All About Gut Dysbiosis

Here we dig into the function, and dysfunction, of the collection of your gut microbes – your microbiome. The word microbiome has gotten a lot of press in recent years. Your different body parts that are “open” to the outside world each have their own unique microbiome. This includes your mouth, nose, lungs, skin, vagina, and bladder. The sum total of your microbes is 4-6 pounds, which means trillions!

However, most of these microbes live in your digestive tract. It’s time to get over being grossed out about this – we live in a world with microscopic critters everywhere, and we need them. We’ve evolved symbiotically with microbes. We provide a nice home for them, and if all goes well, they do a zillion amazing things for us.

Do your gut microbes work for or against you?

You probably know your gut bacteria are vital to all aspects of mind-body health. It’s ideal to have an abundance of beneficial bacteria, in the right place (large intestine), and rich in diversity.

These are some of the key jobs your gut microbes do for you:

  • Regulate your metabolism and keep you lean.
  • Communicate with your brain and nervous system to keep you sane.
  • Process your food and make all kinds of vitamins and nutrients for your benefit.
  • Regulate and metabolize your hormones.
  • Build a healthy mucosal barrier lining all the way through your GI tract, which prevents food intolerances and “leaky gut.”
  • Prevent undesirable species from taking over.
  • Keep your immune system strong and stable.

What if your gut bacteria can’t keep up?

This is what we call dysbiosis, which means a disruption in your gastrointestinal microbiome that leads to poor health. You can have three different types of dysbiosis: inflammatory, insufficiency, or both.

Inflammatory Dysbiosis

This is an overgrowth of microbial species that cause inflammation, which can be in your stomach, small intestine or large intestine (colon).

Inflammatory dysbiosis is very common and can:

  • Trigger autoimmunity.
  • Muck up hormone balance – think endometriosis, PMS, hot flashes, bloating, and painful periods.
  • Crowd out your beneficial species.
  • Damage your gut lining, which causes leaky gut and food intolerances.
  • Produce toxins that can cause widespread inflammation and pain throughout your body.
  • Cause gut problems, such as irritable bowel, colitis, Crohn’s disease, diarrhea, constipation, bloating, and gas.
  • Create neuroinflammation – think brain fog, cognitive decline, mood disorders, and attention problems.
  • Interfere with the absorption of nutrients.
  • Contribute to colon cancer.

Insufficiency dysbiosis

Insufficiency dysbiosis means that you don’t have enough beneficial species to do the work needed. This will:

  • Compromise the integrity of your mucosal gut lining. Damage to this barrier can be devastating. It leads to leaky gut, autoimmunity, cognitive decline, arthritis, fibromyalgia, colon cancer, and much more.
  • Put you at risk for gut infections (inflammatory dysbiosis).
  • Compromise your immune system – The majority of your immune system’s work is in your GI tract, and beneficial bacteria are essential for proper immune surveillance.

Dysbiosis is widespread in well-nourished countries

You probably know that each time you take antibiotics you wipe out loads of beneficial bacteria. This “kill everything” approach has much collateral damage and definitely causes dysbiosis. There are, however, other things that cause dysbiosis, and one of them is the lack of diverse species.

A diverse microbiota prevents dysbiosis. We’ve lost our diversity.

The United States population has the lowest (meaning the worst) microbial diversity on the planet. We have lost our diversity. What happened to it? Think antibiotics, medications, pesticides, and obsession with sanitization (now more extreme with Covid19). The result of these practices is the indiscriminate murder of all the microbes and the creation of superbugs in the process.

It’s not just antibiotics that wreak havoc with your gut microbiome and cause dysbiosis. It turns out that other medications do this as well! All pain meds, anti-inflammatories, acid blockers, and birth control pills affect your gut microbiome. These drugs interfere with healthy populations, cause dysbiosis, and damage your gut lining.

We don’t know how to get our diversity back.

