Enemy within: gut bacteria drive autoimmune disease | Hacker News Reader

Enemy within: gut bacteria drive autoimmune disease

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It is frustrating how slow medical progress is with respect to gut biota and such personalized medicine.

This seems like the perfect place for machine learning and big data. What exactly is the hold up? Is it regulations? Is it old fashioned doctors unwilling to push boundaries?

Ive been dealing with mysterious stomach issues for a long time myself, and I'm living for the day where I can hack something together to cure myself, at this point I've lost faith in doctors; and my problems in the grand scheme of things aren't even that bad, I can only imagine how other hackers must feel...

Edit: I've been getting my own ML startup off the ground just recently, but if anyone is doing something in this area, even open source, I may be interested in collaborating, let's talk!

But aren't all medical progress pretty slow? Human body is complex and research is expensive.

This place is trying: https://viome.com/

My guess is that human flora are orders of magnitude higher in complexity. They all interact with one another and diet. It’s hard to find numbers, but at least one place indicated over 500 different strains in the human gut.

This type of analysis will probably be a cornerstone in future health assessment. Since there are more cells and genes in the microbiome than in the human body, it seems reasonable that different compositions may have profound effects. Untangling this might take a while, meanwhile, changes in food production, environmental degradation and pollution are probably affecting microbial “landscapes” in detrimental ways. For now, options are limited to experimenting with diets, switching to organic alternatives, and the most radical method, temporarily change environment to isolate or eliminate the causes. All these more or less worked for me, the last one most effective, restoring a dysfunctional gut flora, however not permanently which speaks for environmental factors beyond diet.

One of the prime suspects here runs into an extremely influential entrenched forces with an interesting against this sort of work. For instance nearly all foodstuffs of various sorts in the US today are treated with glyphosate both as an herbicide and as a crop desiccant. On the latter part even various cereals and wheats are generally treated with glyphosate just before harvest to work as a dessicant, or drying agent (which, as an aside, is where the hypothesis that 'gluten sensitivity' is actually a response to glyphosate comes from). The most important point here is that while the impact of such is debate, it is not debated that glyphosate has a substantial and not entirely clear impact on gut bacteria.

Monsanto reacts extremely aggressively against any publication, from anybody, suggesting any potential issue with their products. For instance when the World Health Organization indicated that glyphosate is a probable carcinogen, even they came under sustained aggressive assaults from Monsanto's PR and 'approved science' machine. That sort of pressure is something that, if you're a researcher who's not ideologically driven, is going to work as a major deterrent.

And of course it's entirely possible that glyphosate is not the cause here, but it's something that you presumably would want to extensively research first and foremost due to its ubiquitousness and interactions with gut flora, yet that's not really happening, on the scale it should be, outside of studies with major conflicts of interests.

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EDIT: One quick addendum. The reason I jumped from analyzing gut bacteria in and of itself to examining outside players is because your gut biome is going to a product of environmental factors. So it's not so much the biome that matters as how we are changing it, unless you assume that there has been no real change in incidence rates over the decades but simply more widespread reporting - which is certainly possible and something that would also need to be investigated.

As a fellow ML enthusiast with similar stomach mysteries. I discovered a year ago i had a reaction to milk which resulted chronic hyperacidity and eczema. I silently suffered from this condition for a decade and half. A month ago i discovered this was a product of A1 protein in milk. A2 milk doesnt hurt me as much.

Basically eating clean and eating smart seems the only way out coupled with yoga. Yoga seems to help all these conditions. It seems yoga needs to be studied more from a scientific purpose to see why it works

I see a lot about autoimmune disease on Hacker News. I guess that it's a wide medical area, that many can relate to?

I know of several hackers that have gone through YC have autoimmune conditions, and I would say there is a larger population of people that have autoimmune conditions then our parents generation. I myself have ankylosing spondylitis, and live with chronic pain, back and neck problems. Probably just really interesting to people like us, who want to hack our way out of problems that medicine doesn't have good answers for yet.

I don't think I'd be any kind of "hacker" if it weren't for undiagnosed celiac disease. If I wasn't been too sick to go out and do my normal activities, I never would have sat at home learning to program.

It's incidence also, anecdotally, seems to be increasing.

Isn't untreated Celiac disease also associated with foggy cognition and poor memory?

Yes. That was a bad time in my life.

I've got the same thing - my neck and shoulders are wrecked, with two slipped discs and severe degeneration, more than should be for my age. The two things that worked to remove nearly all of my pain:

* Whole 30 anti-inflammation diet

* Mysore-style Ashtanga Yoga

If both are done diligently together every day, after 2 weeks you will likely see drastic improvement.

