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WARNING - If You Have Crohns and Are Taking Meds, Read This...

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There are more microbes in the human gut than there are cells in the body. This observation means that we are highly dependent on the normal gut flora as they actually make us healthy. However, when the probiotics in the gut are wiped out, the intestinal mucosa is suddenly open to colonization by pathogenic microbes that are known to cause inflammatory bowel diseases such as Crohn’s disease. Certain drugs can strip the gut of its “good” microbes. Unfortunately, these are commonly prescribed drugs and some are even first line treatment options that doctors prescribe for Crohn’s disease patients. What are the meds most likely to destroy your gut flora? This article discusses these drugs and how they are bad for your gut and your health.

The Human Gut Flora

The human gut is always teeming with microbes. And this is actually quite healthy.

It is estimated that there are over 100 trillion microbes in the intestine. This means that there are about 10 times more microbes in the gut than there are cells in the human body.

Of the microbes living in the gut, a large proportion are bacteria. However, fungi and protozoa are known to be resident there too. Although the gut is host to a diverse number of bacteria, most of them really belong to less than 400 species.

The microbes making up the gut flora are no mere residents too. They are actually useful even as they need the contents of the gut to thrive. Therefore, the normal gut flora is a community of symbiotic microbes.

What “Good” Microbes Do In The Gut
  • Break down undigested carbohydrates by fermentation
  • Enhance the absorption of short-chain fatty acids and promote the storage of fats
  • Contribute to the syntheses of B vitamins and vitamin K in the gut
  • Contribute to the metabolism of bile acids and sterols
  • Train the immune system to properly respond to microbial attack
  • Keep pathogenic microbes in check by outcompeting them for nutrients and other resources necessary for growth
  • Regulate the development of the intestine by controlling the production and differentiation of epithelial cells in the gut

The Emergence of the Gut Flora

In utero, the fetus’ intestine is actually devoid of microbes. However, bacteria from the mother quickly colonizes the infant’s intestines. This transfer of microbes is one of the major mechanisms by which the young immune system is trained.

Besides the mother’s contribution to the gut flora, environment is also a big determinant of the kinds of bacteria that natively colonize the gut. Therefore, the nature of the gut flora differs between cultures and even between kids born in different hospitals.

As we grow older, diet also determines the predominant microbes that make up our gut flora.

For example, studies show that people who consume more carbohydrates and simple sugars have a predominance of bacteria belonging in the Prevotella family.

On the other hand, those whose diets are rich in animal proteins and saturated fats are more likely to have Bacteroides bacteria resident in their guts. Most likely because weight loss is caused by reduced carbohydrate intake, studies show that this family of bacteria also increase in number in people experiencing weight loss.

In addition, switching from one type of diet to another can also significantly change the composition of the gut flora.

Throwing the Gut Flora Out of Balance

In a healthy gut, there is a delicate balance enforced by “good” bacteria. The natural gut flora inhibits the growth of pathogenic bacteria and keeps the immune system active against possible sources of infection in the intestine.

However, when this balance is disrupted, the gut can be quickly overrun and severely colonized by harmful microbes including pathogenic bacteria and fungi.

This opportunistic overgrowth of pathogens is triggered when the population of “healthy” bacteria has been drastically reduced.

More often than not, the turn for the worse is caused by the introduction of foreign substances in the gut.

The most important agents that can throw the gut flora out of balance are drugs. Drugs can drastically change the growth environment of the intestines. Such changes are often not ideal for the thriving population of healthy gut flora.

Even more importantly, certain drugs can directly wipe out the gut flora and leave room for pathogens to thrive.

When this happens, the gut mucosa breaks down and the immune system panics against the new invaders. The result is a number of bowel disorders including the inflammatory bowel disease known as Crohn’s disease.

Discussed below are the drugs that can wreck the gut flora and cause or worsen Crohn’s disease.


Antibiotics are the most important drugs that can drastically change the gut flora and worsen the symptoms of Crohn’s disease. Ironically, antibiotic therapy is one of the primary treatment interventions commonly recommended for patients with Crohn’s disease.

Epidemiological studies show that people placed on long-term antibiotic therapy are at least 50% more likely to develop Crohn’s disease than the general population.

Besides long-term antibiotic therapy, broad-spectrum antibiotics are especially linked to sudden and negative changes in the native intestinal flora.

Broad-spectrum antibiotics are prescribed because they are effective against a long list of bacteria. However, they essentially nuke the gut flora. Broad-spectrum antibiotics wipe out both “good” and “bad” bacteria from the gut.

Unfortunately, when their effects wear off, the gut is left with no beneficial bacteria to defend it and, therefore, open to widespread colonization of opportunistic microbes.

Studies show that the gut flora never fully recovers even after antibiotics are withdrawn especially following repeated and long-term use.

There are 2 major ways antibiotics reach the gut. First, by oral administration and secondly, through meats obtained from animals raised on antibiotics.

Chemicals with antimicrobial activities can also destroy gut flora. A 2009 study published in the Journal of Physiology and Pharmacology pointed out that the introduction, popularity and widespread use of detergents in households and emulsifiers as food additives can explain the rising diagnoses of Crohn’s disease.

Antibiotics, Gut Flora and Diarrhea in Crohn’s Disease

Killing off the native gut flora is not the only way antibiotics make Crohn’s disease worse. They can also trigger diarrhea.

Antibiotic-associated diarrhea can result from the antibiotic destruction of the gut flora and also from antibiotics directly irritating the gut mucosa.

