abx and microbiome health

As I travel deeper down the rabbit hole into microbiome health and FMT, I'm starting to realize how important the microbiome is. I'm starting to think it is THE primary cause for a lot of autoimmune and neurological diseases. Your digestive system is responsible for 90% of your interaction with the outside world, and there's the old adage that 80% of your immune system resides in your gut. Not only is the gut important for immune and cytokine signalling, but it is reponsible for creating a lot of vitamins, b vitamins especially, that your body wouldnt get otherwise.

We seem to spend a lot of time testing for infections in our blood, while completely ignoring the 3.5 POUNDS of bacteria in our digestive tract

I've spent some time in the FMT group on FB and met plenty of people with inflammatory neuropathy, neurological autoimmune diseases, and CFS type diseases, all of whom have digestive issues or can link their neurological symptoms directly to their gastrointestinal symptoms or diet.

What concerns me, however, is the high levels of antibiotic and antimicrobial use in this group. The old functional medicine adage seems to be that in order to get your gut right, you should blast it with antimicrobials to kill whatever is in there, and then hit it with probioitcs to build it back.

The more I'm reading from sharp sources, the more I realize this is completely naive and dangerous. Gut health is about *natural* biodiversity. You just cant achieve that from a probiotic capsule with maybe 7-8 strains at most. These do not capture the diversity required for a healthy microbiome, one that we do not fully understand. The risk is that this kind of treatment risks reducing natural biodiversity, which can be extremely extremely hard to fix.

If you're lookin for a solution in a pill, I think that a better approach than "killing things" in the gut with antimicrobials, which risks doing permanent damage, is to try to crowd out the bad guys w/ probiotics. But more importantly, one should try to alter the microbiome through proper diet. And the use of FMT.

I have been looking into that last option significantly. FMT is a useful solution for c-diff infection, and it has proven to be quite successful at curing UC and Crohns. These are obvious places where research has focused since theyre gut related, but there are a few studies showing that FMT can be used for Alzheimers and MS management. I think that neurological and neuropsychiatric diseases are strongly related to gut health, and this is an underappreciated fact.

As an anecdote, I have been having success managing my nerve pain and anxiety using ketogenic diet. The flares had basically went to zero. about 6-7 days ago I went off the diet and had a few bites of indian food. I was also experimenting with methyfolate. One, or both, of these changes had a profound effect on my gut. My stools suddenly loosened and I had gas. Immediately my anxiety went through the roof, and I had an impending sense of doom. My neuropathy upticked big time as well. I think that anyone w/ unexplained neurological or neuropsychiatric issues, especially those treating with abx who are having no results or worsening of conditions, should take a look at their stomach

In addition, I'm realizing that gut health, heavy metals, infections and methylation are very inter-related. Gut health is extremely correlated with methylation. The microbes in your stomach are tasked with creating a lot of the b vitamins that you need to methylate. Poor methylation leads to fatigue, nerve damage, psychiatric issues, etc. But at the same time, the causality doesnt run in one direction. When I supplemented with methylfolate my stomach got worse initially as levels started to shift, telling me that methylation levels also affect the gut microbiota. Those w/ poor methylation and MTHFR probably have problems because their chemistry has trouble supporting a healthy microbiome.

I'm finding, and what I think that the nascent research into the topic fails to realize, is that donor quality is everthing. There are plenty of papers out there about the efficacy of FMT for c-diff or UC, but they fail to recognize the importance of donor quality. We need better metrics for measuring and under standing who is healthy and who isnt. Have been talking with a guy who founded HumanMicrobes.org. Very sharp dude who has a lot of novel ideas on the subject. Found this primer to be an interesting read (although a bit disorganized): https://docs.google.com/document/d/1cagqpzrca7uy8qzyv6niywdhpelblzhxuk1owpr3knm/edit?fbclid=iwar1kzbe2ywej1e8dtlmr4tpctdhurthvre7mfapyh56dvc9c6vl74ntd_rc

If one wants to order poo for an FMT, the main sources right now (not considering the clinics in australia, which are supposed to be good but im unwilling to travel to), are Taymount (bahamas/uk), FMT Solutions in Mexico, MG Infusions in florida, and Microbioma.org. I have read the best reviews with microbioma, and they will send you (relatively in comparison) affordable capsules in the mail. I've decided this is probably how I will try my FMT. Will keep all posted, aiming for a late january or february experiment.

