Dr. Woodson,
This is a complex and fascinating topic and yes, probiotic therapy works to restore the proper balance of normal flora to an intestine that has an imbalance of healthy to unhealthy microbes.
Maybe some bacteria are healthier than others. Maybe some "healthy" bacteria are able to displace the unhealthy bacteria, but horizontal gene transfer is a big wild card, in our opinion, especially for those of us who have a long-range view (decades).
IMO, you and Dr. Marshall are using this statement by the NIH out of context to indicate that it supports the linchpin of your thesis that there are intracellular bacteria that cause many diseases. In my opinion, the NIH statement says nothing of the kind but rather is referring to the normal flora described above. Now there are some exceptions as discussed below but what is important to note is that all these exceptions are viral not bacterial.
I will grant you that is a popular view these days to think the human microbiome is confined to the skin, mouth and especially the gut. However, more recent gene sequencing studies are showing that bacteria occupy almost all the organs. The studies relying on cultivation-based methods reveal but a fraction (some have put it at a single digit percentage) of all the bacteria inside the human body. When the proper tools are used, rich diverse communities of bacteria have been found in the vitreous of the eye, in the amniotic fluid, in the sperm, in the egg, on prosthetic hip joints, etc. Kidney stones (PMID = 15142839) and arterial plaque (PMID = 5142839) have been shown to be composed of dead bacteria. IMO, we have only started to learn the full extent of how bacteria infect the human body. Future environmental sampling studies will reveal much, much more.
Here's a list of reasons, some more compelling than others, we maintain of why chronic diseases are likely caused by pathogens. Naturally, we expect this list to grow:
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:evidence_bacteria
There are viruses that live within the human cell, for instance the herpes and human papilloma families, HIV and others. These viruses are well known pathogens. We have known about them for many years. We have identified their presence within the cell with electron microscopy. We have retrieved their DNA and RNA from within the cells they infect and sequenced their genes and can even make functional copies of whole virons.
The point I am making here is that these virons are very tiny; much smaller than bacteria yet we have been able to find evidence of chronic virally infected cells and can even find tiny snippets of viral DNA called plasmids that have become interlaced with our DNA or is sometimes floating around in the cytoplasm of the cell which is just a tiny piece of a virus. What we have not been able to find are cells infected with a large number of bacteria, which are many times larger that these viruses and have tons more DNA. So, where are they hiding?
Size is not the limiting factor. Koch's Postulates have really pulled a number on us. Read these two articles:
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:microbiota:detecting
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:kochs_postulates
Frankly, and please correct me if I am wrong, I am not aware of any disease or condition where free living bacteria have been found within the human cell as you propose.
Well, the l-form has been found everywhere. That line of research has been around for years and years, but it has fallen out of favor, because people didn't know what to make of it - especially since it violated Koch's postulates. Wirostko took pictures of eyes infected by mycoplasma. Mattman wrote a whole textbook on the L-form.
Have these microbes been recovered from infected cells and cultured?
As alluded to above, we have to focus less on culturing (1-2% effective) and more on environmental sampling and high throughput sequencing.
If so, could you describe to us their properties?
We are talking about a microbiota - almost too many species to count. The one property these pathogens share is that they survive by disrupting the innate immune response or benefit from other pathogens' ability to disrupt the response (co-infections).
How are they cultured, upon what media, do they have special growth requirements, are they facilitative anaerobes for instance since they live within the cell in a low O2 environment but not one that is anaerobic?
According to a recent estimate, 50-70% of bacteria aggregate in bacterial communities known as biofilm.
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:microbiota:biofilm
I am also unaware of the evidence for the ligands the intracellular bacteria are purported to produce in the thesis that bind the VDR. Have any of these ligands been recovered from an infected cell and characterized biochemically and sequenced?
We know at least some of the ligands (e.g. Capnine) and we know the effect certain species/viruses have (e.g. EBV). One exception is Caspase-3, which instead of downregulating Receptor expression seems to cleave the Receptor. Review this article again.
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:vitamind:metabolism
Have you been able to create them In-silico? If so, what are their 3 dimensional structure and where do the bind the VDR?
Capnine has been shown to have a strong affinity and antagonize the VDR ? as has 25-D - using in silico modeling. Marshall has various videos showing this.
Is the binding competitive, strong, or weak? It is reversible or irreversible? Once bound is the VDR permanently impaired or structurally altered by the ligand?
Look at Marshall's in silico representations. Everything is always wiggling, in motion. Even while docked the ligands bounce around. No binding is ever permanent, and yes, the binding is definitely competitive. Every nuclear receptor and a ligand has a Kd, a measure of that ligand's affinity for the receptor. This article should explain it further:
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:innate_immunity
Best,
Paul
This is a complex and fascinating topic and yes, probiotic therapy works to restore the proper balance of normal flora to an intestine that has an imbalance of healthy to unhealthy microbes.
