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How Gut Bacteria Are Shaking Up Cancer Research (bloomberg.com)
197 points by bookmtn on March 14, 2016 | hide | past | favorite | 119 comments



One of the ironies is that a very common side effect of standard issue chemotherapy is a marked and often permanent weakening of the immune system by altering a person's microbiome. Advances in oncology perhaps within our own lifetime will make today's treatments seem as embarrassing as medieval blood-letting.


One of the ironies is that a very common side effect of standard issue chemotherapy is a marked and often permanent weakening of the immune system by altering a person's microbiome. Advances in oncology perhaps within our own lifetime will make today's treatments seem as embarrassing as medieval blood-letting.

It's embarrassing now, never mind later. We just don't often have better alternatives than to pump already sick people full of poison in the hope that the poison kills the cancer faster than the rest of the person. It is horrible, and has (in my opinion) only improved slightly in the last few decades.


A great book on this subject is The Emperor of All Maladies, which goes through the historical development of cancer treatments. I highly recommend it to anyone with even a passing interest in understanding cancer.


My Dad was a melanoma patient. Modern chemotherapy has gotten a little more complicated than just directly attacking cells.

Modern treatments include immunotherapy such as YERVOY[1] and KEYTRUDA[2].

With that said, the side effects of YERVOY put him the ICU with kidney failure.

[1] http://www.yervoy.com/

[2] https://www.keytruda.com/


Fun fact: blood-letting is still used clinically for several forms of blood disorders. In cases of iron overload (hereditary hemochromatosis), blood is removed to maintain a low circulating free iron level. Today we don't call it "blood-letting" but rather "therapeutic phlebotomy".


> pump already sick people full of poison

I don't think it's unreasonable to ask for explanation/references/proof of what you mean when you say 'poison'. I don't know your particular experiences with chemotherapy, but I hear this soundbite parroted too often without any effort to actually research what chemotherapy is actually trying to accomplish. I'm not saying people shouldn't investigate their recommended treatment plans, but this often unwarranted suspicion of modern cancer treatment techniques is mystifying to me.


My mother has had cancer twice. My father: twice. My sister: four or five times. My brother: once. My mother's mother died during treatment for cancer. At least three of my mother's sisters have had cancer. I took care of my sister after her first mastectomy.

They do pump cancer patients full of poison. The patients know it. The doctors know it. Maybe I am a little too deep in the weeds here, but I am astonished this assertion is being questioned at all.


I think the gp just doesn't like this liberal usage of the word "poison".

Most medication is "poison" to people who are otherwise healthy. NSAIDs are bad for the stomach, pills for insomnia will make you fat, narcotics will make you fall asleep, epinephrine can stop your heart. We take them because their ill effects aren't as bad as the good they produce.

Cancer chemotherapy is mostly unique because it produces a lot of suffering to someone who appears to be quite healthy. There are other medicines with horrible side effects, but you'll usually have to be obviously sick with something like malaria in order to be treated with one of those.


it goes deeper than that because of the way our bodies metabolize chemicals we often have to pump poisons in to kill something at far greater toxic levels than to kill that thing if it was outside our bodies


Chemotherapy, for most cancers, achieves tumor shrinkage and a temporary extension of life, at the cost of severe life quality degradation. It's a tradeoff that most cancer patients think is worth it. I think that this therapeutic benefit puts us in a grey zone with regard to the definition of poison. The substances would undoubtably be considered poison in other contexts (e.g. mustard gas) but the doses are carefully calibrated to just-barely not kill a patient. Maybe "poison" is a function of usage intent?


"Chemotherapy, for most cancers, achieves tumor shrinkage and a temporary extension of life, at the cost of severe life quality degradataion."

This is just not true.

I provide you with this list of cases where chemotherapy can cure people (established in phase III double blind randomised controlled trials):

Early stage breast cancer

Early stage colon cancer

Acute myeloid leukaemia

Acute lymphoblastic leukaemia

Diffuse large B-cell Lymphoma

Paediatric neuroblastoma, retinoblastoma, nephroblastoma etc etc

Testicular seminoma and non-seminoma

Testicular germ cell tumours

Note that breast and colon cancer are among the top 3 most common cancers.


Let me revise that: for solid tumors, chemotherapy can cure people, but typically doesn't.

At one extreme, early stage (solid) cancers are primarily cured by surgery. At the other extreme (metastasis), chemotherapy is a terminal rollercoaster.

