Spoonie Radio Ep 16: Ken Lassesen

Dr. Craig:  You're listening to Spoonie radio. I'm your host, Dr Courtney Craig. My guest today is Ken Lassesen. Ken is a mathematician and software engineer who first became ill with chronic fatigue syndrome in 1972, then in 2001, and again in 2012. Each recovery was connected to a treatment that would have altered his gut microbiome. He runs the website CFSremission.com a site where he has chronicled these three separate bouts of CFS, and where he has developed analytic tools to better understand the complexity of our gut microbes. Welcome to the show Ken.

Ken:  Hi, thanks. It's a pleasure to be here as a show. A FYI, one time I was a high school science teacher, so, I have a degree with a general science background.

Dr. Craig:  You wear many hats. Yes. And based on your work on your website, it seems like you're well versed in data science as well.

Ken:  Yes.

How Do You Recover from Chronic Fatigue Syndrome Thrice?!

Dr. Craig:  So from 1972 to 2012, that's a long span of time…40 years span of time. So to start off, can you just briefly give us a, a picture of that health trajectory? What were the initial triggers? How long did the bouts last?

Ken:  Okay. All three events I think even the fourth one, I'm just ending now, a flare now, it could be going back into it, but all that say four incidents are caused by ongoing stress. Stress of a particular type of nature for long ongoing, not having ability to control. So each of the time it seems to have triggered a microbiome dysfunction. The last time was extremely interesting because unlike the earlier times I had a reference microbiome before it happened and then did the microbiome every, four weeks during the whole process.

And the thing that jumped out looking at it was that, the number of, bacterial species and strains I had at the beginning of the bout jumped by about 50%. So, I had just massive number of awful bacteria showing up, which then faded back to my normal number roughly about four to six weeks later, which is somewhat supporting the concept which I have, which is that regardless of the root cause of chronic fatigue syndrome or related things, it causes massive instability in gut bacteria.

The classic study I've seen showing the general pattern comes out of Norway where there had a Giardia infection and it had a significant percentage of people coming down with a diagnosis of chronic fatigue. After treating for the Giardia, and being Giardia negative [Inaudible 03:18], the root cause was treated, but you had a high percentage of people suddenly with chronic fatigue syndrome and they were tracked and thanks to the Norwegian medical systems, you had full population tracking happening and basically you had a declining curve over time of the number of people who stayed in chronic fatigue syndrome and doing so roughly every six months, about 20% of people went into remission, 80% stayed in for a number of six month period.

And then after five or six years, the percentage of people going through remission, basically almost flat line as in the gut disturbance were able to correct themselves with that. Using that as a model, then, we can see how as a whole how some things can happen. Stress can cause it, vaccination can cause it, irregular flu can cause it any type of viral or bacterial infection potentially could be a triggering event, but the catch is once the trigger has happened and perhaps it resolved, doesn't get rid of the problem.

The problem is the microbiome was altered and has not restored yourself to the original condition, so that is the model I’ve been using and for myself. The first time the diagnosis was antibiotic resistant walking pneumonia. It was because I had a chronic cough and which the doctor referred to it as a stress cough, which is very consistent with stress being the inducer. So it was retaking different antibiotics, strong advice to avoid stress, which meant I changed I switched from doing triple honors, to doing a major.

Instead of going on to do a master's or PhD, I went into teacher education. I taught high school for years, but about five years after onset, it had subsided enough that I returned to academics part time. And that onset, the dominant characteristic was loss of cognitive facilities. The physical chronic fatigue didn't happen; it was strictly a cognitive loss dominating. Second incident I was working at Microsoft--talk about stress zone--basically it was a bad boss.

The boss was asked politely to leave Microsoft about a year later. So, my interpretation wasn't off as him being a bad stress-inducing boss. In this case the dominant feature was loss of physical stamina, day after payback from fatigue. Went fine through all the tests or everything else had absolutely no problems. Everything went well, and then the next day I was absolutely exhausted.

