➡ This text discusses the role of bacteria in our bodies, particularly in our gut, and how they adapt to different environments. It explains that bacteria can only survive in specific conditions, and changes in these conditions can affect our health. The text also talks about the concept of stem cells in the microbial world, which can transform into different types of bacteria based on environmental changes. Lastly, it critiques some research methods used to study the potential effects of gut bacteria on our brain and behavior, suggesting that the evidence is not as strong as some claim.

➡ The article discusses the impact of gut bacteria on health and the effectiveness of probiotics. It suggests that while gut bacteria are essential for health, it’s unclear how they interact with our bodies. The article also questions the effectiveness of probiotics, citing a study that found only a minor impact on constipation. It concludes by recommending a clean diet, free from processed foods and toxins, to maintain a healthy gut microbiome.

➡ Modern farming methods use herbicides that can harm our gut bacteria, so it’s healthier to eat organically grown food. Certain drugs, especially antibiotics, can also damage these bacteria. For issues like heartburn, a clean diet and detox can help. Fermented foods like yogurt can be beneficial, as the fermentation process can reduce toxins and create nutrients. Lastly, bacteria found in other parts of our body, like our skin, also play important roles in our health, but more research is needed to fully understand this.

Recovering physician, plandemic whistleblower, natural healing pedagogue and legal code talker. You can call me the Truth Doctor. I’m here to shift your paradigm as I perform a radical forensic dissection. Discerning fact from fiction, science from pseudoscience, medicine from poison, law from legal fiction, and individualism from collectivism. This is your channel for unraveling the truth about health and science. This is the Healthy Living Livestream. Hello everyone and welcome to the Healthy Living Livestream. I am, as usual, your host, Dr. Andrew Kaufman. And today I’m going to try to dispel some common myths about the so called gut microbiome.

Now this is a term that is often thrown around loosely and even some serious podcasters are saying things based on some of the research that are in really the hypothetical stage rather than any conclusive scientific facts. So I want to help go through some of the research. And this is a vast subject, of course, so I can’t cover everything in one live stream. But I want to hit some of the major points to help you understand how this may actually mislead you when it comes to seeking out things that will improve your health. So for example, I’m going to talk a little bit about probiotics and are they actually useful or helpful? But also many health products out there advertise or make claims that they improve the gut biome or gut bacteria.

So do those claims actually stand up to scientific scrutiny or are they simply marketing gimmicks to attract you to this fad? Now it’s I think this whole topic is very interesting because certainly we have known about bacteria for quite a long time, since really the invention of the microscope, and have found them to be ubiquitous in nature. And there are lots of observational studies describing how bacteria work in nature, but it wasn’t really until recent decades that it was shifted in the thinking that bacteria actually in organisms is an integral part of health. It was known of course, that there were microorganisms in our bodies for many years and in animals.

And in fact the first germ free animals used in some of the research we’re going to discuss today were developed in the 1950s, but it really there was no consensus or thinking at that time that these organisms were helpful or even integral to our health and survival like there is now. So let me start out by telling you what exactly I’m talking about when I say the gut microbiome. So that of course refers to one the gut. And many of us think of the gut as primarily the stomach. But really, the gut includes everything in the entire tract.

So we’re talking mouth to anus and everything along the way. So the small and large intestine, the stomach, the esophagus, the pharynx or the throat, as well as the mouth itself. And we can include some additional digestive organs like the pancreas, liver and gallbladder, potentially in this definition. And what’s interesting, if we just consider from the mouth to anus, the tube that goes all the way through us, that we could see that there are different chambers in the gut, and they’re separated by sphincters, which open and close. They’re essentially muscular valves. Right. So we may be familiar, for example, with the lower esophageal sphincter, which is the doorway between the esophagus and the stomach.

And if we are familiar with reflux disease, for example, we know that the fluids from the stomach actually go backwards and get into the esophagus. And of course, that’s a state of abnormal function, of course, although there is a normal time for that to function, for example, with vomiting, where we have a reversal of the flow. But because we have these separations by the sphincter, we can actually have different micro environments in different compartments of our gut tract. So that would also lead to, of course, different variety of microbial organisms that might be there. So here’s a great example between the esophagus and the stomach, which I already mentioned.

