So probably I wasn’t really clear when trying to explain what I don’t understand, so please bear with me as I try again.

I wasn’t talking about sequencing bacterial genomes, but rather genetic testing of humans for diseases.

Suppose I undergo genetic testing, and it comes back positive for a mutation associated with some chronic disease, whose symptoms I am actually displaying.

Are you suggesting that I probably didn’t inherit that gene from my parents, but rather sustained the mutation myself in my somatic cells, caused by the same bacteria that were also causing the illness?

If so, then this mutation will be present in only some of my cells, but not all (probably mostly in the infected, inflamed tissues).

So if genetic testing is performed on blood or hair or other cells which are located remotely from the site of the infection, would it still be reasonable to assume that those remote mutations would show up in the hair/blood samples?

Thank you for your patience.

Best,

Andy

Take a look at this paper I wrote that was just published in Autoimmunity Reviews:

http://autoimmunityresearch.org/transcripts/AR-Proal-Metagenome.pdf

In the paper I explain how humans are superorganisms – 90% of our cells are microbial while only 10% are human. This means that we have millions, and possibly trillions of bacterial genomes in our body when the human genome only consists of around 30,000 genes.

What this means is that there is an endless number of interactions between our genomes and the genomes of the bacteria we harbor. Since bacteria can live inside our own cells they can interfere with translation, transcription, and even DNA repair. All these events lead to what are currently perceived as inherited genetic mutations.

Aside from the sex cells, every human is born with a new set of DNA. So bacterial mutations can only be passed from generation to generation in the sex cells. But what is passed from generation to generation are the bacteria that cause genetic mutations. Different species of bacteria mutate certain genes in different patterns which is why we see low levels of identical mutations in people who harbor the same bacterial species.

DNA sequencing of bacterial genomes is a complicated topic to attempt to explain in a few paragraphs. Take a look at this article that I wrote after visiting the Venter Institute, I took a course in how to sequence bacterial genomes and the article describes what I gleaned from the process:

http://bacteriality.com/2008/08/17/jcvi/

Best,

Amy

As a layman, I don’t really understand one thing that keeps coming up. You seem to say that “genetic mutations which result from active infection” are often mistaken for inherited genetic mutations, and are mistakenly thought to be causing diseases.

So are you saying that gene sequencing of sick people just picks up mutated genes that are only present in some of their somatic cells, and are therefore not identical with the sets of genomes inherited from their parents?

I might be using the wrong terminology here, so let me rephrase my question. Are you suggesting that a patient who had her genes sequenced, and was found to have a gene (set of alleles) associated with her chronic illness

1. may not have inherited that gene (those alleles) from either parent;

2. the gene indicative of the disease may actually be due to a mutation caused by pathogens, and is therefore present only in some of her cells, but not in all of them;

3. so she may have a different (=”healthy”) set of alleles in most of her somatic cells and gametes;

4. and the sequencing just randomly picked up a cell that happened to have the mutation in its nucleus?

I don’t know how sequencing works, how many cells it’s usually performed on, and if any effort is being made to eliminate random mutations that may be only present in some cells but not in others.

It would be great if you could provide some explanation that the “wide public” could understand to some extent… I wonder if there are any articles, explanations or papers available that you think might be accessible to those who haven’t extensively studied biology.

It definitely seems like your claim, i.e. that genetic research is often on the wrong track, is surely a controversial one, and I can only imagine how happy those involved in trying to find gene therapies are about it…

Thank you for your time again. You’re a great educator and advocate.

Best wishes,

Andy

I’m sorry to hear about your problems with Candida, fibromyalgia, and other symptoms. However, the MP uses antibiotics in a way that will not make you Candida worse. In fact, the opposite is true. Since the MP works to activate the immune response, Candida actually gets better or resolves when patients are on the treatment. The medication Benicar that MP patients take four times a day is the driving factor allowing the immune system to keep the pathogenic yeast under control.

As hopefully you’ve read in other pieces on this site, Benicar activates the Vitamin D Receptor – a fundamental receptor of the body that controls the activity of the innate immune system (the branch of the immune system that rapidly targets pathogens such as Candida).

So by strengthening the immune response against Candida, the yeast forms have a much more difficult time surviving and are generally killed as people continue taking Benicar (of course they must be taking the standard MP dose of 4 pills a day). A die-off reaction can often be expected when Candida die, as the immune system mounts a temporary inflammatory response to their death.

Because the MP antibiotics are taken in a pulsed, low dose fashion they do not promote Candida growth in the way that a standard regular antibiotic might. Most patients on the MP report that their Candida is improving or gone. I had terrible Candida when I started the MP and haven’t felt symptoms for two years.

If you have Candida it is almost certain that you harbor disease causing bacteria, as these bacteria are what slow your immune system to the point where Candida are able to proliferate. Fibromyalgia is also a result of infection with these same bacteria.

So your best option to target both your Candida, fibromyalgia (and related symptoms) is to do the MP.

You can ask for a list of MP doctors in your area by posting at the following website:

http://www.curemyth1.org (Th1 refers to diseases caused by bacteria. The patient advocates on the site will also answer other questions you might have about the MP free of charge.