My MD had seen me for a check-up two weeks before the onset and then two weeks after. And, and she, remarked to me, she was at first; she had dealt with chronic fatigue patients before. But she said I was the very first patient she had actually seen before and after, who has literally seen a dramatic change happening in the space of four weeks from one degree of fitness and energy to a totally different state. So it was very informative for her. She was good in that she confessed that she had no clue of what to do, but also said, look, you smart, go off and research and I went up and research and in 1999 there were two studies which had a high reported probability of causing remission. Which means me being a statistician. I said, okay; well let's try doing both of them.

The first one was the antibiotic protocol coming out of South Africa by Cecile Jadine who was a Rickettsia. Her model came from the Pasteur Institute for Tropical Medicine, which her father was working at and she remembered this type of problem when a friend of hers came down with the same symptoms. I said, wait a minute, I know that pattern and I remember the treatment that was used. It was successful in causing her friend’s chronic fatigue syndrome to go into remission. The first problem was just persuading the MD to even start giving antibiotics. Since nowadays giving antibiotics tend to incur a lot of justification.

Read the Jadine Protocol Here >>

Dr. Craig:  Right.

Ken:  My success in persuading her to be willing to start was saying, look, you prescribe long term antibiotics for acne, and you will have no problem giving a prescription of doxycycline for a year for a kid with acne. Compare that to the impact of chronic fatigue syndrome on a person and on their family and you really have a problem not prescribing doxycycline?

Dr. Craig:  And I take pause in that because I was that teenager prescribed doxycycline for years for skin conditions and I think that was a big trigger in initiating my own diagnosis of CFS. So yeah.

Ken: Jadin’s protocol was, no more than one or two weeks on it and then you rotate. Regarding rotation, everything else I looked at a few statistical models available, and there is lot more now. It absolutely made sense to rotate because other studies have shown it to be the most effective way of altering bacteria, infection, bacteria and number of types of bacteria is doing the rotation. So that was the procedure to start.

Case Reports of Remission with Antibiotics >>

The second one came out of Hemix labs in Phoenix, Arizona. They were a lab that specialized in treatment of infertility, so it sets an interesting spots for it to come from. And what has happened was he, D. Berg, had noticed to a lot of the doctors he dealt with, and most of these were people who were having problems conceiving, that the blood test showed that they had coagulation issues. So they went on low dose of Heparin, which resulted in conceiving.

But he kept noticing that the doctors mentioned that by the way, my patient’s chronic fatigue syndrome or fibromyalgia disappeared while on the treatment with little dose of Heparin. So he proceeded at his own expense to do a study and found that 80% of people with chronic fatigue syndrome have some sort of coagulation defect as part of the formula.

The result was I went on low dosage Heparin done first actually by needle but then sublingual alone with ordinary heparin rather than the expensive, low molecular weight one that helped. Recovery time in that case was just over a year instead of the five years.

Read about coagulation problems in Chronic Fatigue Syndrome here >>

The third time I was over at another software company by the name of Amazon…. I had not heard that Amazon has a reputation for stress, again it was a combination of bad boss, bad group dynamics. Once it hit…I delayed the hit impact-wise because I was doing all of these standard kind of treatments.      

But I also noticed there was a new symptom that appeared, which I had not experienced before, which was gastrointestinal issues. I contacted first, a MD who specializes in Lyme. But he was pretty booked up, but he had an associate, a naturopath who was working with him. I ended up going to her. She wanted to protect herself about the prescription of antibiotics. So we did a Lyme test. I had suspicious positive results on the Lyme test and I won't go over the accuracy of Lyme test results which is a whole…

Dr. Craig:  That's a whole another interview.

Ken:  Oh yes. However that provided her the clinical rationale and then I've sat down and we work using Jadin's protocol, to select which antibiotics to use. However, at the same time, my wife unfortunately happened to have come down with atypical Crohn’s and we happened to have a supply of MutaFlor in the house.

So in my rereading all the literature on chronic fatigue syndrome, which I think I've done four or five times in my life, a lot of reading there and it's getting worse every year. I came across a 1998, study from Australia where it found that there were distinctive microbiome shifts, one of which was the disappearance of E. coli, bifididobacteria and lactobacillus was a signature, and then overgrowth of others.