It's not a cure - if I stop, after 2 days I'm back in excruciating pain. But when I do these regularly, I can go through the day forgetting that I have neck problems.

I'm currently on the "low-lectin" diet which seems to be the most extreme of the anti-inflammation diets.

Even though the doctor (Gundry) provides mostly anecdotal evidence in his book The Plant Paradox - you might want to try cutting out cashews and nightshade vegetables which are approved on Whole 30. I felt a difference when I cut those two things out.

Is there any authoritative source on nightshades and inflammation/digestive issues?

After extensive testing, I believe they cause serious issues for me (fatigue, bowel issues, etc)

But when I search for info, I just find sites from sort of woo-woo sources. (Chiropractors, naturopaths, etc)

I'd like to read something more definitive. Both for my own purposes, and also to point people to, as the category itself makes people skeptical.

Spicy food, sure, people get that. But potatoes? That's a weird one for most.

Nope. The only studies are in mice/rats. I was disappointed that The Plant Paradox "references" linked to articles on the web like this: https://www.dietvsdisease.org/nightshade-vegetables/

I see. What's your personal view on eliminating them? I'm trying to rule out the possibility that I've given myself a nocebo effect.

(I've had enough cases where I didn't realize something was a nightshade and I had a bad effect from it that I don't think I'm merely fooling myself, but the quality of articles about it is disturbing).

What did the rodent studies find?

Could you elaborate a little bit on how you got started with Ashtanga Yoga ?

Any book or yogashaala recommendation ?

A coworker introduced me. I was already looking for a place to practice yoga so when a recommendation came in I latched onto it quickly.

Ideal book for the Whole 30 diet? Tia

That and probably most people with autoimmune diseases have been surprised how little is known about these diseases. Just getting diagnosed with one often takes months if not years and multiple specialists all telling you that it's "all in your head".

Also hearing that there's nothing that can be done except watch your body deteriorate is a slap in the face to any one. What you're left with is trying the "unconventional".

I think it depends on the type of autoimmune disease. Some are fairly obvious, such as alopecia areata.

>multiple specialists all telling you that it's "all in your head"

This has been my experience since I started having systemic inflammatory symptoms since the age of 12.

It has wrecked my life in as literal and as figurative a way as one can imagine.

A lot of doctors blur the lines between their own hypotheses and facts. It's always "all in your head" until it isn't, but few ever admit they were wrong even after the facts come out.

Many also have such an ego that they prefer to concoct convoluted and implausible explanations for irregular test results and obvious symptoms rather than to concede that their prior implications about the patient's character (as being one who makes up symptoms) were unacceptable.

Not to get off topic but when science (i.e., doctors) act this way it undermines the broader faith in Science.

It would be more accurate to say, "We're not sure. We're sorry. We can't help you at this time." But instead they blame you? The person who brought them opportunity?

Science could stand a heavy dose of humility. No one trusts an egotistical bully.

Note: I'm not a Luddite. I think the scientific method is a great tool. It's enabled us to do wonderful things. But humans being human do make mistakes, there a false flags, etc. My rub, despite history, is there's a (false) belief that Science can do not wrong.

That disconnect - and the ongoing insistence it doesn't exit - only undermines Brand Science (if you will).

The irony is, there's plenty of Science to show how such denial is a mistake. It's as if Science won't listen to itself. But blames us for not listening? Huh?

It's a set of conditions where most doctors' best answers are "beats me", where conditions are extremely variable from individual to individual, and where lifestyle changes can have drastic differences in outcome.

It is the ideal playground for the lifestyle hacker.

Wow, great summary as to why people are interested. Seriously.

I also think the autoimmune system contributes largely to the overall system. To understand the autoimmune system is to do things like “beat” cancer, aids, possibly some brain disorders, and so on. I personally suspect even life extension could be affected with a full understanding- ie maybe we’d be able to genetically engineer an organism that would repair our telomeres or clean our brains of damage as a symbiosis. It sounds crazy, but I got the idea after hearing about fungi providing nutrients to tree roots in a symbiotic relationship. But first we’d have to find a way for our immune systems to allow it.

I would prefer taking a snapshot of our DNA and then making a retrovirus to go in and restore it, and then get flushed out.

>most doctors' best answers are "beats me"

i take your "beats me" doctors and raise you the gastroenterologist i saw recently - he said straight out, end of discussion, "our infectionist doesn't believe in candida in the gut"

As we have that saying in Russia - "the duty to save the drowning person lies solely with the drowning person" ("spasenie utopayuschih delo ruk samih utopayuschih")

My nephew gave a stool sample your gastrointerologist’s infectionist might want to have a look at.

because the symptoms of the disease come and go with frustrating unpredictability, it’s easy to imagine that lifestyle changes can have drastic differences in outcome, and easy to sell desperately sick people on that idea, just like praying to the gods for rain.