When antibiotics destroy the delicate balance of the gut flora, they allow the overgrowth of microbes such as Clostridium difficile and Salmonella species that are known to cause diarrhea. Furthermore, the destruction of gut flora affects the metabolism of carbohydrates and bile acids. Undigested carbohydrates in the gut can cause osmotic diarrhea.


Antacids are alkalinizing agents for neutralizing stomach acid. They are used to treat heartburn or acid reflux.

Basically, antacids act by raising the pH of the stomach. Unfortunately, they disrupt the gut flora.

The gut flora depends on the pH of the various parts of the intestine. For example, the production of hydrochloric acid in the stomach keeps the pH low in the stomach enough to allow digestive enzymes to work properly.

This optimum acidity range is also ideal for the growth of the microbes in the gut. Therefore, the pH of the stomach is one of the factors that support the thriving population of probiotics in the gut.

When antacids neutralize stomach acid and raise the pH of the environment, they kill off a lot of beneficial bacteria as well as impair the digestion of food. This creates the right environment for pathogens to thrive and for probiotics to die off.

At first, the body responds to antacids by releasing even more acid into the stomach. As the doses of antacids are raised, the parietal cells responsible for producing stomach acid get exhausted and steadily produce less acid.

While the body battles with antacids, there is such wild fluctuations in stomach pH that the gut flora has no time to adapt but is rather eroded over time.

Acid as the Protector of the Gut Flora

The acidity of the stomach also acts as a protective mechanism against the pathogens and toxins that get into the gastrointestinal tract every day. Antacids remove this protection.

In a joint study conducted by researchers from the Food and Drug Administration (FDA) and Mississippi State University, the negative effect of antacids on digestive juices was clearly demonstrated.

The researchers first demonstrated that without antacids, stomach acid can eliminate the pathogen, Vibrio vulnificus within 30 minutes of reaching the gut. However, in the presence of an antacid, the lethal bacterium survived for 2 hours.

This study showed that antacids increase the odds that pathogens will harm the gut and break down the mucosa barrier keeping out pathogens and toxins from the bloodstream.

The pathogen survived for so long because the antacid prevented stomach acid from destroying the bacterium and also because the gut flora was weakened and could not quickly inhibit the pathogen.

Birth Control Pills

Birth control pills are widely popular among women seeking to avoid getting pregnant. However, they can have some serious side effects. One of these is their negative effect on gut flora.

Pills can destroy the balance established by healthy bacteria in the intestine. Most of the negative effects of pills are caused by their ability to significantly affect the hormone levels in the body. For example, pills supply the body with estrogen constantly. Therefore, it disrupts the hormonal cycle in which estrogen levels rise and fall.

Studies have shown that the dominance of estrogen in the female hormonal system can lead to yeast overgrowth.

Specifically, pills make mucosal surfaces ideal for the growth of Candida albicans.

Overgrowth of candida can cause candidiasis. The two major sites of candida invasion are the vagina and the gut.

By disrupting the balance of the gut flora, birth control pills allow C. albicans to thrive in the gut. This yeast is one of the pathogens confirmed to increase the risk of Crohn’s disease.

The destruction of gut flora by birth control pills is especially worrying when the women who use them decide to get pregnant. Since infants first inherit their mothers’ gut flora, an unhealthy gut flora may leave affected infants with poorly developed immune systems and increased risks of certain chronic diseases.


Steroid drugs such as prednisone are commonly prescribed for patients with Crohn’s disease to suppress the immune system and reduce intestinal inflammation.

Like antibiotics, long-term use of steroid drugs can negatively affect the gut flora.

Already, intestinal bacterial are involved in the metabolism of steroids which are transported to the liver and excreted into the gut through bile acids. After these bacteria metabolize the steroids, the metabolites are reabsorbed into the body.

With long-term steroid intake, the intestinal bacteria responsible for the breakdown of steroids start to dominate over the other probiotics in the gut flora. This changes the composition of the gut flora and reduces its effectiveness in providing other benefits.

Besides directly changing gut flora, steroid drugs are immunosuppressants. By suppressing the immune system, steroids reduce the body’s ability to quickly and effectively eliminate pathogenic microbes.

In fact, prolonged administration of steroid drugs can increase the population of candida in the gut. This pathogenic yeast has been repeatedly proven to contribute to the development of Crohn’s disease.


NSAIDs or non-steroidal anti-inflammatory drugs may not be steroid drugs but they can destroy the gut flora anyway.

The major side effect of NSAIDs (common examples are aspirin, ibuprofen) is injury to the intestinal mucosa. This is why these drugs are not recommended for people with high risks of gastrointestinal ulcers.

Studies have shown that NSAIDs can induce Crohn’s disease or bring the disease out of remission.

When steroids and NSAIDs are combined, the risk of upper gastrointestinal tract toxicity is significantly increased and the destruction of gut flora is guaranteed.

NSAIDs can also damage the lower gastrointestinal tract (small and large intestines) although most studies concentrate on their effects on the upper gastrointestinal tract. In fact, the damage to the intestines almost always involves pathogenic microbes as the gut flora is extensively destroyed in the lower gastrointestinal tract.

Studies show that the major presentation of NSAIDs’ effect on the gut flora in the small intestine is increased permeability.

This shows that the native gut flora has been completely stripped away and the activities of pathogens are so well established that they are breaking down the mucosal wall of the small intestine.

Therefore, the result of the destruction of the gut flora by NSAIDs is “leaky gut syndrome”.

Curiously, some researchers recommended broad-spectrum antibiotics for clearing out the pathogenic bacteria in the small intestine and restoring the structural impermeability of the breached mucosa. However, as explained above, antibiotics can wipe out the gut flora too.





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