Faecal Microbial Growth Inhibition in Chronic Fatigue/Pain Patients >>

I sat down and looked at Jadin's protocol, the antibiotics, and found that, wait a minute, guess what? That set of antibiotics generally had no effect on the ones which were undergrowth, but did affect just about all of those that were overgrowth. The light just went on that saying, wait a minute. Her treatment is correct, but her model may be incorrect, it may be a clear microbiome dysfunction, and then started with the MutaFlor. Other things to address the microbiome dysfunction, assuming that was the best explanation that took me about 6 months for recovery.

Can I have a Microbiome Problem without Gut Symptoms?

Dr. Craig:  Well, that's quite a story and for our listeners, if you go to the podcast link over on my website, you will see the show notes. I will link out to all of those studies that Ken just referenced. That's really interesting, so my question though is, and I think a lot of our listeners will have this question, I'm a CFS patient, but I don't have any digestive issues. I don't have any gastrointestinal symptoms. Do you believe that a lot of these classic CFS symptoms can manifest themselves in the absence of an overt gut problem?

Ken:  Absolutely. Okay, my reasoning is very simple. I had two incidents with no gut problems with the third one it did, which caused me to revisit the research because I was ignoring anything dealing with gastrointestinal because I didn’t have any. Simple direct logic. But as we understand the gut bacteria, one of the main thing it does, it produces metabolites. All the metabolites floating around alter greatly. One of the recent research papers dealing with Alzheimer's, I sort of chuckled at because before my Amazon incident, my treating physician was not believing in chronic fatigue syndrome. I finally persuaded her to send me to get a SPECT scan.

The SPECT scan report came back. She looked like a deer in the headlights and totally at her wit's end. The SPECT scans all just read my brain scan as being early Alzheimer's, which simply means somebody's presenting with the appearance of Alzheimer's before age 65. Recent studies with Alzheimer's has made a major implication for gut bacteria in terms of the rate of progression of Alzheimer's.

For myself, I interpreted those clinical results as saying that my metabolites being reduced by the ultra-gut bacteria basically triggered something that looked like Alzheimer's, but once I corrected it, it auto corrected itself inside the brain and I do not have early Alzheimer's or even Alzheimer's now that I'm old past the magic age of 65 . The metabolites impact, it can be horrendous it because it can affect things like brain fall, it can affect things like high blood pressure, it can affect a ton of things, none of which were present itself as a gastrointestinal issue.

Dr. Craig:  That's right. And I think also the average person is going to be stuck on this kind of germ theory model of one bug, one problem. And that's not at all what you're describing here. In your own journey and understanding this it's not just too much of one bug or not enough of one bug. It's not also just one bug that you're talking about complex shifts one way or the other. So is that more correct?

Ken:  Very much so and not only complex shift. Frequently the shifts could almost end up with the same results of seeing the same metabolites being reduced, but a totally different combination on bacteria. Because, each bacteria breaks down the strain, each strain has different characteristics.

A real simply example, which may be of interest to people who have histamine issue is that every strain of lactobacillus reuteri which is human source, it is a histamine producer. However, if you get all L reuteri from a chicken or from a pig, it doesn't reduce his to histamine. So, the same species will produce different sets of metabolites and only when you go all the way down to the very bottom strain level do we actually determine that is this a histamine producer or is this not. They're the same species but different strains. And that's where the complexity comes in its having to walk several layers deeper than what traditionally has been done with dealing with bacterial infectional alterations.

You have a whole stack of things that could be involved, many of which interact with each other. So it just becomes an interesting case, if you are trying to approach it through the traditional way. And for myself, I fortunately had been trained in data science and artificial intelligence. So I went and applied my skill and said, wait a minute, this is a solvable problem. Not an easy problem, but it is a solvable problem and went off in that direction.

The Microbiome Beyond the Gut

Dr. Craig:  Getting back to this, having symptoms without overt gut problems. A lot of patients also maybe have issues with other areas where microbes might be populated, like the nasal passageways, the oral pharynx. Do you find that these are also contributory?