>sick peopLe praying to gods...

You may be on to something. Many religions in times of prayer also have fasting and special diets. Such a large change in diet would influence gut bacteria and the person would attribute the change to their god.

Autoimmune diseases used to be very rare a century or two ago. For a long time they were doubling in prevalence every decade or two. But that will not happen again, because over half the population now has at least one (eczema.) Doctors obviously haven't had much to offer during this debacle.

It’s an extremely interesting field where decieses act in extraordinarily ways. An ex boyfriend of my best friend got an autoimmune response and went from perfectly healthy to lying in a respirator close to death in one week, only to be fully out of the hospital two weeks later. And as it went on the doctors seemed to have next to no clue about what was happening just saying that he needed to “ride it out”. Another close friend had an autoimmune condition where she woke up one day partially blind on one eye. It looked like her body was attacking her own eye. But today there is no issue anymore. I think that for anyone who’s come across the subject it’s just intensely interesting.

Immune responses to bacteria colonizing unusual tissues doesn't seem like "autoimmune disease". That is, unless there's cross-recognition between bacterial and host epitopes. But there are known examples of such molecular mimicry.[0] Such as "Campylobacter jejuni lipooligosaccharide (LOS) mimicry of human GM1 ganglioside and mimicry between the dietary antigen butyrophilin and myelin oligodendrocyte glycoprotein". So maybe this is another example.

0) https://www.sciencedirect.com/topics/immunology-and-microbio...

I have hashimoto's thyroiditis autoimmune condition and I read somewhere that one possible cause could be very subtle gluten allergy. So antibodies are produced to attack a specific gluten protein, but this protein is similar in molecular structure as the protein thyroid is made of, thyroglobulin, so at the same time thyroid is attacked. Is this what molecular mimicry is ? I know next to nothing about human microbiology, feel free to educate me. I really should pick up a book on it if I want to experiment with my health, any suggestions where to start ?

> Is this what molecular mimicry is ?

Yes, but it usually works the other way around, i.e. the immune system should not recognise the "specific gluten protein" because it looks like self. After all the microbe(?) that produces it is trying to survive by looking like its host, it isn't trying to induce thyroiditis in its host.

Another common case is mimicry of the A, B blood antigens and the Rhesus factor. Patients that are AB+ treat A,B and Rhesus factor as self and so can accept blood from any donor (i.e. AB+ is the universal recipient). In contrast, O- patients who do not treat A,B and Rhesus factor as self and due to mimicry will likely treat them as foreign bad (as opposed to foreign neutral), so if they receive a transfusion from any other blood type the immune system will attack the transfusion. Since O- lacks A,B and Rhesus it is the universal donor.

> any suggestions where to start?

The topics fall under microbiology / immunology, so Ugrad textbooks, Wikipedia etc.

Yes, that could be molecular mimicry. I hadn't heard of the thyroglobulin gluten similarity. But Hashimoto's thyroiditis is associated with celiac disease, which is clearly gluten related.

As the immune system matures in late fetal development, there's a stage when all cells that can target self antigens get killed. However, some tissues are isolated from the immune system, and so there are antigens there that don't get on the "self list". The thyroid is one of them.

Everything is OK until the thyroid gets damaged, infected or whatever. Then the immune system can see it, and may develop cell and antibody mediated responses.

Like all proteins in food, gluten is normally digested, and never makes it out of the gut intact. Only the component amino acids are transported to the bloodstream. However, in celiac disease, where the gut lining is damaged, I can imagine that some gluten gets across intact. Also many other proteins and complex carbohydrates.

Then the immune system could respond to all that stuff. And some of it could share epitope with thyroid components. So if there is an association between gluten and Hashimoto's thyroiditis, it's hard to say whether gluten shares epitopes with thyroid stuff, or whether it's just damaging the gut.

I have no useful references, but I have a friend with Hashimoto’s who seems to be controlling it by avoiding gluten, brassica, and a few other foods, without any meds. IIRC the set of foods is gluten + known/suspected goitrogens. Definitely do your homework before trusting me on this.

I have the same condition and have improved it significantly by removing gluten from my diet and adding fibre and natural probiotics from fermented foods. I am also not a biologist of any sort. I get regular blood tests done (yearly) to monitor, read and experiment. Not cured but levels generally heading in a better direction.

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