Post Edited (dcd2103) : 12/24/2020 10:51:47 AM (GMT-7)

dcd2103 said...

Gut health is extremely correlated with methylation.

And methylation is extremely correlated with gut health. It goes both ways. Good post.

Good post, but I’m hoping Gut Health is not news to people that are regulars here

I will check out your more detailed links I’m always interested in seeing new information on the subject so far it’s been the same old stuff just recycled over and over

Yes there is a risk with antibiotic use as they say you weigh the pros with the cons.

As a newbie when you first come here in the lyne world and want results when you look at the Internet - the natural protocols are just way too overwhelming in my opinion everyone thinks their protocol works and says they are doing the best thing etc. that’s why I went with abx.

Funny thing is when there’s people that think their protocol is the best and they’re still using it and not much better obviously they need to change.

The gut has been been functional medicine’s number one thing ever since the term functional medicine medicine was invented , health starts in your gut, even serotonin comes from your gut and goes to the brain.

My functional lime doctor got your gut going first or at least better than it was before treating Lyme.

I was at an MS group meeting one time just to pick their brains To get some doctors names,and only one guy in about 20 of them was functionally medicine thoughtful , for lack of better words, the rest of them were eating brownies and cookies for comfort food during their meeting - It was encouraged to do so as a kind thought little did they know that this is not good for them apparently.

Post Edited (astroman) : 12/24/2020 2:20:16 PM (GMT-7)

One little detail about gut health which you kind of mentioned here I’d like to think that gas is not normal. I always feel the best all over when I don’t have gas.

And conventional medicine has the gall to say gas is normal, I say BS. Another prime example that conventional medicine doesn’t know much about overall health. at least 50% of people in America are ill in someway or another, Some just don’t know it yet. That 300 pound person everyone knows who eats like a rabbit - somethings obviously not right with their gut or something else. And that person everyone knows who if was a comic would look like pigpen from snoopy , who is constantly farting 24 seven but they refused to clean up their diet - well that’s the problem, Their diet.

After cleaning up my diet it did not fix everything 100% but it certainly did help noticeably through feeling in lab testing so with that I just can’t believe how many people refuse to clean up their diet apparently comfort food really means that much to them but if they had a better diet their mind might be more healthier as well the average person just doesn’t get it and refuses to except this fact.

Fortunately the word is getting out and people more prone to making more healthy food choices are doing so now since the information is out there available to them.

It still blows my mind though the reluctance that some people have to eat healthy. I worked in Hy Tech and engineering places for quite a while and what do they do on special events and Fridays hand out free pizza donuts whatever. They know I don’t eat that stuff but they don’t connect the dots when They go “wow you’re 50 something , you look like you’re 35 or 40” as they are chomping down on their free doughnut and adjusting their belt out another notch. So obviously in America and the rest of the developed world , people tend to judge others health on their outside’s so if they can’t even connect the dots that way how do they connect the dots with convincing them that eating healthy is number one better for your insides. Some people just will never get it. I’m kind of on a rant here above and beyond the lyme community ha ha .

Hey Astro, interesting comments as always. You're right, I dont think its news that the gut is important, but I guess my point was 1.) its not just important, it really is one of the deciding factors, and the amount of attention paid to the microbiome within the chronic illness community is vastly out of proportion to the size of the role it plays. I guess it felt it important to stress that this is not some theoretical exercise, there is a very obvious, very powerful 1:1 correlation there that most people ignore. This deep dive really opened my eyes 2.) You mention functional medicine, but I was highlighting that even within this community, the approach tends to focus on antimicrobials, which may be the wrong approach. I liked reading your rant and agree with all of it

Georgia, thanks for the compliment on my post, I tried!