There’s a great difference in the ph, where the PH of the stomach being highly acidic, but not in the esophagus and also not in the small intestine. So the stomach, as a contained compartment, can have very different environmental conditions from other parts of the gut. And that’s very important to understand because that’s a major factor in what bacteria may or may not survive in those different compartments. So I want to mention that it doesn’t just include bacteria, but also includes other types of microorganisms, like various fungi, including yeast species and archaea. But these have been much less studied in terms of how they relate to our health.

So I’m not going to focus on them today. I’m going to focus primarily on bacteria. Now, it’s certainly said that there are trillions of bacteria just in our gut alone. But of course, bacteria are present in many, many other part, in fact, probably in all parts of our body, but they tend to be concentrated at higher numbers in the gut. Trillions, in fact, outnumbering human cells substantially by factors reported of up to 10 or perhaps more. Now, most people still think that these microorganisms, they look at them as separate from our body. But I kind of take a different view because we know, for example, that these are present in all organisms and they outnumber the cells that are attributed to the organism.

Like the human cells, right, are outnumbered substantially by the bacterial cells in our body. So could it be that these microorganisms are actually part of our body and not a separate entity? Although it seems that their shape and size and function is different from many of the other cells in our body? However, even if we just look at human cells, we also see a huge variety in the shape and size of cells. So it would not be a large leap of logic to think that perhaps these microorganisms, as we call them, are really just another type of cells of our body.

And this, you know, line in the sand is somewhat arbitrary. And we have some clues to this because of the health status of, you know, so called germ free organisms, as well as understanding that at least part of the toxicity of antibiotics is related to destroying or killing many of these organisms. Of course, if we are killing part of our own body, it would make sense that that would damage our health. So let me jump into some of the research and I’m not going to show the articles or papers this time because I think it’s not really necessary.

And I want to describe it so that any of our audio listeners out there will be able to find this as well. So the first study or paper I’m going to bring up is called the Gut Microbiome in Health and in Disease. And this is a review article from the Current Opinions in gastroenterology, the 2015 January 311 issue. And this is from the Department of. The authors are from the Department of Internal Medicine at the University of Michigan Medical School. And what they did is that they reviewed the literature about the relationship between the gut microbiome and health and disease.

And this brings up the first major point that I’d like to make about this research. And this is actually a quote directly from this paper that I’m going to mention here. And then I’ll discuss this subject and what I’m really talking about. And this is a prevalent point of misconception throughout much of modern science, which is the confusion about cause and effect relationships, which is really what the scientific method is geared toward validating. So I’ll read the quote. However, the relationship between dysbiosis, which means dysregulation of the gut bacteria, and disease pathogenesis, which is the initiating disease.

Pathogenesis is uncertain in the majority of examples at this time, it is often not clear what microbiota changes associated with disease are meaningful. And distinguishing between cause and effect is inherently challenging. Okay, so in other words, when we review the research literature, looking at the gut microbiota or microflora in populations with healthy subjects and with various disease states, we’re essentially only able to make associations. So we see that there might be a difference in the composition of the specific numbers and variety of bacterial species in the guts of those organisms, but we are not able to establish whether those changes are a result of whatever caused the disease state, or if they are part of the cause of the disease state.

And this, you know, is also known as a covariate or a confounding variable. And so we can see associations, but they don’t prove causation. And I think this is the major thing that of course, the. It is well known that the variety and numbers of bacteria change in organisms depending on their state of health or their physiologic state. However, this could simply be that the change in the bacteria is also a result of whatever produced the state of disease or health. And there’s really no conclusive research showing any type of causality. And I’m going to mention a specific example of that in a little while.

But I just want you to know that this is one of the major limitations of this research. Now next, I want to talk about a little bit about bacteria and how they behave in nature and what’s known about them. And for this, I just pulled up a generic introductory biology textbook that I found on Libertext, which is a website that has a number of free textbooks that you can access for your own self education. And here what it states is, not every microbe can survive in all habitats. Each type of microbe has evolved to live within a narrow range of conditions.

