What’s Wrong with Your Gut Bugs?!


In my video about causes of Leaky Gut, I mentioned that an imbalance in your microbiota (i.e., dysbiosis) can cause your intestine to become more permeable than it should be. And I briefly mentioned that there can be an imbalance in any number of ways.

Since there is no one-size-fits-all solution to dysbiosis (or any other health related issue, for that matter!), here are some more details to help you understand what might be wrong with your gut bugs.

Oh wait! Before I get into the different ways your microbiota can be unbalanced, let me tell you what the right variety and numbers of good gut bacteria does for us:

  • Stimulate the intestine wall to generate new cells, which is important because an enterocyte (i.e., intestinal wall cell) only lives for one week from the time it is differentiated (i.e., born) in the crypt until it reaches the top of the villi and is sloughed off
  • Educate the immune system by communicating with M cells and dendritic cells along the intestinal wall which relay messages to the rest of the immune system that these bugs are friends or foes
  • Digest some foods for us in the small intestine (it is believed that a change to our microbiota may be one reason that more and more people can’t handle gluten… the good bugs that can digest it for us are no longer present!)
  • Metabolize different kinds of fiber in the large intestine to give us nutrients that we need like vitamin K, biotin and short-chain fatty acids
  • Maintain a healthy intestinal environment by keeping bad bugs in check (The problem isn’t that there may be a few bad bugs present, the problem comes when there are too many good or bad bugs.)

Now that we know we need good bacteria and don’t want too many bad bacteria, viruses, yeast or parasites, let’s identify the different ways that your microbiota could be out of balance…

1. Overgrowth of bacteria in the stomach

Although we usually hear about bacteria that lives in the large intestine (i.e., colon), we have bacteria that lives throughout the digestive tract… from the mouth to the anus. Although many species can’t handle the acidic environment of the stomach, researchers have found over 120 different phylotypes in the stomach, including H. pylori for many people. (There’s loads of research to show that its presence does not always result in ulcers or gastritis or other problems, in case you were not aware.)

Overgrowth of stomach bacteria most often occurs when there is a change in the environment of the stomach such as a reduction in the amount of acid produced (ex: use of proton pump inhibitors [PPI]), a change to the shape of the stomach (as happens with some gastric-bypass surgeries), or use of enteral nutrition (i.e., tube-feeding).

2. Small Intestine Bacterial Overgrowth (SIBO)

The small intestine is primarily for digestion by our own enzymes and absorption of nutrients, and as such there are not a lot of bacteria living here either. However, just like with the stomach, when the environment becomes right for these bacteria to reproduce at a more rapid rate than normal, we can end up with an overgrowth of good and/or bad bacteria.

Situations that can lead to SIBO include slowed intestinal motility (maybe due to stress, inadequate vagus nerve stimulation, head injury or medication), PPI use, intestinal surgery, scleroderma, diverticuli (outpouchings in the intestine where bacteria can “hide”), autoimmune diseases (including rheumatoid arthritis and celiac disease), Crohn’s disease, hyperparathyroidism, hypothyrodism, organ dysfunction (liver, kidneys, pancreas, gall bladder), diabetes (types 1 and 2), moderate or heavy alcohol consumption, food poisoning and multiple rounds of antibiotics.

Testing for SIBO is done using a hydrogen and methane breath test. It works because bacteria (not human cells) give off gas as part of their metabolic process. The amount and type of gas released following ingestion of an appropriate substance tells the trained professional how many and what kind of bacteria are present.

3. Overgrowth of bacteria in the large intestine

As mentioned previously, we often think of the microbiota strictly in terms of the large intestine… and for good reason! Most of our good bacteria resides there and there’s plenty of talk these days about the importance of good bacteria to help us maintain a healthy weight, a good mood, and nutrient sufficiency, among other things. But even in the large intestine, situations can arise in which the good bacteria get out of control or bad bacteria can take hold.

Overgrowth of bacteria in the large intestine can be caused by slowed intestinal motility (maybe due to stress, inadequate vagus nerve stimulation, nutrient deficiency or medication), inadequate digestive capacity (so more food makes it to the colon instead of being absorbed), diverticuli (outpouchings in the intestine where bacteria can “hide”), pH imbalance (influenced by food choices), intake of certain foods (like processed foods, refined carbohydrates and sweeteners), constipation (can be a cause and an effect!), and multiple rounds of antibiotics.