Pots, thanks as well for the compliment I havent spoken to Mary in December as she's been travelling. I briefly mentioned it in November, but I hadnt done much research at that point. She said that she has seen many miraculous recoveries with FMT, but that I probably wouldnt need it unless I couldnt get there using diet alone. Tbh I dont normally like to make too many changes at once, and I do kinda wanna see how far diet can take me first by itself, so it's possible I may push it back til mid 2021, that would be the scientific thing to do. Well see where I am in a month or two i guess.

Dude, I was curious if you could expound more on your experiences with diets, and which you think hurt or helped? Its very frustrating to me because of the amount of contradictory information and studies out there...some of the smartest people out there come out on completely opposite ends of the spectrum, some arguing vehemently for all-plant diets, and others all carnivore, and they each present their studies and cases well. Based on my research I just cannot get behind the idea that quality (organic, grass fed) meat is bad for you. Quite the opposite, but I still see this idea touted. Similarly, i do not think that all plants are healthy by virtue of being plants. I guess the right answer is just that what all of these diets share is a focus on quality, organic whole foods, and the best diet for any microbiome is probably a whole food diet rich in both plant and animal meats, to support diversity of microflora...and one that limits sugar. So thats what I've been doing.

Even as a child.. EDIT: (my gut) was never that good so there is something wrong to begin with. It’s pretty hard to remember under the age of 10 but I do remember first time I went to Mexico with my parents I suppose I was 11 or 12, it just ripped my gut apart and I was never right after that. I went quite a few times after that and on my own as a young adult every time My gut was a mess. It’s just not worth it.

For that reason I really have little interest in visiting Third World countries again. Even if you drink only bottled water you still come in contact with their water somehow from the food they rinse or whatever. Maybe I’m just more susceptible to it I don’t know.

Post Edited (astroman) : 12/24/2020 10:38:35 PM (GMT-7)

Yes Astro!!!! Your Mexico anecdote is everything right there! That kind of captured my point in its essence, and it also reveals why the tests Adam B is referring to don’t work.

I too had gotten sick on a trip. In Costa Rica, totally screwed me up. And I developed neuropathy right after that. I did stool tests, kept saying I must have some bad bacteria down there. And if you remember even a few weeks ago I was asking in this group, what are the “bad bacteria”? Does anyone even know, or is this just a made up thing? Because there seems to be no definite answers as to what’s bad

It wasn’t until I started reading some of the comments in the FMT group that it all hit me. It’s often not one bad pathogen or bacteria that is the problem. And for that reason it doesn’t show up on a stool test. It’s more complicated than that. It’s biodiversity. It’s about having a diverse, functioning, natural ecosystem in your stomach that can live in harmony, break down everything you eat and keep each other in check.

And often times one of the things that can completely destroy this biodiversity and balance is a stomach infection like you had in Mexico or me in Costa Rica. Sometimes it abx. Or a western diet. Or all of the above. Was just watching a video by the Dr. Will Bulsiewicz, the guy Dude Abides recommended, and he was saying that there’s evidence that stomach bacteria (most likely through methylation I assume), control your epigenetic shifts. And sometimes what happens is someone gets sick, a bacteria temporarily takes hold and completely changes the microbiome, both short term and with long term diversity implications, and the flip is switched.

This is the point I was trying to make with antibiotics. You have a diverse natural roster of micro flora and it thrives. But kind of like a lake, if you dump some toxic substance in there even temporarily and kill everything, it doesn’t grow back healthy...it turns into a swamp w gnats and snakes and and sludge

Post Edited (dcd2103) : 12/24/2020 7:36:04 PM (GMT-7)

"This is the point I was trying to make with antibiotics. You have a diverse natural roster of micro flora and it thrives. But kind of like a lake, if you dump some toxic substance in there even temporarily and kill everything, it doesn’t grow back healthy...it turns into a swamp w gnats and snakes and and sludge"

Well, ....yes....unless you change your input, the output remains the same.

