How Do You Know If You Have Bad Gut Bacteria?

You’ve probably heard the words “microbiome”, “gut bacteria”, or “flora” quite a bit these days.

Maybe you’ve even read a few articles on why you should pay attention to your gut bacteria and how important they are for your overall health.

You know that “bad bacteria” aren’t great for your health…But now you’re wondering – how do I know if I have bad bacteria? Hint: you might have bad bacteria even if you don’t have digestive issues.

Let me walk you through it!

What is Unbalanced Gut Bacteria?

When you hear the terms “bad gut bacteria” or “unbalanced gut flora”, this can refer to a number of different conditions. The most common include small intestine bacterial overgrowth (SIBO), an imbalance of gut flora in the large intestine (commonly referred to as “dysbiosis”), pathogens, or parasites.

Let’s do a quick rundown of each of these conditions:


The small intestine should be relatively sterile when compared to the large intestine, which houses the majority of our bacteria in what is called the “microbiome”. When bacteria translocate to the small intestine for any reason and overgrow, you now have an overgrowth of bacteria in the small intestine; hence, “small intestine bacterial overgrowth” or SIBO. This is a very common condition and one I see a lot in my practice.


The term “dysbiosis” simply means an imbalance of bacteria (which could be anywhere in or on the body), but it’s commonly used to describe an imbalance of gut bacteria in the large intestine, specifically. I like to break down dysbiosis into two categories (well, 3 really, but we’ll talk about the 3rd option – parasites and pathogens – next).


This is when you don’t have enough beneficial bacteria like Lactobacillus or Bifidobacteria hanging out in the large intestine. These should be present in high amounts, but it’s very common to see folks with very little or no growth of these beneficial microbes.

General Imbalance

This is when you have too few beneficial bacteria and overgrowths of one or more commensal bacterial strains. Commensal bacteria are bacteria that are normal to find in small amounts and typically don’t cause any harm to you. However, when they start growing in high amounts, you might start developing symptoms.

Parasites or pathogens

Specific strains of bacteria that, when present, can cause harm or disease. With potential pathogens, you can usually have a small amount that won’t necessarily be problematic, but they may start to cause symptoms as their numbers grow higher.

Symptoms of Unbalanced Gut Flora

Okay, so now that you know what different types of unbalanced bacteria you might have, what are some symptoms you might experience if you were to have any of these types of bacterial issues?

The symptoms that can accompany the different types of imbalance are quite diverse. However, there are a few general symptoms you can look for with the different imbalances that might clue you in to whether you’re more likely to have one or the other.


The most common symptom for SIBO is bloating. This is because when the overgrowing bacteria in the large intestine are exposed to carbohydrates or fiber from your diet, they ferment them and produce gas as a result. As you can imagine, this can not only cause bloating but it can also lead to symptoms like excessive flatulence or belching. The increased pressure in the GI tract can also lead to reflux. (1) SIBO is also associated with diverticulitis. (2)

When you test for SIBO, there are two different types that will show up: methane-positive or hydrogen-positive.

Constipation is highly associated with methane-positive SIBO, while diarrhea is associated with hydrogen-positive SIBO. (3)

You can also exhibit no digestive symptoms when it comes to SIBO. This is because having an infection in the gut can cause disease outside the digestive system. We’ll talk more about these different conditions in the next section, but I just want you to know that you can have absolutely zero digestive symptoms and still have bacterial imbalance in the gut.

Large Intestine Dysbiosis

The symptoms for dysbiosis of the large intestine vary a lot, and I find that a lot of the time dysbiosis is associated with disease states that occur outside of the digestive system. However, there are certainly people who develop gastrointestinal symptoms when they have dysbiosis.

With insufficiency dysbiosis, the most common symptom I see is constipation. Symptoms of just a general imbalance of bacteria in the large intestine vary widely. They can include constipation, diarrhea, bloating, or general pain or sensitivity in the abdomen.

Pathogens and Parasites

These have more specific effects depending on which parasite or pathogen you have. For example, if you have H.Pylori you might have reflux or ulcers, while klebsiella pneumoniae is associated with ankylosing spondylitis. Other pathogens and parasites can simply cause ongoing digestive symptoms like diarrhea or bloating.

Conditions Associated with Imbalanced Gut Bacteria

As I mentioned previously, you do not need to have digestive symptoms to have imbalanced gut flora. I think imbalanced gut flora is more common than most people think because of this – after all, it’s strange to think that the bacteria in your gut have anything to do with the rest of your body.

Here’s just a sampling of the conditions/diseases associated with SIBO:

Conditions/Diseases associated with dysbiosis:

Specific pathogens/parasites and their associated symptoms/diseases:

Test, Test, Test!

Testing your gut for imbalanced bacteria is hugely important. I wish it was cheaper to do so (and hopefully we’ll see prices go down on these tests in the coming years) because I think everyone should do it!

Because there are so many different symptoms of bacterial imbalance, I find it’s very useful to test so you know what bacteria you actually have and what might be missing.

Because not all bacterial imbalances show themselves in the way of digestive symptoms, you may not think you need to worry about your gut bacteria, but hopefully, you’ve learned a thing or two in this article that makes you think twice about that assumption!

To take a look at your gut bacteria, I recommend doing two types of tests: a SIBO test and a stool test.

I’m currently using the SIBO test from Biohealth in my practice, which I like a lot. If your doctor is familiar with SIBO or is open to learning more about it, you may be able to get them to order a SIBO test for you that might be covered by your insurance plan.

However, many doctors won’t test for it, unfortunately (though this is becoming less and less common as the topics of the microbiome and SIBO become more popular). If your doctor will order a test for you, I recommend asking to make sure it’s a 3-hour test that looks at both hydrogen and methane gas. Remember I said that which gas you produce dictates how you deal with it, so it’s important to get that information!

As for stool tests, I’ve recently begun using the GI-MAP test from Diagnostic Solutions Laboratory. It seems to be a very accurate test, needing only one stool sample for parasitology. Other stool tests companies recommend getting the higher sample rates (for example, Doctor’s Data offers a 1 sample, 2 sample, or 3 sample kit).

I still think other options for stool testing are good, like Doctor’s Data, Biohealth, and Genova, but personally, I’m using the GI-MAP now! These tests tend to be a bit harder to get from your doctor unless you’re going to a functional medicine doctor. I’ve seen some tests be covered by insurance (at least partly) before, but a lot of times it’s difficult to get these tests from someone who can help get it covered by insurance, sadly!

If you want to test your gut bacteria, I recommend asking your doctor about your options first. If you can’t get it covered or they can’t or won’t order them, you’ll need to find another healthcare practitioner to order them for you.

In my online program, Build Your Biome, you can order these tests (with a discount) and I’ll educate you on what everything means!

Gut health is so crucial to overall health, as I hope you’ve learned by reading this article! Imbalanced gut bacteria is associated with many health conditions and diseases, and clearing bad bacteria can make a world of difference if you’re suffering.


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  1. […] now, go through this checklist to see if you may have a serious gut imbalance that could impact your health in a negative […]

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