since inflammatory diseases are becoming more and more an epidemic, more research is being conducted to help better understand chronic inflammation.

More than 80% of our immune system is located in the gut. Therefor, it makes sense to start looking to the gut and the role of our microbiome to find out more about chronic inflammation. Because one thing is remarkable: Inflammatory diseases have one thing in common and that is they are all linked to gut dysbiosis - the imbalance in the microbiome with more pathogenic than commensal bacteria.

So what is the connection between gut bacteria and chronic inflammation? And how does our diet impact our gut health and therefore the amount of inflammation in our bodies? What are symptoms of an unhealthy gut and how to improve the gut naturally? This is what we’ll learn in this article.

Does disease start in the gut? The connection between diet, gut microbiota and inflammation

The term gut microbiome describes the microorganisms living in your intestines. A person has trillions of microorganisms residing inside the gut, with about 300 to 500 different species of bacteria. They affect how well we absorb nutrients from our food, how efficient our immune system works and even the extent to which we feel anxious or relaxed.

Not all microorganisms are created equally. Some may be harmful to our health, while others are beneficial and necessary to keep our bodies healthy.

Many factors may alter the gut microbiota, from extrinsic stressors such as the use of antibiotics, sleep disturbance, physical activity, and psychological stress to environmental stressors such as pollution or toxins. The factor most commonly-studied though is our diet.

Our diet has a huge impact on the composition of our gut microbiota and on the growth of organisms that are best suited for metabolizing food that we commonly eat.

What we eat can affect the gut microbiota greatly. Ingested nutrients are used as an energy source by gut microbiota in fundamental biological processes. A change in our diet may naturally lead to a change in the composition of our gut microbiota as new types of bacteria are needed to metabolize the novel diet type while other species become less abundant. A change in the composition of the gut microbiota may not only affect your physiology, but also your disease resistance. 1

There are several studies that suggests that the composition of our microbiota influences our immune system and that changes in it may contribute to chronic inflammation. 2

The typical western diet consists of a mixture of fats and is high in simple sugars, which impacts the gut microbiome composition significantly. The high consumption of sugar and fat also often leads to the development of gut inflammation and other related diseases. 3

When looking at the vegetarian, Mediterranean and FODMAP diets, we can see that they have one significant thing in common: They are rich in prebiotics and fiber. This promotes the growth of healthy intestinal microbiota which in turn reduces the risk of intestinal inflammation and diseases. 4

Healthy microorganisms, known as probiotics, are also found in certain foods, such as fermented foods, yogurts and some dairy products. They provide several benefits and can prevent and even cure intestinal inflammation and disease. 5

Probiotics have an anti-inflammatory effect by promoting the secretion of anti-inflammatory factors. This may aid the recovery of the intestinal barrier, protect against harmful bacteria, and improve the immune response, consequently reducing intestinal inflammation and mitigating the symptoms of IBD. 6

A healthy gut is able to prevent the invasion of pathogenic bacteria while letting normal gut microbiota pass. However, an imbalance in the gut microbiota leads to an altered immune system which in turn leads to the activation of an immune response. This causes the induction of a disease state. And that’s not all: this dysbiosis also increases the number of harmful bacteria in the gut 7, leading to more inflammation.

Summary: Maybe Hippocrates was wrong in suggesting that all disease starts in the gut, but many chronic metabolic conditions are believed to be caused by chronic gut inflammation. For some chronic diseases it has even been suggested, that rather than a single organism, the disturbed microbiota is the pathologic agent.

Which bacteria are the ones driving inflammation?

So if a dysbiosis in the gut microbiome is hypothised to be the cause of many chronic diseases caused by inflammation, we should take a closer look at the bacteria driving gut inflammation.

Gram-negative bacteria: Gram-negative bacteria contain lipopolysaccharides (LPS) in their cell walls, which are large molecules also known as endotoxins. These endotoxins can leak from the gut into the bloodstream either along with with dietary fat or they make their way past the tight junctions that are actually supposed to prevent invaders from getting across the gut lining. The invaders are recognized by the immune system, which starts the attack.

Through the interaction of LPS and macrophages (a type of white blood cells), pro-inflammatory cytokines such as TNF-alpha, IL-6, and IL-1 are released, stimulating chronic inflammation and causing issues over time. 8

You see, our gut microbiota plays an important role in the development of inflammation, emphasizing once again the importance of a healthy diet.

Summary: Some bacteria, called Gram-negative bacteria contain lipopolysaccharides (LPS) in their cell wall. Another name for these bacteria is endotoxins. When they leak into your body, they trigger inflammation. A condition where endotoxin levels are 2-3 times higher than normal is called metabolic endotoxemia.