In between those extremes (e.g. some limited local progression), adjuvant chemotherapy seems to be useful for breast cancer, but has only a very small effect for colon cancer (http://www.sciencedirect.com/science/article/pii/S0140673607...) and none for lung cancer (http://jnci.oxfordjournals.org/content/95/19/1453.short).


When you say adjuvant chemotherapy 'seems' to be useful in breast cancer, what exactly do you mean? How does a meta-analysis of 20,000 patients in randomized controlled trials showing a persistent reduction in risk of recurrence and death equate to 'seeming'?

http://www.ncbi.nlm.nih.gov/pubmed/25917869


It seems like a lot of the "chemo = poison" arguments are part of an ill-informed appeal to nature. Which is an especially stupid argument considering cancer is a natural process run amok.

The dose makes the poison. Even water can become toxic with a high enough dosage. Calling chemo drugs poisonous isn't really helpful. At best, it's like saying water is wet. At worst, you wind up misinforming people and contributing to decisions that are based on bad information. The side effects of cytotoxics make chemotherapy difficult on the patient, but the alternative is a good deal worse and permanent to boot.


Which is an especially stupid argument considering cancer is a natural process run amok.

We don't actually know this. We don't really understand what cancer is. We know that in some cases viral infection is the cause of a specific cancer, but we don't really know the exact mechanism behind what makes cancer, cancer.

I am not a fan of the idea of "auto-immune disease." I think that's bullshit. I think it basically is an admission we have no fucking clue what we are talking about.

The body does things for a reason. Just because we don't understand it does not mean the body has simply lost its mind.

We fundamentally need a better mental model of these things.


You are talking about chemo provided via infusions. We are seeing increasing number of chemo in pills that are noted for being far more bearable for patients while still being effective.


I saw 'local delivery' through surgically added path ways (basically planting metal tubes through your skin into the tumor or organ). A bit violent for tissue but I bet a whole lot better for the overall system. I'm still surprised medicine didn't find a way to craft this kind of thing in a more organic way so they can interact with the tumor as locally as possible without requiring such barbary.


> I'm still surprised medicine didn't find a way to craft this kind of thing in a more organic way so they can interact with the tumor as locally as possible without requiring such barbary.

But this is the holy grail of oncology, is it not? To reach cancer cells non-invasively with spot-on accuracy so healthy cells are spared?


Sure, ability to target a bad cell and only a bad one is. There are many way, membrane markers etc. But they all involve using the main vascular system with potential harmful leaks. Now if you can create your own 'chemo vessel' to reach into a tumor. Erf sounds naive even to me now.


That's how chemotherapy works. Primarily it just kills cells. Typically it has a more potent effect on faster reproducing cells. Because cancer cells often lack the repair mechanisms and support systems of healthy cells they are sometimes more susceptible to being damaged than healthy cells. That plus the focus on fast dividing cells means that sometimes the cancer cells will die off while your non-cancerous tissues persevere and are able to recover after the end of the treatment. It's also why chemotherapy has its notable side effects though (weakness, paleness, nausea, and hair loss) because hair follicles, the digestive tract lining, and new blood cells are also targeted.


That's a neat, simple explanation. Thanks :)


It's a sound bite because it's true. That's not a reason to avoid chemotherapy--it's probably the best method we have right now of fighting cancer--but the biggest concern with prescribing chemotherapy is how much and how long can the patient sustain it, and does the benefit outweigh the costs.


Classic chemo drugs are cytotoxic which is safe to refer to as a poison. Modern targeted therapies can take different approaches


What if the side effect of the chemotherapy (on appetite, etc) were actually responsible for more of the therapeutic value than the primary effect?


The gut constitutes about 70% of your immune system. I don't have cancer (though, as noted in a different comment of mine here, many of my relatives have had cancer) but I do have a genetic disorder that significantly impacts gut function. I have done a lot of reading and self-experimentation in this area. I also have a relative who was Patient Zero in a cancer study and another relative who was interviewed on tape for two hours by a doctor and whose views and practices changed the way two different cancer clinics dealt with certain issues for their patients.

The path forward here is to come to a completely different understanding of the problem space. Allopathic meds have their uses, but it comes at a known high cost. This is why medications routinely have a long fold-out of warnings, provisos and explanations of the side effects.

We know that chemo can permanently impair brain function as well. We know that it does all kinds of bad things to the body. We also know that overuse of antibiotics both harms the gut function and promotes antibiotic resistant infections.

