>>Sorry for being a thread hog but thinking this information may be helpful. :>
The gut environment has been a long study for me, and I am constantly updating my protocols and knowledge base for what that is worth. It is interesting to see new studies coming out more and more as opposed to a scant of knowledge years ago.
The research articles today are clarifying that diversity of the gut is much more than what was thought years ago, and they know that the diversity is like a cocktail meaning that everyone has a mix of microbes in the gut that is doing things that is not quite fully understood.
Pathogen Invasion
I have a fair working knowledge of the pathogens that can harbor the gut, at least the classifications such as rogue bacteria, yeast/fungal, viral and parasites. I hosted a parasite forum that was mainly targeted to protozoa infections which technically are parasitic but act more like bacterial strains. Protozoa are the orphans of the gut environment and usually overlooked. Traditional stool testing will include the 2 most common protozoa in North America which are giardia and cryptosporidium. But these tests seldom look for other species. And then, there are the rogue species that are either unknown or unrecognized. Protozoa are well known to be disruptive of the gut environment except for commensals.
Commensals are known to inhabit the gut but do not create a hostile immune response. Then there are the subtypes which are variations (DNA variations) that are not studied enough. Those are another topic altogether.
The
gram negatives are problematic and for good reason. They as also known as ESKAPE pathogens. Gram negatives all have one thing in common which is the bilayer membrane as opposed to gram positive which are comprised as single membrane organisms.
The double membrane makes them more difficult to kill off so a different standard of antibiotics are used to control these. I think there is another facet to those, in that they can possess resistance strategies such as genetic structures, and efflux pumps are another Gram positives are easier to get rid of with some simple pharma antibiotics and there are plenty of natural antibiotics that can attack them. I would suspect that there are many "probiotics" that could neutralize them. Though gram negatives are in a different class.
There is ongoing research in PubMed about gram negatives and strategies that can attack them. Of particular interest is the use of certain botanicals that have been proven in countless studies that can disrupt them. On a short list is cinnamon and preferably as Ceylon Cinnamon. Regular cinnamon you buy at the store is Cassia, Ceylon has fewer toxic properties. Typically, these substances are paired with antibiotics that provide the killing power. But not antibiotic can work which is another story.
Biofilms are another possibility as
@bizzoc mentions. Biofilms are really protective membranes that pathogenic organisms can hide in. As a side note, there are known bacteria that can proliferate a stronger biofilm environment such as pseudomonas (gram negative). If an organism is locked in biofilms, it makes it difficult for the antibiotic (or immunity) to penetrate. There are a number of methods that can disrupt biofilms, and I have tried nearly all of them.
Of some interest
Quorum Sensing is an interesting topic in that QS is sort of an internet communication system that bad bacteria use to protect the community. There are a number of natural things that can disrupt the QS.
Cell adhesion is another trick some bacteria can use. CA just means that certain bacteria can produce an adhesive that makes them stick to the human cells (I suppose walls) that make them somewhat resistant. In general terms, plants that are considered astringent can reduce their stickiness. Witch hazel is used externally for skin care, it is known as an astringent. Green tea is something that could be safely used internally that has an ability to disrupt the stickiness. And there are others.
Butyrate production is among the latest articles released. Butyrate is manufactured by certain bacteria that seems to be absent in CFS/ME people. Butyrate is healing for the gut wall which reduces inflammatory events. To be more specific, cytokine production is lessened with butyrate which is important systematically. There are some wicked cytokines such as Nf-Kb and others that are quite damaging to the body. For instance, these damage mitochondria which leads to fatigue and other issues.
The butyrate producers cannot thrive in a hostile environment. This means if you have a bad bacteria in the gut that is causing the immune system to react, it makes it difficult for the butyrate producers to proliferate. Without enough butyrate, the barrier function becomes damaged which leads to more inflammation. I covered that in my butyrate post. I also listed some protocols I found helpful.
Binders have always helped me and those can come in a few varieties. These binders sweep out the toxins created by the immune system. Those toxins not only recirculate in the body which puts stress on a number of systems but also disrupt the microbiome.
The gut environment can be complex but new information is helping to unravel this dynamic system.
Again, sorry for being a thread hog!