Endotoxemia and a high-fat diet

Your gut always contains a certain level of these gram-negative bacteria and pathogenic varieties. Usually though, the commensal bacteria outnumber them and therefor keep them at bay, preventing them from triggering an immune response or causing other issues.

Your diet is directly related to the makeup of your bacteria and it therefore plays a major role in the amount of circulating endotoxins.

Imaging your bacteria being those tiny organisms that need to be fed. Some of them prefer to consume protein, sugar or fat, while others prefer carbohydrates in the form of fiber.

If you eat a high-fat diet, you’ll feed those bacteria, that prefer fat and naturally end up with bacteria that like fat. If you consume more fiber, you will have more of the bacteria that thrive on that.

Our western diet usually consists of high fat and a lot of sugar and the bacteria that prefer that seem to produce more toxic metabolites. On the other hand, a diet high in fiber feeds the commensal bacteria. These produce beneficial metabolites and other protective properties.

It seems like a high-fat diet is the fuel source most commonly correlated with an increase in gram-negatives in the gut and the amount of LPS in the blood 9, 10.

A study in mice showed, that a diet high in fat increased the LPS concentration in the blood, causing endotoxemia. This induced systemic inflammation, which in turn initiated a process leading to obesity and diabetes in the mouse. 11.

This effect doesn’t just show in mice. In another study, eight healthy human subjects were put on a typical western diet for a period of four weeks and then put on a one-month washout period, consuming a prudent style diet, which consisted of more fiber and less fat. The caloric intake of both diets was similar, with 2209 calories for the western-style diet and 2214 for the prudent-style diet. In the western diet, 40% of calories were coming from fat, 40% from carbs, and 20% from protein. It contained 12.5 grams fiber and 20.8% of total calories came from saturated fat while the prudent-style diet contained 20% of calories from fat, with only 5.8% from saturated fat. It also contained the same amount of protein and 60% of calories from carbs, with 31 grams of fiber.

So, we have the western-style diet with:

  • 2209 calories
  • 40% fat of which 20.8% is saturated
  • 40% carbs
  • 20% protein
  • 12.5 grams fiber

and the prudent-style diet with:

  • 2214 calories
  • 20% fat of which 5.8% is saturated
  • 60% carbs
  • 31 grams of fiber
  • 20% protein

Consuming the traditional western diet led to an increase in the levels of endotoxins in the blood of 71%! The prudent-style diet on the other hand lead to a reduction in endotoxins of 38%. 11

When we’re talking about a high-fat diet, it’s important to specify the type of fat consumed. A study showed that an increase in the omega-6 to omega-3 fatty acid ratio resulted in a higher production of LPS and other pro-inflammatory bacteria in the gut which in turn leads to chronic inflammation. 12

Conversely, higher amounts of omega-3 fatty acids increased the number of LPS-suppressing and anti-inflammatory bacteria and therefore preventing systemic inflammation.

In our western diet, the ratio of pro-inflammatory omega-6 to anti-inflammatory omega-3 fatty acid is close to 25:1. Ideally, you’ll want to get it as close to 1:1 as possible.

Summary: Studies have shown that a typical western diet that is high in saturated fats can raise endotoxin levels in your blood.

Effects of inflammation

Inflammation is your body’s response to foreign invaders, toxins or cell injuries. By activating an immune response, your body attacks these unwanted invaders and starts to repair any damage done to tissues or cells.

Generally, inflammation is a good thing, as long as it is acute inflammation. Acute inflammation is only a short-term inflammation that after a bug bite or an injury. Only through the process of inflammation is your body able to remove pathogens like bacteria and viruses, that could otherwise cause serious sickness or even death.

However, the other type of inflammation - chronic, low-grade, or systemic inflammation - is the one to watch out for.

Long-term chronic inflammation is connected to so many health problems and diseases. It increases the risk for heart and cardiovascular diseases, and non-alcoholic fatty liver disease (NAFLD). It also increases the risk of cancer and dementia. Obesity and diabetes 2 are also characterised by a low-grade inflammation though it is still not clear if the inflammation is the cause or the consequence of it.

Summary: Inflammation is your body’s immune system response to foreign invaders. Chronic inflammation is the lead cause for many serious diseases.

Gut problems that trigger inflammation

Unfortunately, with our bodies being so complex and our microbiome being so diverse, it is not always easy to heal the gut through clean eating. You may be eating a healthy diet but still experience health issues. This is when you have to turn your gaze towards some underlying gut issues.