I think a first step in the right direction would be for conventional medicine to counteract the drug side effects after therapy is done. I have never had a doctor tell me that I should consume yogurt after being on antibiotics, though that is common knowledge in some circles. We just issue drugs and even when the side effects are known and some fairly easy counter to the side effects is also pretty well established, few doctors tell their patients "You need to undo the damage the drugs do to you and here is how."

If we at least did that much, we could ameliorate some of this. That approach is totally within reach and essentially ignored.


The pathways involved in chemo destroying fast growing cells (traditional cytotoxic CTX) are pretty well understood. It isn't dissimilar to how T Cells work in your immune system.


Well, correct me if I'm wrong: you can understand the mechanism by which the chemotherapy acts in the body, but when trying to understand the effectiveness of the treatment you couldn't really isolate the "side effect" from the primary effect in terms of its therapeutic value. Unless you had chemotherapies which were effective despite a lack of those side effects.


You can compare it to more targeted forms of chemo (for a narrow range of cancers) that don't have those side effects, and to surgical procedures. The common thread here being that killing or removing the cells remediates the problem. You can also demonstrate that other things that cause similar side effects don't affect apoptosis (programmed cell death).

I mean, it isn't like researchers pull these ideas out of thin air. Some forms of cancer are more thoroughly researched than just about any other topic in medicine.


Incontrovertible proof that we deserve to be the laughingstock of the universe.


Blood letting was benefitial, it saved many limbs from amputation. Leech releases enzyme to prevent thrombus formation. That improves blood circulation.


"Bloodletting (or blood-letting) is the withdrawal of blood from a patient to cure or prevent illness and disease. Bloodletting was based on an ancient system of medicine in which blood and other bodily fluids were regarded as "humors" that had to remain in proper balance to maintain health." - Wikipedia

I am pretty sure leeches are still used, they are highly effective for the reasons you describe, but bloodletting is a dangerous practice of trying to get rid of blood from the body to cure someone.


Just because Wikipedia says something doesn't make it true. Bloodletting was also practiced as part of Acupuncture in China - without any "humor" theory. Interestingly, when you talk to people who have actually practiced it (I was hanging out with Traditional Chinese Medical practitioners), you hear lots of stories about how effective it often is - even though it is frowned upon since it lacks any modern theory to explain why it often works. (I did recently read about how blood has been found to "group" based on characteristics. And Traditional Chinese Medicine uses various techniques to choose the location of bloodletting. There are lots of things to be discovered - or rediscovered.)


Idk about bloodletting, but Acupuncture and most if not all of TCM in general is frowned upon not because it lacks modern theory on why it works. These things are frowned upon because evidence suggests its all placebo effect and not medicine.


I guess you haven't read any of the studies of Acupuncture. The World Health Organization endorses Acupuncture, and there are decades of studies showing how Acupuncture is effective for particular problems. Some insurance companies even cover it. Similarly, it was just a few decades ago that it was illegal to practice Chiropractic, and many Chiropractors were imprisoned for practicing medicine without a license - but people slowly realized that it helps for some things. The same thing is true for Acupuncture.


I did say it had a placebo effect and yes placebos are "effective for particular problems". Other than that the science isn't as solid as you seem to think it is.. the same is true of chiropractic "medicine", homeopathy and vision quest duck rubbing.

Here is a good overview:

http://onlinelibrary.wiley.com/enhanced/doi/10.1111/j.1365-2...


That "critical review" says: "The best current evidence suggests that it is effective as a symptomatic treatment of dental pain, fibromyalgia, nausea/vomiting, knee osteoarthritis, insomnia, epicondylitis, chronic back pain, idiopathic headache, resolution of breech presentation and as an aid during gastrointestinal endoscopy" and then goes on to say that it may all be placebo effect. So the "critical review" is clearly intent on being critical. I trust that most people will have the judgment to read this "critical review" for what it is.


Yes, and I hope people read the study better than you did. It highlights how that list of false positives you listed is due to lack of controls in their trials.


I'm pretty sure jcot is aware of the problemmatic theoretical foundations for historic bloodletting, and the attending reputation that persists. However the interesting part is that it could have therapeudic uses, but physicians are understandably adverse to performing a procedure considered typical of medieval quackery.