Ken:  Not only contributory, there was a study in the last two years of the oral microbiome that is the mouth bacteria of chronic fatigue syndrome patient and it was distinctly different than the control group. That does all surprise me because before the study came out, I actually written that what is a most likely reserve for repopulating dysfunctional gut and that is the mouth and the nasal cavities. One of the things by my own experiment I have discovered, is that there are a few probiotics which comes in hard tab that forms: Miyarisan and Shin Biofermin, both of which are from Japan, which you can put sublingually. Both of which cleared up sinus problems for me and I have on my website, people say the same thing has occurred for them. Basically, the result was duplicated by Bioflorin, which is designed explicitly to be used as a gargling mouthwash type of probiotic.

Visit Ken’s Blog for more on these specific products

And the Symbioflor 1 and the Biofermin are the same species of bacteria. It would appear that one of the starting points may well be trying to reduce the risk of repopulation from the mouth of the gut bacteria, which may be contributing to the lower digestive problems. At the moment, there are 3 things which appear to be good choices. Bioferrin which comes out of Japan, using it sublingually as in putting that hard tablet underneath your tongue.

The over one is Miyarisan and the mechanism is slightly different, but it's also significant. Miyarisan produces butyrate. Butyrate encourages the growth of a human antibacterial compound called LL33 which increases greatly with people with gingivitis and the logical aspect is by increasing the butyrate in the mouth, you increase the production of this particular human antibacterial, and your mouth health will improve and probably also significantly alter oral bacteria. We have 2 probiotics, two of which are actually quite cheap. Relatively speaking from Japan well-proven for years of usage starting from the 1930s, and then we have Symbioflor 1, which is available from Germany and available worldwide from Paul’s EuroMart, which is on the web and he will ship worldwide.

Dr. Craig:  I want to talk more with you about probiotics, but before that I want to talk about testing. There are a few director to consumer microbiome testing companies out there in the U.S.: uBiome and Thryve are two of the main ones. There are some others. What is your opinion of these? What are the differences?

Ken:  Okay. Number one difference is that the mechanism they're using for getting the raw data is very similar and there's no differentiation between them. Where differentiation comes is how they take all these bits of data and deduce, keyword here is deduce, which bacteria are involved. So the result is you will get different results from different companies because they use different algorithms to deduce, it doesn't mean they’re more or less accurate. There's also one company in Europe which I think is doing direct to consumer now, which is in Spain, which is called Zenagene.

There's other companies besides those, personally, my key criteria is you want to have a company who is open about the results. That is that the data is easily downloadable in a format which you can either upload to my site or other sites to do further analysis rather than being a closed shop and they look at it and they tell you what the conclusions are with absolutely no access to the raw data. So the result could be different from different companies on the same samples. I'm not particularly surprised.

The thing is you want to do time analysis, you want to do it every month or every two months or every three months and see how things are changing because things will change over time. If you track symptoms and the microbiome, you will strictly find there are first strong associations. At present, I have something like 800 samples uploaded by people of which 400 of them the people have also contributed the symptoms they had when they took the samples.

The interesting thing is that of something like 250 symptoms, 80 symptoms were found to have strong association with particular microbiome patterns, by significant, I mean statistically significant as in well less than one chance in 10,000 of being by accident. The result is symptoms and bacteria go together, which is different and the traditional way, which is you get the disease diagnosis and then you look for patterns of people with that disease diagnosis rather than looking at the symptoms and looking for patterns of people with those symptoms.

And that is what I'm doing and I’m finding surprisingly strong number of resolved. My very first post when I saw them was Eureka! I can't believe it. It just goes on and on. As in wait a minute. Bacteria shifts are directly and strongly tied to how the symptom presents itself.

Dr. Craig:  So patients that have done these direct to consumer microbiome tests on their own, they can go to your website, cfsremission.com and upload the raw data?

Ken:  There is a link to the site, the upload site which is different. The CFSremission site as we mentioned, is a WordPress site. The site for uploading is raw data called microbiomeprescription.azurewebsites.net.

Dr. Craig:  Again, you can check the website show notes for direct link to that. So once the data has been uploaded to the site, what can patients then see based on their result?

