The 5 Little Known Side Effects Of Probiotics

Even though the term “bacteria” often makes people think of illnesses and infections, there are many species of bacteria that are essential to the survival of the human body. When the number of bad bacteria grows larger than the number of good bacteria species in the body, then you should be concerned. When you keep your good bacteria numbers up, you are at a lower risk of infection and other complications. 

To maintain a healthy balance of bacteria in the body, probiotics are essential. These are the good bacteria that thrive in your gut and helps with the absorption of nutrients, as well as ensures your digestive tract can function properly. There are different ways to obtain probiotics – from both food and supplements. 

While increasing your intake of probiotics has many benefits, there are also potential side-effects that many people tend to overlook. We shed some light on these side-effects that some people may experience when they increase the number of probiotics they obtain – and look at some effective ways to cope with these adverse effects. 

Why Do People Take Probiotics?

To understand why people are increasingly opting for getting more probiotics into their lives, we should really start by considering what they do. Essentially, probiotics contain live microorganisms. While the majority of these microorganisms are the good bacteria that need to thrive in the gut, there are sometimes other types of microorganisms too. The goal is to bring about a better balance in the gut flora – also known as the gastrointestinal microbiome. 

The main goal is to ensure the number of good bacteria in the gut becomes more than the bad bacterium species that are present in the digestive system. This essentially helps to keep harmful bacteria in check and helps to reduce the risk of these “bad” microorganisms from taking over and causing sickness. 

Many studies have been conducted to help the population understand exactly what probiotics can – and can’t – do for them. Some of the possible benefits that you may experience when you increase your intake of probiotics include:

  • Digestive health may improve due to the balance of good bacteria in your gut
  • You may experience a reduction in diarrhea
  • Probiotics may also effectively prevent the development of diarrhea, especially in cases where you are required to take antibiotics to treat a bacterial infection
  • Heart health could also be improved with the use of certain probiotic strains
  • There is also evidence that certain probiotic strains may be beneficial for certain types of mental health diseases, including depression
  • There may be an improvement in symptoms associated with allergies
  • Some people also experience an improvement in symptoms caused by a skin condition known as eczema

Side-Effects Linked To An Increase In Probiotics

Most people tend to focus on the benefits they could experience if they start increasing the number of probiotics they consume. Probiotics can come from both fermented foods, as well in the form of a pill that is taken by mouth. 

Even though probiotics are critical to your health, there are also some side-effects that you could experience. The unfortunate fact is that most publications that focus on probiotics fail to mention the specific five side-effects that we will take a look at today. 

The good news, however, is that these side-effects are generally considered temporary. If you are unfortunate enough to experience these adverse effects, then you should be able to find that they go away on their own as your body gets more accustomed to the higher concentration of good bacteria in your gut. 

Let’s take a look at the five little known side-effects associated with probiotics. 

1. Headaches

The first side-effect of probiotics that we want to mention here is headaches. This is a relatively common adverse effect that people tend to experience when they decide to increase the probiotics they consume in their daily meals suddenly. 

It should be noted that this particular side-effect will not be present in all cases, as it really depends on the sources of probiotics that you decide to consume. 

One study published in the Journal of Frontiers in Microbiology looked at how the use of probiotics affected certain chemicals that are naturally found in the human body. Researchers behind this study found that there is an increase in tryptamine and antihistamine among people who consume fermented foods that are rich in protein. 

The reason behind this is due to the production of biogenic amines. This only happens when you use high-protein foods that were fermented to increase your probiotic intake. 

These amines seem to have an impact on the central nervous system in the human body. The result is a change in blood flow. When blood flow changes due to this particular mechanism of action, you may experience headaches. In some cases, it may also lead to migraines. 

With this in mind, it might be a good idea to switch to fermented foods that are not rich in protein. This means the foods will not produce amines, leading to a lower risk of experiencing headaches as a potential side-effect. You can also choose to use a dietary supplement instead. 

2. Bloating

Bloating is another very common adverse effect that many people tend to experience when they first start taking probiotics. In fact, gastrointestinal side-effects, with a primary focus on bloating, is actually considered one of the most common side-effects that people suffer during the initial weeks with probiotics. 

There is a name for the bloating that occurs as a side-effect after you start using probiotics. The adverse effect is known as a Herxheimer Reaction. 

What happens is your gastrointestinal tract needs to get used to the increase in good bacteria that you are introducing into your body. This also means that your gut needs to work overtime and harder than usual. The result is usually bloating as a complication of this effect that the probiotics have in your gut. 

The best solution here would be to consider drinking a lot of water during the day – especially for the first couple of weeks once you start your daily dose of probiotics. Avoiding sugary foods and alcoholic beverages can also be helpful. An anti-inflammatory diet may also be a helpful way of reducing the bloating that you may experience. 

