Hi Holly's Daughter

Here are some general notes of the education I had in the Gut Environment. Keep in mind that this is educational and not a directive to treatment or diagnosis. 

As a side note, I spent an inordinate amount of time in this pursuit based on my own situation. I went to countless doctors and specialists to "resolve" my issues with little to no help. I personally have done these therapies countless times. I also hosted a forum on protozoa parasites and dives into antibiotic resistance. 

I did many stool samples (microbiology) to detect what bug I had contracted and did many therapies including antibiotics, probiotics and the like. Here is what I know.

The Gastrointestinal Tract:

The GI system is rather a complex organism that has many features that Western Medicine is just acknowledging at this point. The GI tract houses 70% of the immune response and these immune responses can react to both pathogens that enter the gut but also systemic infections (example a viral infection). In fact, recent studies have shown that Covid 19 changes the diversity of the gut bacteria, they will find that bifidobacteria is lower in the gut after a Covid infection. Many believe that bifidobacteria is largely linked to immune function. 

Localized Infection:

The gut is very vulnerable to pathogen invasion likely by foods and/or water supplies. Dr. Galland believes that is why so much of the immune system lies in the gut. There are a variety of pathogens that can inhabit the gut which included bad bacteria, protozoa parasites (giardia, cryptosporidium etc.), nematode parasites, fungal and viral infections. 

Stool Testing:

Stool testing is considered a necessity but there can be faults with the testing. I saw on the forum multiple people testing with many companies, some with mixed results. Many people bypassed the tests and began treatment blindly.

A hospital test stool would test for known enteric (gut) pathogens such as variations of e. coli, klebsiella (bacterial) and a few known parasites that are endemic in North America. That would include giardia and cryptosporidium, and they would check for certain roundworm species as well.

In my case, these were negative, and I moved to other labs. One was able to detect a rarer protozoa species.  

Biofilms:

Biofilms are known more in the medical research, and they tend to form in mucous membranes, the gut is a perfect place for biofilm development. Biofilms is a mesh that forms from certain bacteria that is sort of a Saran wrap. That wrap provides a place for bad bacteria to live. The wrap offers a shelter for them so they can evade the immune response. 

When bacteria (or other bugs) are locked in the biofilm, the immune system can detect them but cannot kill them. This creates a constant inflammatory state. 

Kicking the bad guys out: (Cycling)

Biofilms only have room for so many bugs and when the house gets full, it kicks some of them out. This is called Biofilm Dispersion. You may have noticed that cycles of ok feelings then sick feelings. This is likely caused by biofilm dispersion.

Western Medicine 

typically, does not have many answers regarding this but typically treat symptoms rather than root causes. As to date, I don't think they have any way to measure biofilm activity and how to eradicate biofilms, though there are many strategies that have been developed outside of Western Medicine that are logical and safe. I would be happy to list those out for you if  you like. 

Many bowel diseases can be attributed to unwelcome pathogens in the gut and likely biofilm environments. Western Medicine calls it Crohn's or IBS, IBD etc. I would likely label it as a dirupted microbiome. 

Cycling bombs:

Cycling bombs is the explanation for the fallout from biofilm dispersion. The immune system is a powerful system that when excited, produces some very toxic byproducts. There are a million published papers (peer-reviewed) on PubMed using the search query "inflammation". They are quite aware of the damage inflammation does to the body (cells, tissues, organ systems) and they know that many degenerative diseases have the origin in inflammatory responses. This inflammation arises from immune activation that creates ROS and RNS molecules. 

The body has a set of chemical reactions that can neutralize and diminish the damage caused by these inflammatory storms that are vastly created by biofilm dispersion. These systems are dependent on nutrients to perform their task. Antioxidants can also be donated via supplementation. 

Cycling bombs also drain energy, sleep and create pain. This again is directly impacted by strong inflammatory reactions that attack the mitochondria of our cells, meaning energy dips.

NEI Supersystem:

The NEI (Neurological, Endocrine, Immune) system is an interlinked system meaning one system change alter the other system. Immunity is the strongest force in the body and can move the other two. So, cycling storms will likely impact the neurological system (brain fog, depression, mood disorders etc.) it can also alter the endocrine responses.

I will stop here but willing to drive a little deeper into the subject if you like.