The enemy within: Gut bacteria drive autoimmune disease | Hacker News Reader

The enemy within: Gut bacteria drive autoimmune disease

sciencedaily.com

232 pointsmontrose83 comments

If anyone is interested in a way to treat E. gallinarum—and other potentially pathogens—without antibiotics, you should look into phage therapy. Phages are viruses that attack specific bacteria, have been used for decades, are commercially available (even on Amazon) and are generally considered safe for human consumption.

Granted, phage therapy typically targets gut pathogens, and in this study the E. gallinarum had traveled to other parts of the body. But many people I have talked to who use phage therapy have reported improved symptoms and in some cases even reversal of autoimmune disease.

And yes, phages that you can buy today without a prescription target Enterococcus bacteria, which includes E. gallinarum.

The gut is a wonderful, mysterious place that most of us neglect.

Sounds interesting, but how would you know which species to attack?

Most commercial phages in the US (can't speak for the rest of the world) are comprised of these 4:

LH01 – Myoviridae LL5 – Siphoviridae T4D Myoviridae LL12 – Myoviridae

You can research all of these, but these 4 specifically target a specific but broad range of potentially pathogenic bacteria, including E. Coli (though not all E. Coli is bad) and other species. Generally if you take them together they provide effective treatment against a broad range of inflammatory agents.

Disclaimer: Not a doctor, just someone who suffered decades of gut problems and eventually healed himself.

Would these bacteria show up in a stool test? It would have my preference to first test myself, with the benefits of not taking any therapies I don't need, AND also for getting an objective measure of the effectiveness of the therapy.

By the way, I've read that phage therapy is big in Georgia: https://www.nature.com/news/phage-therapy-gets-revitalized-1...

To a degree. Also, depends on the service you use for testing. For example, Ubiome will show your bacteria down the genus level (e.g. Enterococcus) but not the species level (e.g. Enterococcus gallinarum)

cyrusshepard, I have 2 questions:

-How long did you suffer from gut problems, and what exactly wer the symptoms?

-How long did it take for the problem to resolve after you started taking the phages?

Do you know where to find more information on that? (If you would be willing to answer a few questions about it, my email address is on my profile.)

FWIW, I started learning about phage therapy from John Herron, who runs the Gut Health Protocol. He sells a phage product so keep that in mind, but he's gathered a lot of research here: https://www.theguthealthprotocol.com/wp/phage-therapy/

I think gum disease could be a really powerful application for phage therapy. As I understand it there’s really just one or a few species causing the inflammation. Most bacteria in your mouth is good and just wants to mind it’s own business.

The gut is the new "great unknown." Understanding it takes a more holistic approach. Western medicine / science is typically not very holistic-centric.

It's not going to surprise me if many of the cures / remedies offered by "non traditional medicine" (read: lessons from human history) little by litte get more credit for their worthiness.

I don't know why people are downvoting you. Things like microbiome, calorie restriction, diet, and water fasting are very promising "non-traditional" areas for dealing with systemic inflammation, and they definitely can work. Researchers should be paying more attention to those areas. Doctors often have no good answers for those diseases -- they often don't even diagnose them promptly and correctly.

There is some research, but not enough yet. And some of the previous studies were not designed well. I'd put water fasting in a "non-traditional" approach that should be looked at more closely, though many other "non-traditional" things, like homeopathy, have been debunked.

This is very interesting:

https://news.usc.edu/63669/fasting-triggers-stem-cell-regene...

I'm a skeptic, but knee-jerk skepticism is sometimes as bad as woo. I'm guessing that the downvoters have no experience with these kinds of conditions or what it's like to deal with the medical system around autoimmune conditions.

I could tell you many stories about it. I know one person who didn't get his autoimmune disease correctly diagnosed for 20 years. He now has serious problems due to lack of treatment for all that time. Even today, many doctors do not know basic information about those conditions (or sometimes even basic anatomy). The current state of autoimmune diagnosis is still absolutely terrible.

Woo is dangerous, but so is knee-jerk skepticism. I'm not complaining about modern medicine -- just that you shouldn't necessarily be so quick to downvote something if a medical doctor hasn't given their stamp of approval. Science does not have enough information yet to confidently and safely treat these problems, and it has provided many clues about the microbiome, intestinal permeability, and water fasting on the immune system. If you haven't heard of those things, I suggest reading some studies before downvoting.