Although the vast majority of microbial diversity remains undetermined, it is globally understood that the effects of microorganisms on their environment can be beneficial and is almost always beneficial actually. So what we can see here is that bacteria, particular species or varieties of bacteria can only survive within narrow environmental conditions. And this would suggest that it is the environmental conditions that determine the variety of species and the number of bacteria in our gut, rather than those changes being driven by the bacteria and thus bringing about a state of illness or disease. Okay, and this, you know, this is very well established as the basis of microbiology.

So this kind of leads into a discussion of what the importance or the recognition of the importance of the gut microbiome is, which really is a revival or a call out to terrain theory. Right? And terrain theory is the theory that states that the environmental conditions actually determine health and disease states. And we can see that the bacteria are affected by changes in that environment, which is analogous to this whole issue itself. Now, there is in the terrain body of research a concept that’s been well observed by different scientists that can help explain how these changes come about.

And it is the pleomorphic cycle. And what this is is essentially it is the microbial version of stem cells. Now, we’re all familiar with the reported miracles of stem cell treatment, and perhaps in the future I will analyze the research on that topic. But nevertheless, stem cells are immature. They’re. They’re said to be immature or undifferentiated cells. So they don’t have a specific shape and function like many of the cells that actually do various work in our body. And as they reproduce or divide through mitosis, they can actually differentiate into different cell types. So, for example, in the bone marrow, we have bone marrow or hematopoietic stem cells that can divide and become all the different types of blood cells in the body, like various white blood cells like neutrophils, basophils, eosinophils, also red blood cells, which, there are different path, you know, different steps in the pathway, like reticulocytes, and then they lose the nucleus and become erythrocytes, as well as megakaryocytes and platelets.

So in the microbial world, there also are stem cells, and they have some specific names like protid or somatid, from different scientists like Gunther Enderlein and Gaston Naissance. But they also can differentiate as they divide into different species of bacteria that have different functions and can survive in different environments. And this is most likely more realistically what happens in response to changes in the environment that bring about tissue damage and disease, that they also affect the microorganisms that might differentiate into different species that are adapted now to that new environment as a result of the change.

So let me give you kind of an example about this or related to this, which is the example of C. Diff colitis or pseudomembranous colitis. And this is a very severe type of colitis or a disease of the colon that occurs exclusively in medical patients that are either treated with a variety of antibiotics and or have a lot of tubes going into their body that are connected to the outside world, like indwelling catheters for Example and what happens there is that we observe a specific bacteria, Clostridium difficile, that grows and predominates in this condition. However, C Diff, or, you know, clostridium is often abbreviated as C diff is present in healthy people in the gut.

So why does it suddenly, you know, overgrow or become a more predominant species? And I think that we can easily reason that there’s a change in the environment, either from the antibiotics or from having indwelling catheters in the body and usually in a hospital setting, that changes the environment of the colon. And as a result, different species grow favorably. And this is, you know, a way that we can see that the change in the species are really a result of some other cause, because this condition doesn’t occur without the medical interventions. Okay, very well. So let’s also, I want to mention that a lot of the research that is done and a lot of claims that are made, like, for example, gut bacteria make certain chemicals or that maybe have physiologic activity, like hormonal chemicals, neurotransmitters, a lot of that is based purely on genetic research that they find gene sequences from gut bacteria that supposedly represent a gene that can bring about the synthesis of a certain chemical.

But that is a very different type of evidence from showing that the chemical is actually present, you know, in the gut, made by the bacteria. Okay. So if we look at a particular study on that, we can see some very interesting measure ways that they look at this. So there is one study that. Let me see if I can find the title here. Yeah, it’s called Alternative Pathway for Dopamine Production by Acetogenic Gut bacteria that O demethylate 3 methoxy tyramine, a metabolite of catechol O methyl transferase. Now, that is a very complicated title, but this was published in the Journal of applied microbiology on June 1, 2022.

And the leading author is Barry E. Rich. And this study, what they did is they took commercial lines of bacteria that are said to live in the gut, and they cultured them with artificial media in a petri dish. And in one set of these bacterial cultures, they added a chemical, 3 methoxy tyramine, which is supposedly is a metabolite of dopamine synthesis. So it’s an intermediary in the human synthetic pathway of dopamine. Okay. And then this undergoes a reaction in our body that is catalyzed by the COMT enzyme. Right. Catecholomethyltranslate that does transferase. Sorry, that does a demethoxylation reaction, or demethylation, sorry, reaction.