Ken:  Okay. They can see a fair amount of things. First of all it gives some suggestions on what you should avoid taking or should be taking, including down to which probiotics. Now these are suggestions and I have a big warning on every page. These should be reviewed always with a knowledgeable medical professional. And the reason is simple, that there can be other factors involved which should impact what the tests are one way or another. Okay, so let's go through what is on the site.

The site gives you a set of immediate suggestions based on your shift. So what we do is we simply go in and say, okay, what from medical literature do we know, what we do if this bacteria is particularly high. Okay, toss that in and then we have to go and do some back and forth to see what the other side effects are.

Dr. Craig:  I want to talk more with you about probiotics, but before that I want to talk about testing. There are a few director to consumer microbiome testing companies out there in the U.S.: uBiome and Thryve are two of the main ones. There are some others. What is your opinion of these? What are the differences?

Ken:  Okay. Number one difference is that the mechanism they're using for getting the raw data is very similar and there's no differentiation between them. Where differentiation comes is how they take all these bits of data and deduce, keyword here is deduce, which bacteria are involved. So the result is you will get different results from different companies because they use different algorithms to deduce, it doesn't mean they’re more or less accurate. There's also one company in Europe which I think is doing direct to consumer now, which is in Spain, which is called Zenagene.

There's other companies besides those, personally, my key criteria is you want to have a company who is open about the results. That is that the data is easily downloadable in a format which you can either upload to my site or other sites to do further analysis rather than being a closed shop and they look at it and they tell you what the conclusions are with absolutely no access to the raw data. So the result could be different from different companies on the same samples. I'm not particularly surprised.

The thing is you want to do time analysis, you want to do it every month or every two months or every three months and see how things are changing because things will change over time. If you track symptoms and the microbiome, you will strictly find there are first strong associations. At present, I have something like 800 samples uploaded by people of which 400 of them the people have also contributed the symptoms they had when they took the samples.

The interesting thing is that of something like 250 symptoms, 80 symptoms were found to have strong association with particular microbiome patterns, by significant, I mean statistically significant as in well less than one chance in 10,000 of being by accident. The result is symptoms and bacteria go together, which is different and the traditional way, which is you get the disease diagnosis and then you look for patterns of people with that disease diagnosis rather than looking at the symptoms and looking for patterns of people with those symptoms.

And that is what I'm doing and I’m finding surprisingly strong number of resolved. My very first post when I saw them was Eureka! I can't believe it. It just goes on and on. As in wait a minute. Bacteria shifts are directly and strongly tied to how the symptom presents itself.

Dr. Craig:  So patients that have done these direct to consumer microbiome tests on their own, they can go to your website, cfsremission.com and upload the raw data?

Ken:  There is a link to the site, the upload site which is different. The CFSremission site as we mentioned, is a WordPress site. The site for uploading is raw data called microbiomeprescription.azurewebsites.net.

Dr. Craig:  Again, you can check the website show notes for direct link to that. So once the data has been uploaded to the site, what can patients then see based on their result?

Ken:  Okay. They can see a fair amount of things. First of all it gives some suggestions on what you should avoid taking or should be taking, including down to which probiotics. Now these are suggestions and I have a big warning on every page. These should be reviewed always with a knowledgeable medical professional. And the reason is simple, that there can be other factors involved which should impact what the tests are one way or another. Okay, so let's go through what is on the site.

The site gives you a set of immediate suggestions based on your shift. So what we do is we simply go in and say, okay, what from medical literature do we know, what we do if this bacteria is particularly high. Okay, toss that in and then we have to go and do some back and forth to see what the other side effects are.

But in short, there's a whole bunch of calculations done and the best choices are suggested to reduce what your high in or bring up what you are low in and then they are applied and you get a list of food, diets, and everything. Everything is linked back to the original PubMed study. That's one of the things that I’m being very adamant about making sure that everything is absolutely public as possible so that the MD can come in, look at the results, click and say, okay, oh here's the study that this information come from.

I'm not sure if this information is correct. I can go and read that study. A couple of other things that are available is there is a nice chart showing where you are compared to other people for each bacteria, all the way down to strain levels. I reported, so that you can see where your shifts are visually and how far extreme are for some things.