As a matter of fact, I do know what you're talking about (AS). And I can't downvote, but I would ! ;) Promising mountains with "diets" is as bad or worse than doctors not really considering what's it like to live with autoimmune diseases / having trouble establishing diagnosis. Please link to peer-reviewed, serious papers showing results in double-blind studies if you wish to convince fellow hackers.

You're reading too much into what I'm saying. I didn't promise mountains with "diets". I said that "Researchers should be paying more attention to those areas." I'm definitely not saying that the answer is going to be "just stop eating" or curing yourself with woo like homeopathy and goji berries.

I don't think that something like water fasting will cure the autoimmune conditions of most people, but it's something that has such a dramatic effect on some autoimmune conditions that there should be more research in that area.

Have you ever done 3-5 day water fasts with nothing but water? Hold your reaction until you have investigated the dramatic effects (but not cures) it has on many people with autoimmune conditions.

I'm working this afternoon and don't have time to find links for you, but you can find my email address on my profile if you have questions about it.

Edit: please send me an email if you read this. I will email you some links later if you will send me your constructive opinions after you read them. I think you may find the information interesting and possibly useful.

Thanks for the clarification. I will look into it !

This is a very dangerous way of thinking. I can think of at least five people in my social network who have died as a direct result of seeking naturopathic medicine for their serious illnesses instead of proper medical care. Please do not encourage more people to do this.

I can think of 250,000 people in the United States alone who died last year because they sought proper medical care but died because of medical mistakes and bad prescriptions. In addition there were those that were harmed, but not fatally (of whom I know several).

https://www.hopkinsmedicine.org/news/media/releases/study_su...

That's a very misleading statistic, many of these people might have lived with the best possible care but would have still died without treatment. Heathy people rarely seek major surgery for example.

I think both examples need to provide a denominator.

Any particular naturopathic medicine in common?

There are conditions that are considered incurable by "proper" medicine (e.g. Alzheimer's disease) and discouraging people from looking elsewhere (e.g. http://www.aging-us.com/article/100690) in those cases is just as dangerous. People are capable of considering multiple options simultaneously, and should be encouraged to inform themselves about the available treatments. In cases when two medical theories are truly incompatible, give people the right to decide what gamble they want to take, and understand that, in both cases, outcomes are uncertain.

A "more holistic approach" doesn't necessarily mean "naturopathic medicine" or not seeking proper medical care.

Exactly. Thank you.

I did not say naturopathic medicine. What I said was, things that were "scientifically" dismissed are rventuallt redemed. Acupuncture comes to mind. As do other approaches that help strengthen the gut. Etc.

That said, how many people have died, suffered or lived otherwise uncured from the tunnel vision of traditional medicine? I wish I had $20 for every time I heard "...the doctors aren't sure what it is..."

Your point is a good one. Let's just be fair to apply it evenly to all those who offer cures.

Oh! And let's not forget the "opioid crisis." Not only is that driven by the misunderstanding of pain, but the so called cure kills time and time again.

Let's be fair. Please.

The medical establishment offers the best preventative cure for many of these diseases: eat a variety of food and exercise regularly. Further; be born through the vagina, drink brest milk, and eat dirt.

The problem is people aren't educated about the Hygiene Hypothesis and often succumb to bad habits and addictive food.

My mom has Hashimoto’s which she's managed successfully for years using a low daily dosage of doxycycline. This suggests a mechanism for why that seems to work for her.

Did her endocrinologist prescribe her antibiotic?

I'm asking this because I have Hashimoto's myself and none of the endocrinologists I've seen recommended anything else besides levothyroxine.

Depends on the pharma rep in their area.

No, she and my dad just did their own research online and gave it a try. Seems to have worked out really well for her. Her goiter shrank and she had to reduce her thyroid meds.

Low dose doxycycline seems who tolerated, and has an interesting side effect of reducing inflammation to near zero in the body (CRP levels of actually zero). Given the role of inflammation in heart disease, that might be helpful for longevity too.

There's actually a drug, periostat that's prescribed in this way for oral health. It's 20mg doxycycline taken daily long term. There are studies on it available online.