I tried various probiotics, and I went by feel. SB made me ill, scratched that off fast. Many basic ones seemed to have no effect. VSL3 had a slightly noticeable better feeling down there effect. You then need to recognize the effects of specific foods you re-introduce. Gas and bloating? Some Drs say thats normal, which again, in my opinion and experience that is total BS lazy talk, and your brewing up something in your gut not just digested fiber. More likely underdigested foods. FODMAPS are perfect example. I can air up the Goodyear blimp if I consume enough of them. So I dont do that....anymore. Did I once have the enzyme that could digest these? Did this change from the Mexico bug? Im not sure. I was a kid. Drs were worse then vs now. If I could go back in time, there are a few tests I would ask for if they had them in the late 70's.

This is not just about digestion, its also about inflammatory gut wall effects/porosity (micro-villie). And this is where autoimmune possibly makes up its playground, possibly in play with gut candida. Why did my c4a inflammatory marker (its not just mold) drop from 55,000 (highest ive seen here when this place was super busy and via googling the web) to normal of 14,000 a few months after dropping gluten and treating candida? Had I not done this simultaneously I would know the answer. Or was it the combination of both.? Probably.

I wonder how important eating seasonally (different sets of foods for months at a time) is to creating/maintaining diversity.. I heard Mary emphasize this in a podcast I listened to (thanks, Dude for the link). Thinking there would be some microbes that would only be able to colonize in certain environments, and when environments change for other microbes to flourish, the one's that colonized previously would at least be able to stick around in a more limited capacity.

potsnpans said...
I wonder how important eating seasonally (different sets of foods for months at a time) is to creating/maintaining diversity.. I heard Mary emphasize this in a podcast I listened to (thanks, Dude for the link). Thinking there would be some microbes that would only be able to colonize in certain environments, and when environments change for other microbes to flourish, the one's that colonized previously would at least be able to stick around in a more limited capacity.[/quote

Interesting idea, Might be easier planting different bacteria with different probiotics, of course wouldn’t it be nice if there was an easy test that could tell us what’s inside already, besides the bad guys.

If replant lawn seed in the spring . I mix up several types - northern mix, shade tolerant, drought tolerant and blue grass. There are less bare and dead spots throughout the year using this approach. Now I will be thinking about my gut when I do this ha ha.

DCD - The relation of Fofmaps And gas or bloating is - number one: a missing enzyme that would normally digest these sugars. It’s assumed that we either have or don’t have these enzymes no one ever talks about if they actually change in time or not. That said what isn’t digested becomes food for bacteria in the small intestine And of course gas.A.k.a. Non-FOD map veggies Are said to create gas from the fibers, But I think this is over exaggerated., we are all different because of these reasons, but in my experience it’s
certainly way way less then the effect from FODmap foods. I remember times when I could eat several apples in a row when I was a child and years were only one apple created huge stomach bloating and all the other effects. Apples are a fodmap. For some people an apple a day will not keep the doctor away ha ha.

Enzyme health population , types etc. is never talked about. Like probiotics there are obviously supplemental Enzymes, just talked about less than probiotics. I fooled around trying various brands of those too.

To go further down this rabbit hole you also have to include stomach acid and pH.. It is well known that stomach acid gets reduced as you get older which not coincidentally is why so many middle-aged and older people are mis-diagnosed with high stomach acid and put on PPIs which make the problem worse, if more of these people took HCl, They would find some relief.