There's also a nice little chart which shows you where you are compared to other people in a particular bacteria. Why am I high in this one? and it will go and show you all the related bacteria which are known to influence this particular bacteria in a positive or negative way. So you will see they are four bacteria, which are very high. You look at one of them and you see the other four, which contribute are also high, so you now get a pattern of what is causing it, so that you can see that is not just one bacteria involved, it is a group of bacteria reinforcing each other.

There are some experimental pages because I don't have adequate numbers to feel confident with any more than experimental saying which metabolites are being produced. There’s also a whole series of pages which allows you to look at a timeline of how your microbiome has changed over time and you can do that for any particular microbiome level down to species or bacteria. A lot of it is to provide information for people to do their own analysis and understanding. One thing which I've been very careful about and almost at times dogmatic about, is that my site is educational only.

I will not give people suggestions to what they should do. That's crossing the line into practicing medicine and that is something I want to absolutely avoid doing. I will give them the information. I will give complete explanation as to why and how I come to the suggestions or should I say how the AI-engine comes up with the suggestion and link to the studies, so I've wrote everything that is there ideally for a knowledgeable medical profession to go and look and says, okay, it does make sense. Let's go with the suggestions or let’s go with that suggestions, but let’s take these things out because you have another condition, which I'm pretty sure will be impacted negatively by doing this particular suggestion.

Dr. Craig:  This is also an excellent tool. I think for many patients that are very sensitive to certain things. Some patients are sensitive to supplements that they don't really understand why. Probiotics, again, a lot of patients report adverse effects with probiotics and they give up on probiotics entirely. But using your tool, if you have adequate data to input, you can actually pinpoint because of your microbiome, this might be why you're sensitive to this brand of probiotic.

Ken:  Great. Yeah on the site, there is also a listing of which ones are histamine producers and which one are known lactic acid producers, both of which are subsets of people who are very sensitive. So the purpose of it is to try and figure out which probiotic you want to take. You look through that list and say, okay, this one isn't a histamine producer, this one isn’t a D-lactate producer and I have problems with both of those. I will avoid it or I will take it. The main purpose is to make life much simpler for people to figure out which ones they should or shouldn't have been taking. Unfortunately, most probiotics are tossed together by marketers as to which species go in. Some of them basically try putting in everything as a universal cure or to advertise that we have more strains and species that anyone else so buy us which is not the best way of resolving what is the best probiotic.

Dr. Craig:  And that brings up another idea, when you talk about treating this or doing something to shift the microbiome, do you take a kind of umbrella approach that takes these global truisms we know about diversity or do we want to instead be as precise as possible and hone in on specific species and specific metabolites?

Ken:  I would suggest you will probably get your best results by zoning in because the complexity is such that yes, you make it lucky, but throughout every study I've seen, it is 60% get positive results, 40% gets no or negative results. That sounds like it's almost like a multi correlate simulation of treatment and the problem is you are basically almost doing what in operation research is called a random walk through treatment protocols, trying to get back to health, because you try one thing, it doesn't work, you stagger off in another direction, does work. Okay and now you stag up in another direction, it doesn't work and you go back and forth, so it ends up being random. What I've tried doing is building an AI-engine that works on fuzzy logic, because the information is fuzzy, but with optimizing the probability of success. In other words, trying to stack the deck so that everything you try has a much higher probability of being successful than of having no or negative effect.

Dr. Craig:  Now with this tool you mentioned you have 800 uploads of people's samples. What is your goal moving forward? Do you intend to improve this tool even further and get more data of course… or even share this with any of the research institutions?

There’s a Strong Association Between Symptoms & Specific Gut Bacteria

Ken:  Let start with last part. When you upload, there is an acknowledgment this information will anonymously be available for citizen scientists is to use, all of the microbiomes, which have been uploaded, are available free of charge for download by anybody who wants it, including with the symptoms associated. There's no personal identification information there, but the microbiomes and the symptoms are there, so that any researchers can grab the data.

You don't have to be a data scientist or researcher it is there openly. I am very aware of data security issues and I've been very careful to make sure that upload has as much information without revealing personal identity as possible. So all the data is available for anyone right now and will continue to be available. I don't have enough time to work on a full time and believe me; the amount of rich research it can be done from it is very large.