This is why we have drug resistant bacteria, in a nutshell. Glad your mother's health is better, but if even a small number of people started following this regimen, it would be come useless in a relatively small number of years.

edit: I would love it if just one person could tell me how I'm wrong instead of downvoting. Long term low dose antibiotic treatment (doxy is a tetracycline) is how this happens. If you look up how I'm wrong before downvoting, I suspect you will end up not doing so, and perhaps learn something new.

So... People shouldn't use drugs that work for them because the bacteria will develop drug resistance to the drugs which are already useless because you can't use them otherwise the bacteria will become resistant?

Just because there are some bacteria that are already resistant to doxy doesn't mean that shifting the entire ecology of human bacteria so that resistance against doxy is selected for is a great idea.

If you have a garden and use pesticides, there are probably some weeds that will be resistant to it. But the mere existence of resistant weeds is not an argument for continued indiscriminate use of pesticides, as you will end up with even more. Degree matters.

Not sure why you're getting downvoted actually.

Yes, this treatment can probably help some people, but it's probably also true that deploying this en masse would not be a great idea from a long-term ecological perspective.

Low-dose antibiotics are already widely used today in farm animals because it lets them gain weight more quickly ( = more profit for the farmer). And now the bacteria have spread out of farms and into the ER rooms and are killing people. Another form of socialized externalities.

I found a few NIH papers after posting, and it appears the available data shows it doesn't result in drug resistance at these dosages. There are a few studies that tracked resistance among patient populations for several years and saw fewer changes than periodic high doses. I don't know.

This is my understanding as well.

I Was going to downvote but I’ll respond instead.

These people have legimate medical needs for this antibiotic so this isn’t a case where we’d want to withhold it.

We’re better off spending our resources discovering new antibiotics instead of neggling who’s deserving of what.

Hashimoto's is awful, but it can also be treated with an oral form of the thyroid hormones to restore appropriate levels (levothyroxine as the original poster mentioned earlier). I believe this is completely effective (I don't know if the underlying condition still causes an uncomfortable/visible goiter).

It's generally not fatal when treated. I'm sure you know that bacteria don't have to do traditional reproduction to exchange genetic material so they can pass along traits like antibiotic resistance very rapidly. It can also spread between different species of bacteria (see plasmids, bacterial conjugation/transformation).

So this is why I'm against using antibiotics for non-life saving applications, generally. You have widely drug resistant staph (eg, MRSA), e. coli, chlamydia, tuberculosis (XDR TB), et al. causing massive problems in healthcare systems across the world and killing quite a few people.

I am not sure if you know this, but given the absence of the selection pressure, bacterial populations can lose drug resistance. It has higher ongoing metabolic requirements to have that trait, and is a evolutionary disadvantage. Also, I don't know if you appreciate the difficulty to find new antibiotics (particularly wide-spectrum and low side-effects/toxicity). I would encourage you to research that topic carefully because it's a subject with a lot of poor information written about it.

Finally, I will underscore that I took my own advice, and found multiple papers hosted by the NIH about emergence of drug resistance in patients using very low dose doxy (not in Hashimoto's, but rosacea, where its non-antibiotic properties are also useful, though I'm not sure it's the same mechanism). So I was wrong, it seems. I learned something new in the process of researching my response.

Hashimoto's relatively easy to live with (at least, compared to other autoimmune conditions). If properly medicated with replacement hormones, no observable change in life expectancy. If goiter forms (which is a complication of undiagnosed/under-treated Hashimoto's), it's solvable by surgery.

It may very well be that either: these people think they have a legitimate need for the antibiotic or it is helping for a narrow portion of population.

The problem is, people without medical background cannot really evaluate if a treatment recommended by random blog is worth it, in terms of possible risk-reward. This can lead to all sorts of social phenomena, of which the most visible is anti-vaccination movement.

Interesting. Also have Hashimoto's. But the only thing they give me is Levothyroxine.

Though, I suppose it's in the mild category. I mostly only experience lethargy, swelling in my neck, and itchy calves.

See the paper here: https://sci-hub.tw/downloads/2c98/10.1126@science.aar7201.pd...

Is the suggestion that this particular bacteria is behind all forms of systemic lupus or merely that this bacteria can cause such a response? Thats an important difference.

Similarly, this headline makes it sound like all autoimmune diseases stem from gut bacteria. That sounds unlikely.