If you feel exceptionally bloated, then stop wearing skinny jeans for a week or two. Instead, try some pants that are made from stretchy material. This will help ease the pressure that your clothes may put on your abdomen. 

3. Gas

Gas and bloating actually go hand-in-hand when looking at the little known side-effects that probiotics can cause. When you experience an increase in gas as a side-effect of probiotics, then it will generally form part of the Herxheimer Reaction that we mentioned earlier. This also means that gas is one of the more common adverse events that people do tend to experience if they are still new to the increase in probiotics in their daily lives. 

The development of gas can be linked directly to the fact that good bacteria causes your digestive system to work overtime. Due to this overactive digestive system, there will generally be an increase in gas accumulation in your gastrointestinal tract. 

The good news is that the increase in gas will generally not last for long. Expect the side-effect to clear up in just a few days – in some cases; it may take a week or two, however. Drink lots of water and increase your exercise routine to help clear this side-effect faster. 

4. Diarrhea

You may have heard that probiotics are highly effective at treating diarrhea. This is most often the case when you are told to take a daily dose of antibiotics to help fight against an infection that you have developed. For this reason, diarrhea as a side-effect of probiotics may come as somewhat of a surprise to you. Still, it is an adverse effect that you need to take note of. 

Note that not everyone will experience diarrhea when they decide to take probiotics. Furthermore, diarrhea will usually only last for a couple of days. This is just a side-effect caused by the healthy bacteria going to work – which means your gut is still adapting to the presence of these microorganisms. 

The best way to counteract diarrhea as a side-effect to probiotics is to get the timing right. Avoid taking your probiotic supplement with food. Instead, take the pill on an empty stomach – perhaps right after you get up in the morning. 

5. Allergies

This is another side-effect that can cause some confusion. We previously mentioned that probiotics seem to be a good natural treatment for allergic conditions – including general allergies and even eczema. 

What you may not know is that your allergy symptoms could actually worsen for a few days when you just start to increase your probiotic intake. 

This is generally because the probiotics may cause an increase in the production of histamine in your body. The histamine, in turn, may cause you to experience itchiness in your eyes. Your nose may also be runny for a couple of days. Some people may also experience shortness of breath. 

If you do find that probiotics are causing a more significant increase in your allergy symptoms, then consider the source of the good bacteria you are using. Kombucha, kimchi, yogurt, and similar fermented foods are more likely to cause this side-effect. You may want to consume foods that contain other strains of probiotics to reduce the risk of suffering from worse allergy symptoms. 

How You Can Cope With These Side-Effects

Now that you know about the side-effects that may occur with probiotics, you at least understand what you should expect. As we did mention previously, you will find that these adverse effects start early on after you decide to take a daily dose of probiotics. The side-effects will also start relatively quickly after you decide to implement more probiotic-rich foods into your daily diet. 

These side-effects are mostly temporary. Most people will still be able to increase their intake of probiotics without experiencing side-effects. If you do develop side-effects, then coping with these events does not mean giving up on the probiotics. You simply need to wait it out – your body should be allowed some time to adapt to the new bacteria that are introduced into its gastrointestinal tract. 

There are also certain strategies that you can use to minimize these adverse effects. 

First off, consider the fact that many of these side-effects are more prominent in people who decide to increase their probiotic intake through fermented foods. Certain fermentation processes can cause these side-effects to develop. Thus, deciding on a high quality probiotic dietary supplement is one way to reduce the impact of the adverse effects associated with the good bacteria. 

You should also get the timing of your probiotics right. If you decide to take a supplement, try to drink it without food. When you take your supplement on an empty stomach, there may be a reduced risk of experiencing diarrhea, for example. If you drink adequate amounts of water with the supplement, but still take it on an empty stomach, you are also less likely to find that the product makes you feel bloated. 

Another important strategy is to watch what you eat during the first few weeks once you have started to increase your probiotic intake. Eating a diet that is rich in anti-inflammatory foods and avoiding unhealthy foods, such as those drenched in sugar and hydrogenated oils, can help to make you feel more comfortable. This means less bloating and a reduced chance of feeling gassy. 


The use of probiotics has become very popular, especially among people who are more concerned with their general health. It is possible to get probiotics from both fermented foods and in the form of a dietary supplement. While most people are able to tolerate the addition of good bacteria species to their gastrointestinal tract well, there are some who may experience adverse side-effects. 

We looked at five of the little known side-effects that some might experience when they decide to take probiotics. We also considered effective ways to counteract these side-effects and improve your experience when you decide to start relying on probiotic supplements and fermented foods. 


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