So that's the first question, I keep getting more uploads. People upload to get suggestions or to get better understanding and with their upload, it adds more data to the database which allows better resolution. The bigger the sample, the better the resolution, the better you can detect weak patterns. So it's ongoing. What I do ask people for, but they don't require it, is to add your symptoms.

Because symptoms and bacteria seem to have the best association, some diagnosed conditions I've looked at and basically I cannot get any patterns from them. However, for a symptom I can get a strong pattern showing up, which means that symptoms as a way you really want to go, you want to be treating your symptoms. You don't want to be treating your quantity fatigue syndrome as an abstract collection of things.

Because remember, look into the definition of what chronic fatigue syndrome is through the years. At one time it was anywhere up to four of the following 16 symptoms. Okay, so how are you going to figure out what is the best treatment? Yes. Your test population has an official diagnosis chronic fatigue syndrome but with 4 out of 16 symptoms being the criteria for inclusion, you get a real mixed bag of symptoms being involved. If on another hand is flipped over and restrict it to people with specific symptoms, you will get far stronger results. At least everything I've seen suggests that you will get far stronger results when you focus strictly on symptoms rather than on the official ICD diagnosis.

Dr. Craig:  And this AI model that you have established, do you know of anything similar in other diseases?

Ken:  In terms of dealing with the microbiome? Yes. as in there have been recent papers coming out of the university environment, where they have been very successful predicting certain diseases from the microbiome analysis, not in treating it, just as in giving them batch of samples, they have 80 or 85% success in separating those with specific condition and those who are controls.

Dr. Craig:  Okay. We need better accuracy then, it seems, but I feel like this whole approach is the way that things will be moving forward and we'll see this more in other disease stats. So it has the potential to not just affect the CFS community but many, because we were learning the microbiome is involved in so many disease processes.

Ken:  The second largest group of people who I've been corresponding with are people with autism or kids with autism, which is sort of interesting because that the impact of microbiome is very well accepted in the community. Alzheimer's, the researchers there, but the general Alzheimer's community is still dealing with the older discredited science explanation as to brain plaque as being the cause.

Dr. Craig:  Well, I am certainly going to go over and upload my data. I have some uBiome data that I have from a while ago to contribute and I encourage all of our listeners if you have this data available you to contribute it for your own amusement and analysis, but also for this larger project which Ken has created here. If you could just fill us in again on where listeners can go to upload the site and again, your blog to read about your different projects.

Ken:  The main site dealing with chronic fatigue largely is CFSremission.com. It has currently about 1300 posts. If you search over it, you'll find that I deal with specific things in depth and almost all my posts link all back to the original PubMed or other research studies. For example, this morning I just did a quick update on brain fog and the update was somebody numerated the possible sources for brain fog because brain fog is a big term and it’s actually at least six different causes that could be contributing to brain fog.

I just thought it’d be good to enumerate them so people would know what they may want to have their physician tests for to see if they can identify the root cause. The site dealing explicitly with Microbiome is microbiomeprescription.azurewebsite.net. It basically tends to be very friendly.

There's a bunch of pages which you can use without doing an upload, for example, there is a page which lists which bacteria are known to be associated with certain medical conditions and I think I have about a 100 different medical conditions which have been there, everything from type I diabetes, Grave’s disease, Crohn’s disease. The thing is my model or just website, deals not with chronic fatigue exclusively. It deals strictly with the microbiome, so I looked at, okay, here is the shifts, how do you correct it and the correction is based on this study showing that this particular probiotic, this particular supplement, this particular diet reduces or increases to these particular bacteria.

A lot of things will have no impact on most bacteria, but it does impact a few. As an interesting aside, one of the problems, and this is probably me going off on a soapbox, one of the common problems I see that non-reproducibility of results for medical study.