Quote “the research team found that they could suppress autoimmunity in mice with an antibiotic or a vaccine aimed at E. gallinarum.”

The titles vague to the point of clickbait.

On topic, there is much going on with bacteria. My hunch is this could be a large research area for the next couple decades. We’re talking about a system composed of trillions of individuals and an unknown (but large) number of species and all their interactions. I’m sure there will be bacterial “combinations” that in certain situations are helpful and others deadly, for instance.

Having one autoimmune disease increases the likelihood that you have or will develop another one. They also have cross-reactivity on tests.

For instance, false positives on the TTG/IGA for celiac are 2% for healthy patients, but rise to 20% for subjects with type 1 diabetes.

Celiac patients have a drastically higher rate of Hashimoto’s, autoimmune thyroid disease: https://www.newsmax.com/t/newsmax/article/718160?keywords=ce... and also the liver disease cited in the article: https://www.verywell.com/celiac-disease-and-liver-diseases-5...

Celiac patients also suffer higher rates of MS: https://multiplesclerosisnewstoday.com/2015/05/14/celiac-dis... MS doesn’t seem gut related on the surface, but you can get almost identical neurological symptoms from celiac. I know because this is what drinking beer does to me.

So, the roots of all of these diseases could definitely be related.

> So, the roots of all of these diseases could definitely be related.

Well, yes, but by definition they already have one connection at the root: the immune system. So increased comorbidity could also be explained by having a kind of immune system that fundamentally is more likely to develop auto-immune diseases.

This is not the only research regarding microbiome and autoimmune disease. While this article states that their findings seem most promising for Lupus Nephritis, there are recent articles that point to other microbes which are relevant to rheumatoid arthritis: https://www.sciencedaily.com/releases/2016/07/160711151315.h... and https://www.nih.gov/news-events/nih-research-matters/gut-mic... among many others with the search "rheumatoid arthritis and gut microbes". See this for MS https://www.scientificamerican.com/article/gut-germs-appear-... This is my all time favorite that just came out in Nature which shows that anti-inflammatories may contribute to slow growth of beneficial gut microbes. I have identified at least two first line DMARD's used in rheumatoid arthritis that are mentioned in this article. https://www.nature.com/articles/d41586-018-02780-x?utm_sourc... So, while autoimmune diseases amy not stem from gut bacteria, there is definitely some relationship about which we need to learn more.

I went to an ayurvedic doctor (in India, my friend insisted) and he said the exact same thing. He even said all allergy problems arise because of issuees in the digestive tract. At the time I thought he was just saying it but who knows there might be some truth in what he said.

> ayurvedic doctor

So not a real doctor

Please don't, just because someone mentioned something like that. It only leads to predictable places.

I don't mind being downed for an unpopular opinion, but calling out fake doctors should not be a reason to get flagged... And yes they are fake doctors.

Maybe so, but these discussions are all the same and always turn uncivil, so they're off topic here. There are lots of other places on the internet to argue about them.

Then please flag the original posting as well.

Allowing people to promulgate pseudoscience without following up with a strong counter-response is how we wound up with anti-vaxxers.

As someone with vitiligo, wonder if there is something similar in us.

Another reason why water fasting is highly effective at curing many diseases.

> water fasting is highly effective at curing many diseases

Has this been demonstrated?

I don't know about "curing" but it can be surprisingly effective for systemic inflammation. I think it's one of the most promising areas for autoimmune research.

https://news.usc.edu/63669/fasting-triggers-stem-cell-regene...

"...it can be argued that caloric restriction ... has the potential to accelerate the healing process..."

https://www.ncbi.nlm.nih.gov/pubmed/25881054

"...fasting ... has the potential to differentially protect normal and cancer cells against chemotherapy..."

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815756/

"...Autophagy is sometimes referred to as cellular “cleansing”, and our observations provide an attractive neuronal parallel to the organismal benefits that, historically, are perceived to derive from fasting."

"...short-term food restriction induces a dramatic upregulation of autophagy in cortical and Purkinje neurons. To our knowledge, this is the first demonstration that food restriction leads to in vivo neuronal autophagy."

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106288/

The day Big Pharma finds a way to profit from patients not consuming anything but water for 10 to 40 days and getting rid of diseases that used to require lifelong drug regimen, the research flood gates will open. But ain't gonna happen in my lifetime. There's no money in fasting, and no one can patent it.