Hope this helps!

Amy

It seems as if all you can do is continue searching for a new doctor. CFS is not a mitochondrial disease. It is caused by chronic intraphagocytic metagenomic bacteria. So mitochondrial therapy will do nothing to make you better……which is probably why it hasn’t worked for you.

Not surprisingly the bacteria that cause CFS spread easily among family members which explains why so many people in your family suffer from the disease.

The Marshall Protocol is the only treatment to date that will effectively kill the bacteria making you sick so you need to find a doctor who is open-minded enough to prescribe you the necessary MP medications – a doctor who is willing to let go of their own pet theory about what causes CFS and embrace the research put forth by Autoimmunity Foundation.

I’m not sure how health care works in the UK, but if you can spare any money towards seeing a private doctor who will put you on the MP I feel it’s worth it.

I wish I could offer you more help but all I can encourage you to do is to keep searching for a doctor who is willing to listen to you and to let you do the MP.

Best,

Amy

I’m so sorry I have not responded to you sooner. I’ve been away at a medical conference. Benicar goes a long way in lowering the inflammation that is generated by immunopathology or the bacterial die-off response. However, your daughter with Linea Morphea is still going to experience immunopathology in order to recover. So, her symptoms of the disease are going to flare as she recovers, during the period of time when her bacteria in her face are being killed. What this means is that as your daughter’s Linaer Morphea responds to the antibiotics her symptoms will likely get temporarily worse.

Of course, the key word in that last sentence is temporarily. All symptoms on the MP get “worse” (in the sense that they flare due to die-off) before they get better. So I would expect your daughter’s face to possibly become worse at certain times during the first stages of the the MP. However, once she has killed off many of the bacteria that are causing the condition, her symptoms should stabilize, and then eventually resolve. So I can say with confidence that her Linear Morphea will definitely not deteriorate once she is on the MP (since once on the MP any signs of getting “worse are only a sign of bacterial death), but for a while the disease symptoms will be exacerbated in the way all symptoms are when the MP is initiated.

I am, however, very glad that you are looking into the MP in such detail. You may want to start the treatment on yourself or your children first. It sounds like your husband could benefit from the MP as well. Then, when you get more familiar with the immunopathological response, you can move on to treat your daughter with Linear Morphea.

Don’t forget that if you have any more questions on this issue you should post them on http://www.curemy1.org where they can also be addressed by our patient advocates.

Best,

Amy

Thanks for writing. I’m so sorry to hear that you and all your children are suffering from such a variety of Th1 diseases. Yet, it’s exciting that the MP has the potential to allow all of you to regain a state of health.

I’m very, very, glad to hear that you and your oldest daughter are planning to start the MP. I hope you find a doctor soon…

As for your questions:

1. I am quite confident that Linear Morphea is a Th1 illness and would respond to the MP. We are finding that essentially any ailment/symptom/disease that has no “known cause” is Th1 related. But the fact that the condition is responding to steroids is the give-away. Any condition that improves with the use of steroids is Th1. The steroids slow the activity of the innate immune system. Less bacteria are killed and the patient temporarily feels better (as in your daughter’s case). Plus, your youngest daughter has certainly picked up bacteria from you and your siblings. So the MP is needed for her in any case. When she starts the MP, you will soon be able to tell if her symptoms related to Linear Morphea respond to the antibiotics (if that area starts to herx) and you will have final confirmation if they do.

2) I don’t know anything about Samento/Cumanda. The fact that they elicit herx at least suggests that they arn’t totallyimmunosuppressive (any person with a Th1 illness wants to avoid immunosuppressants at all costs). So perhaps the herbs have killed off some of your daughter’s bacteria. But I guarantee they have not come close to targeting all the bacterial species making her ill. Also, herbs are risky because there is simply no data showing how they might affect the immune system or VDR. But in the time before you daughter does the MP, they don’t sound like the worst option.

3) I would say that you mother probably did not consume as many fortified products (with vitamin D) as you and your kids. Also, she probably wasn’t treated with as many immunosuppressive drugs. But even if the above is not the case, you probably picked up a lot of your mother’s bacteria right at birth. Even though the two of you got sick around the same age later in life, you bacterial load was probably much higher at that point.

When it comes to your kids, they were able to acquire not just your bacteria, but bacteria from your husband in the womb and after birth. Does your husband show any signs of Th1? If so, the extra bacteria from his side of the family could also have contributed to their illnesses.

4) I don’t know how the herbs work. But I wouldn’t worry too much about cardiac herx on the MP. Benicar goes a long, long way, in reducing the inflammation generated by herxing in the heart. So as you mention, extra Benicar can be used if necessary. Also, there is a specific path of treatment for people with cardiac symptoms called “modified phase II” People who take that route of treatment use the MP antibiotics in slightly a different order so that they more gradually wear away at bacteria in the heart. Thirdly, it should comfort you to know that up to this point, no patient, even those with cardiovascular disease on the MP, has suffered from a major cardiac event because of herx.

Hope this information helps! I assume you are also getting advice from the patient advocates at http://www.curemyth1.org? If not, that website is another excellent resource.

Best,

Amy