Taking random over-the-counter probiotics won’t restore a diverse microbiome, because many of the keystone species don’t come in pill form. The keystone species need to be fed – by a widely diverse diet of polyphenols and fiber from colorful plants.

Most Americans are not doing this. We tend to favor foods that won’t feed good microbes (like refined carbs and sugar) and we eat the same small number of foods, over and over, which doesn’t promote diversity. How many different types of vegetables, fruits, nuts, seeds, and beans do you eat? Do you eat 10 servings of these foods a day? These foods feed your beneficial bacteria, and the more diverse your diet, the more diverse your microbiota will be.

Crappy digestion causes dysbiosis

Dysbiosis can result from faulty digestion, in any part of your GI system. Let’s break this down . .


Most of us don’t chew enough. Seriously. For instance, do you multitask while you eat, swallowing large chunks of food before thoroughly mixing it with your saliva? If so, then this food sits and ferments in your gut, which causes problems. Furthermore, it puts more work on your. . .


Your stomach has to work really hard to break down food that isn’t chewed well! It has to kick into gear and make acid and pepsin to break down protein and kill harmful bacteria. Without this, food sits and ferments in your stomach, and bubbles up to create reflux – that sour taste. So you take acid blockers which are meant to be used for two weeks tops. The suppression of acid makes your food ferment longer and changes the pH of your stomach contents. This means you won’t absorb many minerals and vitamins that need an acidic pH, and malnutrition starts. Yes, malnutrition in well-fed countries. The food “bolus” continues down at the wrong pH into your small intestine where it meets your . . .

Pancreatic enzymes:

If your small intestine pH is right, then your pancreas secretes enzymes. However, if food enters your small intestine at the wrong pH (from low stomach acid or acid suppression), as a consequence your pancreas misses the signal. The other organs that miss the signal are your . .  .

Liver and gallbladder:

Your liver and gallbladder are partner organs that make and secrete bile, which breaks down the fat you eat. In addition, bile has another important job: It binds with toxins from your liver and your gut and carries them out with your stool.

However, this process is not always efficient! First of all, your liver needs to function well, and unfortunately, many Americans have a faulty liver function. As a result, bile can be thick and sluggish, and therefore unable to do its job.

Motility (pooping):

How fast or slow are your intestines moving? Slow motility means bacteria can ferment and overgrow. Fast motility means bacteria don’t get a chance to populate and do their good deeds for you.

How to test for dysbiosis

Hands down, the best tests for dysbiosis are the genetic PCR stool tests that clinicians use ( such as Diagnostic Solution’s GI Map). However, you will not find these in your conventional gastroenterology office. You actually need to order these tests yourself or through a functional or integrative practitioner.

These tests show you which types of bacterial species are present, and at what levels. In addition, they detect parasites, candida, and some viruses like H. pylori. You’ll also find out if your:

  • Gut lining is inflamed, and to what degree.
  • Bile system is effectively breaking down fat.
  • Gut immune system is sufficient, overworking, or weak.
  • Pancreas is making sufficient enzymes.

In conclusion, if you want to assess your own gut microbiome, you can order your own GI Map here. Next, book a consult to review the results and get a custom plan for your digestive and microbiome health.

Please add your questions or comments below,

paris healing arts, doctor laura paris, dr. laura paris, dr laura paris

Similar Posts


  1. I have been researching SIBO since I realized my off and on again diarrhea was most likely caused by a really strong antibiotic prescribed by a dentist for a very bad tooth abscess, When I had a really bad bout I finally went to my primary (tooth pulled after 5 days of antibiotics in Feb. went to Doc in late September). My primary wanted to test for c.diff before pursuing SIBO as cause; turned out I had low grade c.diff and she treated it with viocynmin and FODMOP diet. I’m better but still suspect my small intestine is messed up with over growth. Rather than seek out a naturopath who can give the breath test and all that entails do you think the test GI MAP test would answer my questions about my gut and aso does it show c.diff? Do you treat via internet?
    Bobbi (Barbara) Cooper

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.