Regardless of whether or not this is true (and really it seems to me to be a bit more malicious than large groups of people are consistently capable of), this isn't a super useful way of looking at it. Rather than speculate on why things are the way they are (especially if in this case it's pretty much unsolvable without really big changes), shouldn't we look to solve the problems this is causing (which by and large involves "merely" collecting large amounts of data, which is much less difficult and much more attainable in the short term)?

Yes, there is a hospital in South Africa that is successfully using water fasting in autoimmune disease. I'll pull some documentation and post.

Didn't you see all those posts on facebook? Middle-aged women appearently are really heavy medical researcher.

I'm no expert, but here's the sequence (in reverse order) as I see it (for now): bad-things-happening <<< crazed-immune-system <<< crazed-gut-bacteria <<< 1st-world-bad-living

Anything that treats "bad things happening", or "crazed immune system", or "crazed gut bacteria", will be a bandaid.

I think our first world lifestyles create a perfect storm of bad living that undermines the foundations of a healthy human being from a multitude of vectors. Not enough sunlight, not enough unprocessed fresh foods, not enough exercise, not enough fresh air, long term consumption and exposure to compounds and chemicals that work against your bodies natural processes.

A friend of mine had to go every other month to sit in a chair for 4 hours at a clinic to receive an IV drip that included medication to squash his immune system. Why? Because his immune system was attacking every joint in his body. He could not move without extreme pain without the treatment. Eventually he stopped eating the cheapest and most processed of garbage food, started exercising every day, gave up alcohol and diet sodas, and lost 75lbs. He found that he no longer needed the medication after about a year of turning his life around...

I know it's very tempting to blame everything to our "1st world bad living", but please do not spread misinformation like this about autoimmune diseases. I am 27, always ate healthy and was very active, yet I started developing ankylosing spondylytis 3 years ago, a very painful AI disease which attacks your articulations.

And you know what ? We know that many Pharaohs of ancient Egypt had it too, including Ramses II : https://www.ncbi.nlm.nih.gov/pubmed/12548434

So long for the 1st-world, industrialized society as the root of all evils...

Moreover, sounds like your friend was on biologics. Sure, losing 75pds will help lowering the inflammation and pressure on articulations anyway. But there's NO evidence it's not just a pause in flares, sorry for your friend. I met many people with AI diseases and to date have met no one who can prove he "healed" with a change in diet. Happy to discuss about it in PM if some read that comment !

A recent study indicates clinical evidence for remission through diet in IBD:

"Clinical remission was achieved by week 6 by 11/15 (73%) of study participants, and all 11 maintained clinical remission during the maintenance phase of the study."

Konijeti, Gauree Gupta et al. “Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease.” Inflammatory bowel diseases 23.11 (2017): 2054–2060. PMC. Web. 9 Apr. 2018.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647120/

That's really great, but I did that protocol strictly for 3 years straight and it never worked for me. (I continued it because it had a good effect on my sinuses, but not my lymphocytic colitis).

Your comment is incredibly ignorant, and positions opinion as fact.

It sounds like this friend of yours was taking a biologic like Remicade. People take these medications (Humira, Remicade Embrel etc) because they have immune system issues - to make a statement that these things are all caused by "bad living" makes it clear how uninformed you are on the topic.

Immune system conditions are also renowned for coming in waves - people can go into remission for years without a strong link to causation, making changes in diet and lifestyle often appear as if "it was definitely eating hamburgers that gave me eczema/arthritis/crohns disease.

The truth is, the medical community doesn't know the cause of these diseases yet, other than potentially linking these diseases to a reduction in "things for your immune system to do" due to our overly clean and sterile living conditions compared to past centuries.

The years before I developed Ankylosis Spondylitis I slept 8-10 hours a night, walked everywhere (I can't drive), ate a varied diet of food I prepared myself from scratch every day, ran an average of 24 miles a week, spent 3 hours a week in weight training, had a single sexual partner, didn't smoke, barely drank, took no prescription medications, used virtually no over the counter medicine, bathed daily, always wore clean clothes, and read my copy of Tao Te Ching every night.

Not sure what I did to bring this on myself. Must've been all the radiation from my smart phone.

So here we have two anecdotes, one as equally useless as the other for understanding anything about the way the universe works.

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