1. Leaky gut

In leaky gut, your intestinal lining is damaged, allowing undigested food particles and bacterial endotoxins (LPS) to pass. This may lead to systemic inflammation throughout your whole body.

2. Bacterial imbalance

An imbalance imbalance in the microbiome with more pathogenic than commensal bacteria can lead to a variety of health issues. Anxiety and depression for example seem to result from lower levels of Lactobacillus helveticus and Bifidobacterium longum while weight gain is linked to higher amounts of Firmicutes.

3. Yeast overgrowth

Everyone of us has some level of yeast in our microbiome. However, a yeast overgrowth, for example in candida albicans, can lead to chronic low-grade inflammation.

4. Histamine intolerance

Histamine, a chemical that is produced during an allergic reaction, is usually broken down by specific enzymes. However, if there is a dysfunction or deficiencies of these enzymes, histamine intolerance occurs. Without these enzymes your body is not able to effectively get rid of excess histamine which leads to all sorts of health issues.

Summary: Gut health problems don’t only manifest in the gut-stomach area, but may lead to inflammation all over your body, showing in all kinds of symptoms.

What are symptoms of an unhealthy gut?

The symptoms of an unhealthy gut are manifold which makes it harder to really tie them to an unhealthy gut. Here are some common symptoms that may stem from an unhealthy gut.

1. Upset stomach

An upset stomach is probably one of the more obvious symptoms of an unhealthy gut. Gas, bloating, constipation, diarrhea, and heartburn are usually signs that something is wrong in your gut.

2. Sugar cravings

Increased sugar cravings can be a sign of an imbalance in your gut bacteria, more specifically, a decrease of your good gut bacteria. This may lead to a vicious circle, making you eat even more processed, sugary foods, damaging your gut further.

3. Changes in weight

Have you been gaining or losing weight unintentionally without changing your diet? This may be a sign of an unhealthy gut. Your body may face difficulities absorbing nutrients from your food, regulating blood sugar, and store fat due to an imbalance in your gut bacteria.

4. Problems sleeping or fatigue

It may sound weird, but problems with your sleep like insomnia or poor sleep may derive from an unhealthy gut. In the worst case, this may even lead to chronic fatigue. You may wonder how our sleep and the gut are connected. Here’s the deal: The majority of the hormone serotonin, which affects mood and sleep, is produced in the gut. This is why damages to your gut can manifest in sleep disturbances and mood disorders.

5. Skin problems

A damaged gut may lead to skin irritation such as eczema. Due to inflammation of the gut, certain proteins may be leaking out into the body. This then leads to skin conditions such as eczema.

6. Food intolerances

Are you having trouble digesting certain foods? Then you may have a food intolerance. Poor quality of bacteria in the gut is believed to be the main cause here, leading to difficulties digesting certain foods and unpleasant symptoms such as gas, bloating, nausea, diarrhea, and abdominal pain.

7. Autoimmune conditions

Since most of our immune system can be found in the gut, naturally our gut health has a huge impact on it. An unhealthy gut may lead to chronic inflammation and alter the functioning of our immune system. This may lead to our body attacking its own healthy tissues rather than harmful invaders, giving rise to autoimmune diseases.

How to improve gut health naturally?

So, how can you restore gut health and get your bacteria in balance?

The first and most important step is to feed the good bacteria while making sure to create a healthy environment in your gut for your good bacteria to thrive in and limiting bad bacteria.

Basically, there are four pillars to healing the gut:

  • Reducing the gram-negative bacterias to limit the amount of endotoxins in your bloodstream
  • Feeding your good bacteria
  • Preventing and repairing any intestinal permeability or leaky gut
  • Treating the inflammation caused by endotoxins

Naturally, this all starts with your diet. It doesn’t end there though. Still, in this article we will focus on the role of our diet in order to improve gut health naturally.

Take a look at your overall diet

Taking a look at your overall diet is always the first step. Are you eating a lot of processed foods? A lot of sugar or high fat?

Ideally you want to opt for a high fiber diet rich in vegetables, fruits and whole grains. Substituting whole grains for processed grains is one easy step you can take towards a better gut health.

Furthermore, you’ll want to look at your fat consumption. The goal is to opt for healthy fats and balance out the omega-6 to omega-3 fatty acids ratio as low as possible, ideally 4:1 or even lower.

Beware of vitamin/mineral deficiencies

Deficiencies in vitamins and/or minerals are a huge threat to our health. Scientists have looked at the consequences of micronutrient imbalances in human biology extensively. But when it comes to the impact of micronutrient imbalances on gut health, much less is known.

A study in mice though showed, that a deficiency in micronutrients, especially a Vitamin A deficiency, affects the bacterial community structure.