It removes one carbon from the chain. So they added this intermediate to these bacterial cultures in a laboratory, and then they measured if there was dopamine after they incubated the cell lines. And in the control group, they did not add this metabolite. So that is the independent variable, really, that they’re testing here and also measured dopamine. Now, the control cells did not produce any dopamine that was detected by their liquid chromatography assay, but the cells where they gave this metabolite did. Now, here are some of the problems with this research. One is this does not show that the bacteria actually synthesize dopamine from scratch.

In fact, it shows that they don’t because the control cultures did not yield any dopamine synthesis. Another limitation is that these cultures were incubated in strict anoxic conditions because these were largely anaerobic. These were anaerobic bacteria. But in the gut, there aren’t strict anoxic conditions. There is oxygen in the gut. So the mechanism of growth and the anaerobic physiology in this experiment does not directly apply to a living organism. And also, not all the species yielded dopamine, and the concentration of this metabolite were much higher than they would be actually in our colon. So, in other words, it’s somewhat thrice removed from what actually happens in an organism.

And wouldn’t it really be somewhat simple to take out samples of stool or scrapings from the inside of, you know, bacterial plaques in the gut and simply see if there’s any dopamine there? I don’t know why that study, those kind of studies weren’t done, but this is really the closest thing we have to, you know, providing any serious evidence that there may be some synthesis of neurotransmitters by these gut bacteria. But many of the people who speak on this subject talk about this as if it’s a proven fact that our gut bacteria synthesize neurotransmitters. Somehow they get into the blood and make their way all the way to the brain and affect our behavior.

There is additional research that also supports that, this connection that the gut bacteria can affect behavior or brain functioning. And this is also some very flawed research. And I’m trying to find the right study here. Okay, so this paper I want to describe is called Brain Neurotransmitter Modulation by Gut Microbiota in Anxiety and Depression by Fay Huang in the Frontiers in Cell and Developmental biology in 11 March 2021. And this paper reviews quite a number of studies looking at essentially rodents with anxiety and depression. Now, I’ll tell you right now that how does one know if a mice or rat is anxious or depressed? We don’t really even have reliable diagnostic methods for humans, and we certainly can’t ask a rat if they’re feeling panicky.

So this model alone is problematic. And then what they did in this body of research essentially is that they used animals either that were bred completely germ free, and by the way, germ free animals that are used in research, they have tons of health problems, they are not normal animals, or they took other laboratory animals that were not germ free, but they gave them high doses of broad spectrum antibiotics to wipe out all their bacteria, and then they generally measured neurotransmitters in different parts of the brain. So in other words, they had these organisms that don’t resemble nature, like the germ free organisms, or they had organisms that may resemble nature, but they were given toxic drugs right before the experiment.

And they showed, not in all studies and not with respect to all the neurotransmitters looked at like they looked at serotonin, they looked at dopamine and a couple of others. But what they found is that when they had these abnormal animals or with a toxic insult, that yes, in some cases when they looked in the brain, the levels of certain neurotransmitters was different. Now, there are so many different confounding variables that could affect that in these experiments. There’s really no way to reason that it’s specifically the effect of changes in the microorganisms in the gut that are responsible.

So I think we can really take all that research with a big grain of salt. All right, now I’m going to go into two more issues to wrap up this lecture and then I’m going to just make some general recommendations about how you can improve your health. With respect to this issue. But this is perhaps one of the biggest things, is how do we tell if our gut microbiome is healthy or not? Now, I want to say that there are no studies that definitively answer this question whatsoever. There is only opinions of people who are experts in this research and most of the people who are, you know, declared experts in this research would say that it is the variety of different species of bacteria in our gut.