Here's an excerpt from the BMJ:

>Bloodletting was done by the barbers in England at the request of patients and must, therefore, have had some beneficial effect even if it was just a placebo effect. It is very possible, however, that there were very real benefits in selected patients especially those in left ventricular or congestive cardiac failure. In withdrawing blood the venular outflow pressure from capillaries and cardiac filling pressures would have been immediately reduced. The pressure gradient between capillary and interstitial fluid may have been decreased or even reversed if it was elevated(6,7). A reversal of the pressure gradient in oedematous patients would have promoted the mobilisation of oedema fluid and excretion in urine provided renal function was normal. Bloodletting would also have improved capillary blood flow, which can be severely disturbed in septic patients, by decreasing viscosity and improving the rheological chacteristics.

>Repeated epsiodes of bloodletting will cause anaemia which is an independent risk factor for adverse outcome in patients with heart failure (8). As heart failure may cause anaemia by compromising the synthesis in the Krebs cycle of substrate needed for haemoglobin synthesis and blood formation in the bone marrow this risk might be a consequence of the heart failure rather than the cause. In adequately nourished and oxygenated bone marrow haemoglobin pools should be replenished by resynthesis unless the bloodletting was repeated too often.

>In the short term bloodletting achieves what the venodilators glyceryl trinitrate and isosorbide mononitrate achieve, a reduction in venular outflow pressure in capillary beds. In patients with heart failure venodilators improve exercise performance and reduce mortality (9). Whilst ACE inhibitors, angiotensin II receptor agonists and beta blockers may also decrease mortality in patients in heart failure, partly or wholly by similar mechanisms, inotropes and beta agonists may increase mortality from heart failure. These medications have not been established to improve disability-adjusted or un-adjusted longevity.

>Bloodletting might have been much more effective than venodilators and as effective as diuretics for in increasing th tone of the precapillary sphincters and establishing a pressure gradient between interstitium and capillary the excretion of oedema fluid would have been promoted. If in inducing a gastric intramucosal acidosis bloodletting were also to induce preconditioning by, for example, activating anf K(atp) channel, bloodletting might even have had extended benefits not seen with medical therapy. [1]

I wouldn't agree that patients' requests meant that it must have been beneficial, since people willingly do all sorts of crazy things to their bodies based on the most tenuous new age theories. It also doesn't make sense that regular bloodletting would be beneficial to an already healthy subject, since we'd presumably have evolved with a mechanism to dispose of excess "bad humors". However, as an alternate mechanism for achieving results that treat a condition like congestive heart failure, it seems a lot like drilling a hole in your head to treat a head injury — ridiculous sounding, but effective in certain cases.

[1] http://www.bmj.com/rapid-response/2011/10/29/treating-heart-...


That article gives no hard evidence that bloodletting is actually beneficial for the treatment of anything, correct? Observing that some tiny subset of the many things treated with bloodletting can be helped by something that shares some things in common with bloodletting -- but with no evidence that even then the benefits are wouldn't still be swamped by the large negative effects of bloodletting -- is not impressive. Nor is pointing out that some current medications haven't been shown to be beneficial in some situations.


> Blood letting was benefitial, it saved many limbs from amputation.

What is the evidence for this?

I'd say, in contrast, that chemotherapy is analogous to amputation. Both are crude and horrific treatments, but both have and are used with strong evidence that they are beneficial to the patient. Bloodletting, on the other hand, has only weak theoretical arguments that it may have been very slightly useful in a tiny minority of cases, but was definitely ineffective or harmful in the vast majority of cases.


Funny how many 'stresses' trigger beneficial reactions.


Until then, let the blood run.. :(


it's fun, to think of what practices today will seem barbaric or primitive in the future.

surely all "modern medicine" will fall into that category.


It's interesting to think about how much of those changes will be due to new technology enabling new ways of doing things and how much will be due to simply superior knowledge. Consider, for example, what someone going back in time to the early 19th century or earlier would be able to improve just by giving instructions, assuming they'd listen. Pasteurization, sterilization, hand washing, the germ theory of disease, etc, etc. Even things like blood type and how to do transfusions effectively.

I suspect that in the future there will be a few "boil water" or "wash your hands" type lessons learned that will affect how we do medicine that aren't dependent on futuristic technology.


I strongly hope they will be seen as primitive. As for barbaric, I don't think so - our medical practices are based on (mostly) solid peer-reviewed studies and statistics, so at least we know that they do work, albeit in some cases definitely not enough.


