Dysbiosis Basics and Tests

Dysbiosis and SIBO

Every doctor I saw told me I had IBS or my symptoms were all in my head.

  1. IBS isn't a real thing. 
  2. It wasn't my head's brain.

It was my second brain that was messed up.


Gut Biome Basics

The gut is an integrated system composed by immune, endocrine, and neuronal components. R


Second Brain

When someone says go with you "gut feeling", they may not know what they are actually referring to.

The microbiota in our gut, sometimes referred to as the “second genome” or the “second brain,” influence our mood. R 

The gut and the brain are closely connected in certain feeling states and intuitive decision making. R 

The microbiome is intertwined with the immune system, which influences mood and behavior. R

The microbes in our gut influence the brain via multiple mechanisms. R

Gut bacteria produce neurotransmitters such as serotonin, dopamine, and GABA. R

Gut bacteria affect how people metabolize compounds, affecting the blood and brain. R

Gut bacteria generate neuroactive chemicals, such as butyrate, which is linked to reduction of anxiety and depression. R

Some microbes activate the vagus nerve. R

Read all about the Brain-Gut Axis here.

Irritable Bowel Syndrom Isn't Real

If someone has told you they have IBS, they were mistaken. IBS has many causes.

One of those causes has been shown to be a decreased numbers of microbiota and intestinal inflammation is generally believed to be associated with a reduced bacterial diversity. R R R

IBS can usually be caused by a post-infection or yet undiscovered active infection. R


That's me years ago. SIBO can make you look and feel  pregnant .

That's me years ago. SIBO can make you look and feel pregnant.


SIBO, or small intestinal bacterial overgrowth, is as an increase in the number and/or alteration in the type of bacteria in the upper gastrointestinal tract.  R

Patients with SIBO vary in presentation, some are only mildly symptomatic while others may suffer from chronic diarrhea, weight loss, and malabsorption. R

Antibiotics can be bad. They can contribute to intestinal overgrowth by killing your good bacteria.

Taking antibiotics increases the risk of developing IBS. R

Some antibiotics like rifaxamin can be beneficial. This is probably because targets certain bacteria and pathogens.

In cirrhosis, several factors contribute to intestinal bacterial overgrowth.

These include impaired motility of the small intestine, reduced bile flow, and altered secretion of immunoglobulin A and antimicrobial molecules. R

This reduction is accompanied by reduced antimicrobial activity against Enterobacteriaceae. R


The Gastrointestinal  Wall

The Gastrointestinal Wall


Dysbiosis is when there is an imbalance in your microbiota. This can be detrimental if this happens in your gut.

Disorders associated with dysbiosis include:

  • inflammatory bowel disease R
  • irritable bowel syndrome (IBS) R
  • coeliac disease R
  • allergies R
  • asthma R
  • metabolic syndrome R
  • cardiovascular disease R
  • obesity R

Dysbiosis can cause changes in diet, obesity, immunologic, and neurological diseases that impact brain function and behavior. R

It can also cause hypertension. R

Bile (exacerbated by a western diet) can increase tumors, in those with dysbiosis. R

The antibiotic rifampin has shown to help some symptoms of dysbiosis-induced IBS, although it could worsen it. R

Other researchers have focused on a possible unrecognized protozoal infection such as blastocystosis as a cause of IBS, as certain protozoal infections occur more frequently in IBS patients. R

Compromised intestinal host defense might therefore contribute to qualitative and quantitative changes in the enteric microbiome associated with end-stage liver disease. R

Intestinal Barrier Dysfunction

Leaky Gut (AKA Gut Permeability)

Gut permeability is related to body weight, fatty liver disease, and insulin resistance in obese individuals undergoing weight reduction. R

Click here to to learn how to fix a leaky gut and reverse any gut permeability problems.  


These tests will help you find out if you have SIBO and/or dysbiosis.

Eliminate Pathogens



There are two "traditional" ways to get rid of dysbiotic pathogens in SIBO. Rifaximin, or herbal therapy. Rifaxmin is just as effective as herbal therapy. R I did both. 

Here was my protocol:

During my recovery, I was luckily living in Los Angeles where I had a connection to a doctor that was close friends with Dr. Mark Pimentel. Dr. Pimentel, author of A New IBS Solution, recommends using Rifaxamin. R 

Most doctors will implement a low FODMAP diet. This can be problematic since when bacteria don't have food, they can turn dormant and hide in biofilm. R 

The addition of partially hydrolyzed guar gum makes rifaximin treatment more effective. R

Clay has been found to be beneficial, because of its ability to bind to pathogens. R


I had done the Comprehensive Stool Analysis and the results showed high levels of Citrobacter Freundii, a gram negative bacteria. I took an intense protocol to kill it: 

A follow up Comprehensive Stool Analysis showed that this protocol was effective.

Restore Beneficial Bacteria


Restoring your gut biome can be tricky.  

Your gut biome feeds on anything you put in your mouth.

Pathogens will grown on bad foods, while good bacteria will thrive on healthy foods.

There are two things we want to do to restore the beneficial bacteria.

  1. Supplement with the PROPER beneficial bacteria
  2. Support that bacteria with fermented foods or prebiotics

After you have killed your pathogens, it is paramount to get retested (to verify you have actually killed them and that see which bacteria you need to restore).

Doctor's data or SmartGut/uBiome is best for this.

Also, I HIGHLY RECOMMEND getting a Spectracell Micronutrient test, since malabsorption is highly likely after dysbiosis. R


There are many types of probiotic strains on the market you can supplement. I tried a LOT, and I noticed Lactobacillus strains made me sick and constipated. 

My pathogen was citrobacter freundii, which produces a lot of histamine. R 

A few lactobacillus strains also produce histamine. R R (L. Reuteri produces histamine, but may be beneficial.)

I essentially was giving myself histamine intolerance by supplementing probiotics.

A few bifidobacterium strains degrade histamine, so I found trying only bifidobacterium strains (that don't produce d-lactate) helped (Lactobacillus plantarum will degrade histamine too). R

For you it may be different. 


Your gut bacteria feed on prebiotics. Make sure to kill off all the pathogens first, so you don't feed them.

After killing the citrobacter, I went on a raw vegan diet for 6 months, as not to poison my gut and feed the wrong bacteria.

Fiber is good. Bacteria ferment fiber into butyrate in the large intestine, and then the butyrate helps feed the cells that line the gut. Everyone is different, but obviously eat the healthy things like: 

  • Leafy green vegetables
  • Brightly colored vegetables (carotenoids, anthocyanins, lycopenoids)
  • Fermented foods (if you don't have a histamine or d-lactate problem)
  • Nothing fried, no artificial sweeteners, and no processed foods

 More Prebiotics: (consume them in their raw for) R

Here is a whole list of resistant starches and prebiotics

More Research

  • Dysbiosis in the gut flora has been linked with the development of cirrhosis and non-alcoholic fatty liver disease. R
  • Some studies reported up to 80% of patients with irritable bowel syndrome have SIBO (using the hydrogen breath test). Subsequent studies demonstrated statistically significant reduction in IBS symptoms following therapy for SIBO. R R R
  • There may be increased prevalence of intestinal hyperpermeability with SIBO, which may contribute to fibromyalgia. R
  • Biomarkers for Chronic Fatigue Syndrome have been found in a lack of diversity in the gut (amongst other biomarkers). R
  • Gut dysbiosis impairs recovery after spinal cord injury R