Some may find certain result one time and nobody ever attempts to reproduce the fact that it was successfully or unsuccessfully reproduce, which is a major problem, it is contrary to the basics of science. But with the current academic thing is you don't get fame or a permanent tenured job from reproducing other people's results. You only get them from producing new results. That's immediately means that the quality of a lot of studies showing positive results become suspect and often when I read reviews, you'll find that 40% were positive, 60% were negative and nobody knows what the answer is and the difference was that there were other factors that weren't being controlled. As a statistician I understand the problem all too well. The second issue is that often studies are looking to produce results showing a statistically significant positive impact on some conditions and with those words I cringe because the statistically significant positive impact may mean that across the disease group that some measure may have shown a 2% improvement overall on the average and in reality you had 10% of the people major improvement, 90% no improvement or even loss, but because you’re using averages those two which have the major improvement shoved the average and statistically significance and will allow you to have a nice publishable paper.

Okay. Now almost all the studies which I'm using for what shifts bacteria, they were looking at things like that and they're mentioned the bacteria shifts incidentally and because you're mentioning it incidentally, we weren't looking to produce those results. They just observed those results, which means that the quality or the reliability of the data, I personally deem to be far more likely to be correct than studies treating a particular disease directly simply because the information they’re disclosing is not part of their reward mechanism.

This site is going to be continually evolving, I continue to spend probably 20-30 hours programming a week on it, which is fine after the last two years doing it, a fair number of hours there, it's going on. I have made it clear that it's not HIPPA compliant. I do have a couple of physicians who are regularly using it, but all of them happen not to be in the U.S. so they don't have to worry about HIPPA compliance.

The main thing is its educational and the goal is to give information which is being filtered, focused with 100% display of the source of the data, so that there’s no magical waving of hands and you know that every piece of data is coming from a reasonably repeatable study, which has been accepted for PubMed or elsewhere.

Fecal Transplants as an Option for Chronic Fatigue Syndrome?

Dr. Craig:  What is your opinion about fecal transplants as a therapeutic option given all that you've learned through this project?

Ken:  I'll say it's very good, but we are still in early days in the art of doing them. There are multiple issues involved. One girl who I have correspondence with in Australia has had something, like 10 of them. Every single time it resulted in remission for a month or so and then relapse. The problem is a couple of things, first one is the microbiome and your DNA are tied together. They are strongly associated, which means you have the classic problem of organ rejection, when you do a fecal transplant, basically your DNA may basically say uh uh, this is to foreign a microbiome for me to accept and proceeds to get rid of it.

That's one of the most interesting aspects and we have not seen very many studies dealing with DNA to microbiome and it would be an interestingly complex thing. I would say if you have opportunity to do so and yet chronic fatigue syndrome and everything else has failed, yes, I would do it more as a last resort because it could get very frustrating going into full remission for six weeks and then slipping back in.

Dr. Craig:  Yeah, absolutely.

Ken: My preference is if you have a very cooperating MD, my preference would be to go to a microbiome alteration pattern and that is first get your microbiome done. See suggestions; sit down with the MD and glean the best suggestions from there. Try them faithfully, keyword faithfully for four to six weeks and then get another sample done and see if your microbiome had shifted. If it has shifted in a positive manner, then you have positive evidence of improvement in an objective method.

One of the problems with chronic fatigue syndrome is if you are pretty bad, you take something, you improve, four weeks later you have forgotten how bad you were and the result is you stop taking it because it doesn't seem to be helping. It helped, but you forgot about how much it has helped. With the microbiome, you have an objective measure coming in every time and you can see whether or not, you are making progress.

Now the path isn't a straight path. When you shift things one way, something else may shift up. Symptoms may change, but then you simply repeat it again. The first couple of levels I would suggest doing it without any prescription drugs. If you have no major success after four to six tries, then take a look at if any particular antibiotics are strongly recommended. What I found amusing is that from some of my samples from when I had been in relapse, the antibiotics or probiotics suggested were basically the ones which are commonly suggested in the literature for chronic fatigue syndrome, which means, okay, well the study is a consistency there, if the predicted what you should take to improve things and what the literature reports as improving things lining up, then we may have consistency between the two approaches, because both of them are independently done, but with the same results: improvement.

Dr. Craig:  Thanks for listening to another episode of Spoonie radio. Be sure to SUBSCRIBE over on iTunes and for all show notes, go to drcourtneycraig.com/podcast until next time.




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