To take a devil's advocate to that, there's not a lot of evidence that much of modern medicine is that helpful. I read about a study where people were given health insurance didn't do better than those without it, even though they went to the doctor far more, got better treatments earlier, etc. Another study that most surgeries weren't better than placebo surgeries. And we don't even test surgical placebos yet. And then another study that a significant portion of deaths were due to hospital errors.

Of course that's ignoring that there is a lot of medicine that obviously does work and is great. No one is going to dispute that antibiotics are literally the greatest thing ever, or that insulin saves tons of diabetics, or that cancer treatment has saved a lot of lives. On the other hand some things we do are quite horrible, like keeping old people alive long past the point it's worth it. Or not cryogenically preserving everyone because it's "weird".


Great book on the history of pre-antibiotic medicine is "Devils, Drugs and Doctors" by Howard Haggard, available online here: http://www.unz.org/Pub/HaggardHoward-1929

As I recall, you could boil down medical progress up to the publication date as "discovery of germs" as in "washing hands," "cleaning things," "vaccination," "isolate people with plague from the well" and "don't drink water you pooped in" -and the discovery of anesthesia, which made complex surgery possible. I'd say antibiotics is the main further improvement.


This assumes our future doesn't involve a global collapse of society.


Disappointing to see a complex field summarised in this fashion. For some reason, ill-informed individuals love to adopt extreme views about cancer therapy and air them in public. This is totally irresponsible, and I hope nobody making decisions about cancer therapy reads this. For example:

1. 'Weakening' of the immune system is the wrong idea. Preclinical and clinical studies have shown that there is synergy between the immune system and chemotherapy, and also between the microbiome and chemotherapy. For some cancers, combining modern immunotherapies with other treatments including chemotherapy is likely to be necessary to achieve the best outcomes.

2. Your analogy to medieval blood letting is totally ridiculous. The chemotherapy used today has been carefully studied in randomised controlled trials with many thousands of patients. These patients have been followed up for many years with meticulous documentation of early and late side effects, disease outcomes and patient reported quality of life measures. This information is invaluable to patients who have to make decisions about the pros and cons of cancer therapy.

Is chemotherapy pleasant? Definitely not. Do some people experience terrible side effects that may be permanent and life threatening or even fatal? Yes. But it saves lives, and it comes with a host of supportive therapies designed to make the process as tolerable as it can be.


Unrelated gut flora personal story:

Few years ago I was in bad health. Got sick 4 times a year had a lot of pain going to the bathroom and was in a general state of depression. Started taking probiotics in 2 weeks I felt happier and my over all health improved. Did some research and found that it is estimated that 90 percent of the body's serotonin is made in the digestive tract. Who knew, get your body right added some probiotics in your diet.


Another piece of anecdotal evidence. My wife has had allergy attacks constantly for years and years. Every morning she would wake up and have to blow her nose for a half hour. We started making fermented food (saurkraut, pickles, fermented garlic carrots) and at the same time buying/drinking keefir daily. This was just to be healthy and as a new hobby. However, within a week or two, her allergies subsided substantially. To the point where she would go for weeks at a time without having the morning nose blowing session. When she dials back the intake of fermented foods, allergies come back.

We haven't spent much time tracking it closely, but the relationship is obvious enough to be a no brainer for us.


I've heard stories like yours, witnessed a few myself, and have noticed changes within myself as well. Yet no matter how many times I tell people they look at me like I'm an idiot.


I sincerely hope there will be more research into this in the coming years. The problem I think is that we need to do more personalized research and experiments, but somehow figure out the baseline to compare individual results against. Someone who has a system with X properties will respond differently from someone with Y properties, and we don't know enough about those properties to understand the different response types.


That reminds me of the 'hookworm' therapy to help alleviate allergies. http://www.nytimes.com/2008/07/01/health/01iht-01prof.141229...


Thats... really interesting.


Do you have recipes for the fermented foods you make. I'm thinking of trying some for my own health issues.


I really appreciate you posting this and am going to try it.


You're welcome. I almost feel backwards when I tell people about it, but the results are obvious (to us).


Thank you for this note, I will recommend it to someone close to me who has the same symptoms as described.


You're welcome. She's just been following the serving size on the bottles from the healthfood store on the keefir (usually half a bottle a day), with some other random fermented foods thrown in (shredded carrots + garlic, ginger is one of my favorites)


It's really timely information - my girlfriend who has the health/immune issue was just making "Korean carrots" which are shredded and, I believe, fermented or at least pickled (not sure if that's the same). I bought her a bottle of kefir too, it's a popular and commonly sold product here in Central/Eastern Europe.