Finding dysbiosis in the large intestine requires a complete stool analysis. (Beware that the stool analysis by many labs is insufficient to detect all kinds of microbial imbalance.)

4. Growth of yeast or a parasite in the intestine

We’re all familiar with the term Candidiasis, which is an overgrowth of the yeast Candida albicans. What you may not realize is that we all have some yeast in our intestines and some species have been shown to be beneficial (like Saccharomyces boulardii). The key is to not have too  much of the wrong kinds of yeast.

With parasites, it’s a bit different as there are no beneficial parasites. Parasites include worms and protozoa, and while it sounds gross to think of anyone having a parasite, they are not unusual especially in this day and age when we travel as much as we do. (Would it make you feel better to know that I found two amoebas when I did a stool test?)

Detection of yeast overgrowth or a parasite is done with a complete stool analysis.


Now that I’ve told you the ways that your gut bugs can be out of balance, I’m sure you are wondering if yours have a problem. Before I tell you the signs and symptoms, let me say that one of my concerns with a lot of the health information on-line is that it tries to tie one symptom to one problem and state that there is one solution (a drug, a supplement, a diet, etc.).  Unfortunately, with chronic conditions, there is always more than one possible explanation and, therefore, many possible solutions. (This is different from some acute conditions for which the cause is obvious. For example, if you have a bone sticking out of your arm, you have a broken bone. Period. But even for some acute conditions like a headache, there can be multiple causes.)

I want you to take this to heart because, if you have an imbalance in your microbiota, There can be any number of causes, and true resolution depends on removing the cause, followed by rebalancing the colonies of microbes.

As well, having one of these symptoms doesn’t necessarily mean that your gut bugs are out of balance. Some of them could mean you have a nutrient deficiency, a food sensitivity, or some other problem not related to your microbiota. Of course, our bodies are systems, so an imbalance in one area will often lead to an imbalance in another area. As stated above, the key is to figure out what the root cause of the problem is and fix it. (If you’re curious about other causes for some of these symptoms, check out my post Eating Should Not Hurt.)

Okay, now that all the caveats are out of the way, here are the signs that your gut bugs may have a problem…

Signs that you have an imbalance in your microbiota

  • Chronic bad breath
  • GERD / acid reflux and the regular use of acid suppressing medicine (like proton pump inhibitors)
  • Burping often after meals (remember digestive human cells do not produce gas, the bacteria that live there do)
  • Nausea, especially if associated with probiotic intake
  • Bloating, distension or tightness in the belly
  • Abdominal pain
  • Flatulence
  • Diarrhea, especially if probiotic intake increases symptoms (may be diagnosed with IBS)
  • Constipation, especially if fiber, probiotic and/or optiate intake makes it worse or taking antibiotics makes it better (may be diagnosed as IBS)
  • Steatorrhea (fat in the stool)
  • Itching around the vulva or rectum
  • Headache
  • Mood dysregulation including depression, ADD/ADHD and autism
  • Skin problems like acne and rosacea
  • Recurrent yeast infections
  • Urinary Tract Infections (UTI)
  • Sarcopenia (muscle wasting)
  • Joint and/or muscle pain
  • Weight loss or weight gain
  • Edema
  • “Seasonal” allergies
  • Fatigue
  • Nutrient deficiencies, including anemia (based on symptoms or blood tests, where possible)
  • Diagnosis with one of the aforementioned conditions


As with all of my posts, this is not intended to diagnose you or provide medical advice. Rather, it’s meant to give you information that will help you and your healthcare team figure out what is going on with you and why you may be experiencing certain symptoms. After all, our mutual goal is that you feel amazing!

A healthy gut is key to health everywhere else in the body. And having the right mix and amount of microbes is necessary for a happy GI tract.

By the way, if you think you have a problem with your gut bugs and you want to pursue resolution, contact me. Working together, we can figure out what’s causing your symptoms and resolve it, so you can get back to feeling as good as you deserve to feel.


Image courtesy of Gratisography.

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