Maybe some bacteria are healthier than others. Maybe some "healthy" bacteria are able to displace the unhealthy bacteria, but horizontal gene transfer is a big wild card, in our opinion, especially for those of us who have a long-range view (decades).
IMO, you and Dr. Marshall are using this statement by the NIH out of context to indicate that it supports the linchpin of your thesis that there are intracellular bacteria that cause many diseases. In my opinion, the NIH statement says nothing of the kind but rather is referring to the normal flora described above. Now there are some exceptions as discussed below but what is important to note is that all these exceptions are viral not bacterial.
I will grant you that is a popular view these days to think the human microbiome is confined to the skin, mouth and especially the gut. However, more recent gene sequencing studies are showing that bacteria occupy almost all the organs. The studies relying on cultivation-based methods reveal but a fraction (some have put it at a single digit percentage) of all the bacteria inside the human body. When the proper tools are used, rich diverse communities of bacteria have been found in the vitreous of the eye, in the amniotic fluid, in the sperm, in the egg, on prosthetic hip joints, etc. Kidney stones (PMID = 15142839) and arterial plaque (PMID = 5142839) have been shown to be composed of dead bacteria. IMO, we have only started to learn the full extent of how bacteria infect the human body. Future environmental sampling studies will reveal much, much more.
Here's a list of reasons, some more compelling than others, we maintain of why chronic diseases are likely caused by pathogens. Naturally, we expect this list to grow:
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:evidence_bacteria
There are viruses that live within the human cell, for instance the herpes and human papilloma families, HIV and others. These viruses are well known pathogens. We have known about them for many years. We have identified their presence within the cell with electron microscopy. We have retrieved their DNA and RNA from within the cells they infect and sequenced their genes and can even make functional copies of whole virons.
The point I am making here is that these virons are very tiny; much smaller than bacteria yet we have been able to find evidence of chronic virally infected cells and can even find tiny snippets of viral DNA called plasmids that have become interlaced with our DNA or is sometimes floating around in the cytoplasm of the cell which is just a tiny piece of a virus. What we have not been able to find are cells infected with a large number of bacteria, which are many times larger that these viruses and have tons more DNA. So, where are they hiding?
Size is not the limiting factor. Koch's Postulates have really pulled a number on us. Read these two articles:
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:microbiota:detecting
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:kochs_postulates
Frankly, and please correct me if I am wrong, I am not aware of any disease or condition where free living bacteria have been found within the human cell as you propose.
Well, the l-form has been found everywhere. That line of research has been around for years and years, but it has fallen out of favor, because people didn't know what to make of it - especially since it violated Koch's postulates. Wirostko took pictures of eyes infected by mycoplasma. Mattman wrote a whole textbook on the L-form.
Have these microbes been recovered from infected cells and cultured?
As alluded to above, we have to focus less on culturing (1-2% effective) and more on environmental sampling and high throughput sequencing.
If so, could you describe to us their properties?
We are talking about a microbiota - almost too many species to count. The one property these pathogens share is that they survive by disrupting the innate immune response or benefit from other pathogens' ability to disrupt the response (co-infections).
How are they cultured, upon what media, do they have special growth requirements, are they facilitative anaerobes for instance since they live within the cell in a low O2 environment but not one that is anaerobic?
According to a recent estimate, 50-70% of bacteria aggregate in bacterial communities known as biofilm.
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:microbiota:biofilm
I am also unaware of the evidence for the ligands the intracellular bacteria are purported to produce in the thesis that bind the VDR. Have any of these ligands been recovered from an infected cell and characterized biochemically and sequenced?
We know at least some of the ligands (e.g. Capnine) and we know the effect certain species/viruses have (e.g. EBV). One exception is Caspase-3, which instead of downregulating Receptor expression seems to cleave the Receptor. Review this article again.
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:vitamind:metabolism
Have you been able to create them In-silico? If so, what are their 3 dimensional structure and where do the bind the VDR?
Capnine has been shown to have a strong affinity and antagonize the VDR ? as has 25-D - using in silico modeling. Marshall has various videos showing this.
Is the binding competitive, strong, or weak? It is reversible or irreversible? Once bound is the VDR permanently impaired or structurally altered by the ligand?
Look at Marshall's in silico representations. Everything is always wiggling, in motion. Even while docked the ligands bounce around. No binding is ever permanent, and yes, the binding is definitely competitive. Every nuclear receptor and a ligand has a Kd, a measure of that ligand's affinity for the receptor. This article should explain it further:
http://mpkb.mp-dev.com/doku.php/home:pathogenesis:innate_immunity
Best,
Paul