Funny thing, she once went through a phase of making home-made yogurt and also bought some kefir "seeds", little white blobs of culture. I saw that it's quite simple to multiply/generate a regular home production, so I'm going to recommend that she start the hobby again, for improving her health and immune system.

The issue you described of sneezing and stuffy nose every morning affects quality of living, and I hope fermented foods can help clear it up.


A quite note on pickled vs fermenting: pickling usually refers to a vinegar solution that preserves but isn't fermented (so it isn't a live culture). Fermenting is usually just water and salt, promoting the lactobacilus in the air and slowing down everything else.

I wish you the best! Gut health is important, and very much still a black art.


I see, good to know about pickled vs fermenting, I learn something new every day.

Another thing we're trying with regards to allergies and other immune issues, is medicinal mushrooms. But that's a whole topic in itself and maybe only tangentially related to gut flora.

It's fascinating the medicinal/curative potential of bacteria, molds and fungi. The posted article mentioned 100 trillion microorganisms in the human microbiome, that's astronomical.


whoa - I've recently had that problem start happening. I'm going to go build some more anec-data.


I'd love to see any results that you may have. Especially if you figure out a good way to track it.


Similar story about gut health rabbit hole and profound quality of life improvement after understanding gut serotonin... I took 23andme and found out I had HLA-DQ2.5 (Celiac gene) making my risk of developing Celiac around 10% (as opposed to near 0% if you don't have it - everyone with the gene cannot process Gliadin, a wheat protein, Celiac is just the most severe set of symptoms).

Before this point I was highly critical of people with pretend/made up food sensitivites and ate anything I wanted on the basis that if there was a problem my doctor would tell me. Recently (a few months ago) I stopped eating wheat as an experiment as I had some Celiac-like symptoms showing up more and more. It changed my life.

76% of people with this gene who are not diagnosed with Celiac yet and consume wheat have a serotonin-based psychiatric disorder because the undigested wheat starts acting negatively on the serotonin system, making you volatile and anxious. My diagnosed Generalized Anxiety Disorder took a matter of weeks to disappear.

Genetic self awareness and choosing your foods carefully cannot be overstated as a means to improved quality of life.


To what extent did you stop eating wheat, out of interest? I seem to only be affected (digestive problems) by products that are literally made out of wheat flour (bread, pasta etc) and things that "contain gluten" have no discernible effect on me. Have you needed to go "gluten-free", or just avoid obviously wheat-based foods? Trying to avoid everything that has gluten in it does not sound like a fun way to live.

I'm considering trying to cut out wheat-based foods to see how it affects my anxiety, but it'd be good to know whether just cutting out obviously wheat things is pointless.


I basically got rid of all of it at my house but none of the crazy stuff (some people replace their cookware, etc. I think that is a misunderstanding of the problem).

I notice when restaurants use it but it doesn't really ruin my life or make me descend back into bad health. I just notice I am more anxious/blood sugar volatile for a few days after. So I avoid obvious large sources of wheat, but I accept that restaurants regularly use it in sauce, etc. and it causes noticeable but manageable issues.

I have the heterozygote version (1 variant of HLA gene) rather than the homozygote version (2 variants of HLA gene) so it is less severe and only affects some of my cells. If you have both variants, your risk of Celiac goes to about 50% and you normally find out early in life.

I would also confirm it is not some other category of food sensitivity affecting you - my fiance went through a similar process and found some links to IBS which leads to a low FODMAP diet. Wheat is a FODMAP but other FODMAP foods affected her also where for me it is 100% wheat.

TL/DR: obvious wheat things is a big step, I noticed difference in anxiety, skin health, brain fog, focus, migranes, sleep. 80% of those issues for me went away by getting rid of obvious sources at home.


Glad that you found what worked for you, but I find it strange that people would be distrustful when people say they have food sensitivities. Even if it's made up what does it matter? Nobody really has a say over what another person puts into their body (unless infirm, under doctor's care, or young/baby). I find this "if you don't have a doctor's note you have fake food allergies, you're just picky" idea really insensitive.


For me, it was a fear driven response to anti-science rhetoric. I think anti-vaccine narrative really convinced me the extent to which people act irrationally about personal health. I observed parents self-diagnosing their children with all kinds of made-up conditions solved only by avoiding certain categories of food like GMOs.