I don’t regularly take supplemental digestive enzymes anymore but I do take HCI If or when my gut starts brewing up or if eating more meats.

astroman said...
I wonder how important eating seasonally (different sets of foods for months at a time) is to creating/maintaining diversity.. I heard Mary emphasize this in a podcast I listened to (thanks, Dude for the link). Thinking there would be some microbes that would only be able to colonize in certain environments, and when environments change for other microbes to flourish, the one's that colonized previously would at least be able to stick around in a more limited capacity.[/quote

Interesting idea, Might be easier planting different bacteria with different probiotics, of course wouldn’t it be nice if there was an easy test that could tell us what’s inside already, besides the bad guys.

If replant lawn seed in the spring . I mix up several types - northern mix, shade tolerant, drought tolerant and blue grass. There are less bare and dead spots throughout the year using this approach. Now I will be thinking about my gut when I do this ha ha.

DCD - The relation of Fofmaps And gas or bloating is - number one: a missing enzyme that would normally digest these sugars. It’s assumed that we either have or don’t have these enzymes no one ever talks about if they actually change in time or not. That said what isn’t digested becomes food for bacteria in the small intestine And of course gas.A.k.a. Non-FOD map veggies Are said to create gas from the fibers, But I think this is over exaggerated., we are all different because of these reasons, but in my experience it’s
certainly way way less then the effect from FODmap foods. I remember times when I could eat several apples in a row when I was a child and years were only one apple created huge stomach bloating and all the other effects. Apples are a fodmap. For some people an apple a day will not keep the doctor away ha ha.

Enzyme health population , types etc. is never talked about. Like probiotics there are obviously supplemental Enzymes, just talked about less than probiotics. I fooled around trying various brands of those too.

To go further down this rabbit hole you also have to include stomach acid and pH.. It is well known that stomach acid gets reduced as you get older which not coincidentally is why so many middle-aged and older people are mis-diagnosed with high stomach acid and put on PPIs which make the problem worse, if more of these people took HCl, They would find some relief.

I don’t regularly take supplemental digestive enzymes anymore but I do take HCI If or when my gut starts brewing up or if eating more meats.

Good point, some fodmaps require enzymes. The simple sugars do, like fructose that they've lumped into the FODMAP definition because some people cant digest them. We've had this convo before. The definition is non-digestible, and to me my brain automatically thinks fibers. Sometimes it slips my mind that theyve lumped these often very digestible simple sugars into the same definition. My bad! But some, if not most, fodmaps do require bacteria to digest them. But your point stands, the reason you probably cant handle them is because you have trouble breaking down lactulose and fructose.

Post Edited (dcd2103) : 12/25/2020 11:49:55 AM (GMT-7)

Dcd2103, where are you sourcing the fmt? I've communicated with the microbiome project.org person you speak of but he had not been able to locate any donors in a while that met the strict criteria. He had a couple on the line but I chose to forgo because I didn't like their profile.
I've been trying to find a good source for about 2 years.
I know a lot of the do-it-yourself grown and also rate of colitis suffers have used samples from their own infant children which appears to be the best source because in most circumstances they have not received lifelong exposures to antibiotics and are only really contending with whatever viruses and heavy metals were passed on from the mother at birth assuming the mother is healthy.
But as you can imagine this is not an easy thing to try and solicit someone.
I have ponied up the money to try and stool sample test a couple of folks but they ended up having a fairly substantial level of pinworms and roundworms parasites etc so I think in most cases it the best option is to get a small group of people to spread the cost evenly pay the donor and also compensate them for doing free dried shipping.
Feel free to contact me privately if you're interested in going down that road I already have three other people for a total of four that are interested in ready to go usually the stool samplingand blood test markers are between 6 and $900.

Yeah I'm suspicious on the oxalate issue as also being related to the microbiome I just happen to get a stool test very early in my illness earlier than most probably only weeks after my infected bullseye tick rash and I did not have oxalate problems but of course they slowly crept up over the course of the illness deterioration regardless of diet intervention. So we likely have bacteria that neutralize that problem that we've lost or there's some enzyme mechanism that's been blocked.