That is what we can say correlates with health. However, there are no specific parameters like how much variation, how many species, how do we determine it? Are, are the assays even Valid. And then we have other data that shows, for example, when people who are taking probiotics take higher doses, that there can be detrimental effects, for example, on cognitive abilities. Right, like producing brain fog. So is it that there has to be just the right amount of variation or of diversity? You know, this is a very vague determination, so there’s really no way to know it based on looking at some individual specific gut bacteria, if that is a sign of health or not health.

But fortunately for us, we can generally just ask someone some questions and know their health status. So we don’t need this to determine it. But if we’re looking at, you know, this as a way to measure the effectiveness of various health interventions, we cannot make any claims with any certainty. So any products out there that you see that claim that it improves their gut health, one would have to ask the question, how do you know that? Because it’s unknown what constitutes with certainty a healthy gut biome. So this is marketing language, not scientific information. Okay, so the last topic I want to cover is probiotics.

And these are very popular as a health remedy. It’s a huge market, so does it actually do anything good? So I wanted to find some randomized controlled trials, because that is the gold standard for research to see if probiotics can affect health outcomes. And the majority of research is done about constipation. So that’s what we’re going to look at today. And I found a Meta analysis from 2020 in clinical nutrition done by Shang Chang Zhang, and it’s called Meta Analysis of Randomized Controlled Trials of the Effects of Probiotics on Functional Constipation in Adults. Very snazzy title.

Now, in this study, they actually identified over 2,300 studies on this topic. That is quite a large number. So there’s a huge, huge effort and a huge amount of funding in this area of research. Now, this is the other interesting thing, that out of over 2,300 studies, only 15 were actually done well, and only 15 were included in this meta analysis. And they looked really at two main parameters, which was the gut transit time, so how long it takes for food to go through your gut from mouth to anus. And then they looked at the number of bowel movements, and they did that per week.

Now, what they found when they pooled all of the data from all of these studies is that the group who took probiotics had a measurable but very inconsequential effect on constipation. So here’s the big thing, that it reduced the gut Transit time by somewhere between six to 20 hours, based on the the confidence interval, and it created just under one additional bowel movement per week. Now, if you have someone that is chronically constipated and they can have one extra bowel movement per week, do you think that would provide adequate relief for them? I highly, highly doubt it.

So in other words, all this effort, over 2,000 studies, 15 solid randomized controlled trials, pooled into a meta analysis, shows essentially a clinically meaningless outcome of probiotics. I think that really summarizes what’s out there. And there are many reasons for that. One is because our bodies, as I mentioned, through pleomorphosis, can differentiate into any species that would survive in the current environment of our body. And then also we are continually exposed to bacteria from the environment that get into our body, especially into our gut. So food we eat is not sterile. We can have physical contact with other organisms, both humans and animals.

And these things have been shown to affect our gut bacteria. Like if we have a lot of relationship with animals. For example, if you are born via a C section or through the birth canal, because the birth canal exposes you to bacteria species, but just breathing in the air will expose you to bacteria. So in other words, there are plenty of sources of bacteria for our bodies that there is no real justification for purposely ingesting them. And then the other thing is that the actual probiotic preparations themselves, many of the organisms, in fact probably most, are not even alive in that pill when you take it.

And then, of course, if the environment of your gut is not correct for those particular species, they won’t be able to survive there even if they are alive to begin with. So I think I’m, you know, very skeptical of any kind of probiotics. The only time I really consider this is after someone has a course of antibiotics, but I don’t think that’s generally a good idea to do. And also your body will recover its gut bacteria after antibiotics if you simply treat it nicely. So how can you interpret all this information and decide if or what steps you might take in your own health journey to affect this? And I think here are some of the major takeaways.

So one is, you know, I didn’t really talk about this a lot, but it’s very, very clear that these microorganisms play an integral role and most likely are actually part of our body. If we look at animals that are created, that are germ free, they have all kinds of health problems and shortened lifespans, problems with reproduction, with development of their Organ systems and so on and so on. So we know that having these organisms in our body is necessary for optimal health and survival. But what we don’t know is exactly how they are important and exactly how they interact with the other systems of the body.