As someone with immediate family members with autism, people claiming that removing wheat and dairy from their child's diet would "fix" their "autism" was offensive to me. I trust doctors for the most part to be a superior model to the mommy blogger/anti vaccine crusade. GMOs are another example of misinformation and fear mongering trumping science.

I have since learned the value of genetic self awareness and how little we understand about health and diet issues, especially chronic ones, and so have reversed my position towards people with food sensitives, made up or otherwise, to empathize with the fact that we probably don't understand a given issue well enough yet to fix all of the eating problems people have and so people can do whatever they want.


Out of curiosity, which ones do you take? I've been taking them for a few years now and have had similar results as you, although it took a while to find a combination that worked for me personally.


General Biotics: http://www.generalbiotics.com/

Real science behind the strains they choose and I've never seen a probiotic with more of them (115 different bacteria).


I've had those. I think they improved my digestion. I have had IBS-like symptoms for years. For a while it was diarrhea. Then it switched to constipation. I could go to the washroom only with coffee.

Starting taking these, suddenly was able to use the washroom normally. No coffee needed, finally quit that. No diarrhea.

It's been about three weeks. So I doubt it's a coincidence. In a span of that length I would have had multiple problems in the past. Only alternate cause I can think of is that I was reducing coffee before I took them, but still drinking decaf. However, digestion had been entirely the same during this reduction process.

And I was on the pills + coffee for about 10 days, with improved digestion, so I suspect the pills.


Their CEO posted some HN comments in the past: https://news.ycombinator.com/item?id=8600201 I'm waiting for them to post the results of their study.


For me (Colitis), they made me worse. I had tried many brands, then settled on GB for like 3 months, I kept records, they made it worse. Within two weeks of stopping my symptoms improved.


It sounds a little bit disgusting, but have you heard of fecal transplants? I've read that this can help people with clostridium difficle infections if antibiotics don't help (which is kind of 'funny', because patients seem to get clostridum infections after antibiotics therapy...) and research is going on if this can also be used for treatment of colitis and morbus crohn (but I don't know more than that, maybe you can find already published study results about that).


yes, FT sounds like a good idea if done by pills

BTW antibiotics is usually the cause of C. Diff and can be a cause of other bowel diseases


The various Ultimate Flora brands are excellent. They are expensive and you can get them at whole foods. The trick is to get multi-strain LIVE species. Refrigeration seems to help.

Many probiotics are labeled as "active". I think this means they are dead but the remaining proteins are "active". They'll only last as long as proteins are available. The industry really needs to clarify this stuff. Independent evaluators need to check out their claims.

Live strains will reproduce.

There are many tricks to get them to survive the stomach acids: imbed them in gelatin or psyllium. Another trick is to prefeed them in airtight, dark bottle so they're growing before you eat them. Just put it in your pocket for a couple of hours.

Clinical trials need to be done to firmly establish efficacy; but I've given this concoction to several people and they were very happy with the results.

More research needs to be done on which species of fungi, bacteria , and arachea give good results.

The gut microbiome is an interdependent environment. Restoring the balance occasionally may benefit lots of folks.


  Many probiotics are labeled as "active". I think this 
  means they are dead but the remaining proteins are 
  "active". They'll only last as long as proteins are 
  available.
Incorrect. Probiotics are supposed to contain live, active bacteria: the large "CFU" number on the front stands for "colony forming unit": https://en.wikipedia.org/wiki/Colony-forming_unit

Labdoor (which is advertising-supported) tests probiotics based on how accurate their CFU numbers are: https://labdoor.com/rankings/probiotics (These tests, of course, don't say if the probiotic in question is actually good for you or not.)

I've taken both General Biotics Equilibrium and (115 strains, 1 billion CFUs, shipped unrefrigerated) and Renew Life Ultimate Flora Extra Care. (10 strains, 50 billion CFUs, refrigerated)

If either of them had any effect at all, I didn't notice it.


Thanks for the clarification and the link. Not surprising to see Ultimate Flora at the top.

I'd bet that a lot of these species die on the shelf.

The industry might still benefit from consistently labeling as "live" on the bottle if the probiotics are live.

I suspect that not everyone has an imbalance that would benefit the user.

A good strategy might be to try various species until something works.

An over the counter "23 and me" for gut species genomes assays might help; but that's a few years away.