Another study showed the effect of iron supplementation on the gut microbiota. Iron supplementation increased the number of gut bacteria and beneficial anti-inflammatory bacterial metabolite (butyrate)

Take your prebiotics

Prebiotics are non-digestible food ingredients that fuel commensal bacteria in your gut and therefore promoting the growth of beneficial microorganisms.

When you start taking your prebiotics, you may experience uncomfortable side effects such as bloating and excess gas at the beginning. It is therefore recommended to start slowly and build up the recommended dosage of prebiotics.

Probiotics for gut health

Probiotics are beneficial to your gut health by affecting the gut’s makeup. They are able to stimulate the growth of resident bacteria and directly impact the abundances of bacterial pathogens. But be aware that not all probiotics are the same. The effects are based on the strains of the bacteria.

Potential benefits of probiotics have been seen in the treatment or prevention of:

  • diarrhea
  • Crohn’s disease
  • irritable bowel syndrome
  • infection of the digestive tract and much more.

Fermented foods

Fermented foods have been big for quite a while now and for good reason. Foods like sauerkraut, kimchi, yogurt or tempeh have numerous health benefits which might be connected to the beneficial microbes found in fermented foods. Additionally, a variety of other nutrients like polyphenols and prebiotics promote gut health even further, bringing even more health benefits to fermented foods.

When choosing fermented foods, go for those that list several different bacteria strains. Also, be aware of the high levels of sugar, salt, and fat that are often added to fermented foods. Make sure to read the label to make the healthiest choice.


Polyphenols are natural compounds in plants, including foods such as vegetables, fruits, cereals, coffee, tea and wine that protect your body from oxidative stress, UV damage, and pathogenic microorganisms.

Polyphenols that reach the large intestines have been reported to alter the proportions of microbiota. However, they often don’t reach the colon, as they are not well absorbed and rapidly excreted in urine. If they do though, they come in direct contact with the gut microbes, resulting in a complex and multidirectional interaction. Due to the polyphenol’s antioxidant capacity, a healthy gut environment in which gut microbes can thrive is shaped.

They are said to improve dysbiosis as well as the accompanying metabolic endotoxemia by increasing the abundance of Akkermansia muciniphilia, a Gram-negative mucin-degrading bacterium, in the gut microbiota.

To get the advantages of polyphenols in food, it’s important to eat a wide spectrum of colorful, plant-based foods such as green tea, olive oil, berries, red wine, coffee, plums, spinach, apples, black beans, and plums.


Many diseases are believed to begin in the gut, as the microbiota is significant in relation to inflammation, a driving force of so many chronic diseases.

Inflammation in the gut is caused by an imbalance in the microbiome with more pathogenic than commensal bacteria. Specifically, endotoxins play a significant role in the process of inflammation and may be the missing link between an unhealthy diet, inflammation and chronic metabolic disease. Thus, healing the gut microbiota can be a strategy to mitigate inflammation.

Still, chronic inflammation is incredibly complex and so is our gut microbiome. It is nearly impossible to connect all the dots of these complex processes and scientists are just beginning to explore how it’s all connected.

In a nutshell

The composition of our gut bacteria is determined by what we eat. Some bacteria thrive on protein, sugar or fat, some on fiber.

Eating a high-fat diet will feed those bacteria, that prefer fat and you’ll naturally end up with bacteria that like fat. Consuming more fiber will leave you with more bacteria that thrive on that.

A diet high in fiber feeds our good bacteria and makes them thrive. On the other hand, studies show, that a typical western diet full of sugar and fat feeds non-favorable bacteria in our gut called endotoxins or gram-negatives.

When these harmful bacteria leak into the bloodstream, our immune system detects them and starts to attack. Usually, their amounts are too small to cause symptoms of an infection, but they are high enough to stimulate chronic inflammation which leads to several health issues over time.

Thus, healing the gut microbiota can be a strategy to mitigate inflammation.

Gut health is a topic that has become increasingly important. Scientists are just beginning to explore how our #gut is connected to all that's going on in our bodies. Latest studies show, that gut inflammation is one of the driving forces of a lot of most harmful diseases. Read how our gut affects our health, how an imbalance of bacteria may lead to #chronic inflammation and how to heal your gut naturally. #guthealth #gut #gutinflammation #chronicinflammation #healthylifestyle #healthyliving #bacteria

Disclaimer: Please be aware that I am not a doctor or a medically trained person. What you're reading here is information that I researched and summarized to the best of my knowledge and processed it for your digest. Information stated on iamliesa is for educational purposes only, this information is not to replace advice from your health care practitioner. If you have any concerns about your health, always consult your general practitioner.

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