And unfortunately, much of the research that has been done is of quite poor quality and poor methods that we haven’t learned too many specific things. And you know, there are many reasons for that, but this is really true in most of the research of the modern era. So if we want to have a healthy gut microbiome, we simply have to have a healthy body. And that means that the environment or the terrain of our body has to be healthy, which means, of course, that it has the right nutritional elements that our body needs to build and maintain itself and for metabolism.

And there needs to be an absence from toxic elements that would damage our tissues and bring about pathologic changes in our body that would result in, of course, changes in our body’s bacteria. So if we can have a clean diet, I think that’s probably the biggest factor because everything we swallow goes right to the gut. So what I’m talking about here is avoiding processed foods and seed oils, of course, but also with respect to plant foods and animal foods, there are many chemicals used to treat the plants and animals, or it’s in the feed that they give to the animals and then accumulates in the animals bodies that we eat, which are quite toxic to the bacteria.

Glyphosate or Roundup is one of the biggest ones. And you know, there’s a reason that the bacteria are also often called microflora. It is because they have a lot of physiology in common with plants. And algae would be a great, you know, example of sort of a single celled organism that is a plant, but also like a bacteria in many ways. So because of the overlap of different biochemical pathways between plants and bacteria, herbicides that are used in modern agriculture are going to be toxic to the bacteria in our gut. So if we, you know, grow our own food using regenerative farming practices, or if we exclusively focus on organic food, which may not 100% eliminate all these herbicides and pesticides, but they’ll be far fewer or far less.

Then if we don’t eat organic food, that is also going to have a big role. And then of course, exposure to pharmaceutical drugs, especially antibiotics, but there are other drugs besides antibiotics that are also toxic to bacteria that we can avoid. All right, I hope this information has been helpful, useful and cleared up some common misconceptions on the gut microbiome. And I have time for maybe just two or three questions. All right, Bonnie Sammons asks Dr. Kaufman, what is your recommendation for GERD, specifically for silent GERD? Well, I don’t know what silent GERD is, unfortunately, but GERD is gastroesophageal reflux disease or heartburn.

And I think you have to look at the specific factors, but usually this is often diet related. So you have to clean up the diet. And the drugs that are used to treat this, which are, you know, over the counter now, can also very much complicate this issue and be very, very difficult to get off of because of what, rebound reflux issues. So, you know, the biggest thing is to clean up the diet and do a detox protocol. And many people can alleviate this issue completely through those types of processes. All right, Alex, SD how about yogurt, kefir, etc.

Well, you know, these are fermented dairy products. And I think the major benefit of fermentation on foods is that it can take foods that are somewhat toxic or have elements in them that may be somewhat toxic. And I’m not really referring to fermented dairy so much here, but other things like fermented soybeans, because we know that there are a lot of health problems with soy. We have, you know, phytoestrogens like genistein and even, you know, other other issues with respect to lectins. But if we ferment soybeans and make a product like natto, natto can, you know, be very healthy because those toxins have been turned into something else and some nutrients have sometimes been created, like in natto, there’s a form of vitamin K2, which is produced during the fermentation process that has nutritive value for people who eat that material.

So I think similar things may be true with fermented dairy products. And also, of course, they will be lower in carbs because the organisms that ferment the dairy will eat the sugar in there. So that could be a benefit of just having a lower carb version, you know, of milk to ingest. So I have no problem eating these foods. And we can also look at some traditional cultures that ate fermented dairy, like I believe, the Maasai, who have very excellent health outcomes. I just don’t think that it’s necessary to get the organisms in those forms of dairy for your health.

All right, one final question, if we have one. All right. Rachman asks, how about the skin biome? Yes. Well, much of what I taught today about the gut biome can be extended to all the other biomes in the body, right? Because we even in the eye, right in the eyelashes, on the skin and in various other parts of the body you can find bacteria species. And I think overall my understanding or my hypothesis is that these are actually part of our body and have integral functions and that we don’t really know the full functions yet. A few things here and there have been somewhat worked out but I think we really need to investigate this a lot more to understand this issue better.

But it certainly is important for our health and welfare. All right everyone, I really enjoyed this topic. I feel, you know, it’s such a vast area of research and there’s so much misinformation that we need to be sharp and clear up these issues in order to take the right steps for our own health. I look forward to seeing you all again next week for another Healthy Living livestream.
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