  An over the counter "23 and me" for gut species genomes 
  assays might help; but that's a few years away.
Nope, here today.

http://ubiome.com/

Costs $89.


Again. Thanks. Anybody tried this?


yup, not a bad report. I've used American Gut as well, a project from the University of Colorado at Boulder. Concordance between the two results was decent.

I'm not sure I got a lot of actionable information from either, though. Certainly not as much of detailed interest as from the 23andme data.


Out of curiosity, which ones have you taken?


Not GP, but these have worked for me:

L. reuteri ATCC PTA 6475[0]

L. reuteri DSM 17938[0]

Lactobacillus reuteri Protectis[1]

[0]- http://www.amazon.com/gp/product/B01AH3RT9Y

[1]- http://www.amazon.com/gp/product/B001XUQNN4

I was taking others too, as well as some prebiotics but I stopped for awhile and been taking these two again for about a week and already feel much better - at least as good as before when I was taking more.


Out of curiosity, mariodiana, do you take probiotics? If so, which ones?


Ha! No, I don't.


The serotonine in your body isn't able to cross the blood-brain-barrier. So it doesn't affect your mood the way brain-serotonine does.

It does affect blood pressure and a few other things, so you get indirect effects.


That assumes that consciousness only correlates to brain activity, which is unsubstantiated


No, GP's statement assumes only that serotonin in the bloodstream outside the brain has different effects from serotonin in the brain, so let's put that lid back on that kettle of fish.


You don't have MTHFR by any chance do you?


Incidentally, one of those gut bacteria, helicobacter pylori is the leading cause of gastric cancer in the world (and maybe even a deterrent of some forms).

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952980/


Alternative to expensive probiotic supplements: fermented foods. It is easy to:

1.) Brew your own kombucha

2.) Turn milk into kefir

3.) Make your own sauerkraut.

I do all 3 of the above, feel free to email me w/ questions!


Also Kimchi! My gf and I make kimchi about once a season (in a large Chinese ceramic fermentation jar). It's a great ritual; it takes a few hours but is very enjoyable... every batch comes out unique, and the result is delicious.

Or, if you're in a hurry: make pickles. All you need is salt and water (vinegar-based pickles are not actual ferments).


Good point! I've been meaning to make Kimchi but unfortunately my gf hates the smell so much that she's banned me from making it...

Another (banned) item on my list is homemade natto... (https://en.wikipedia.org/wiki/Natt%C5%8D)


One of the best fermented foods to have is the South Indian Breakfast of Idli( Iddly).

This batter can be bought in Indian Grocery stores or prepared at home

A similar batter is used to make Indian pancakes called Dosa as well.

There are also a host of Appams & String Hoppers made with different fermented batters in South India and SriLanka.

In addition many South Indians enjoy fermented rice which is basically leftover cooked rice that gets soaked in water and left overnight. Its a staple breakkie or Lunch for many poor families with some Yogurt, pickle, chutney or a green chilly.

1. https://www.quora.com/Is-idly-truly-the-healthiest-Indian-br...


Idli isn't probiotic unless you eat the batter raw though.


Why would you make your own vs. buying it from a shop?


For me it's a fun hobby. With that said, as a software developer making $XXX,XXX per year, your time is worth more than the money you save by DIY. So it's up to you.

The final caveat is that w/ milk kefir in particular, the stuff you buy in the store is different that making it yourself. Commercially made milk kefir is inoculated w/ ~7 specific bacteria strains whereas homemade kefir is made with kefir "grains" --- a symbiotic culture of 40+ different strains. Interesting scientists have not been able to directly synthesize kefir grains in a lab due to how complex the symbiotic ecosystem is. All Kefir grains around the world today are from other grains stretching back thousands of years to when the first grains were discovered (people suspect in the digestive track of a ruminant).


Because it's very easy, fun, and much cheaper. Any geek or hacker should find fermentation at home rewarding.


I've done 2 & 3. What's the best way to go about doing 1? Pointers to a good guide would be much appreciated.



Brewing Kombucha is insanely easy. Way, way easier than beer or anything else.

1. Buy a large glass dispenser with a stainless steel spigot at the bottom (this is important and will make life WAY easier).

2. Buy a Kombucha starter kit online or locally. I usually use green tea as my base. I buy my kits from Amazon and they come with the scoby (mother) and tea bases. Some come with glass jars, etc. I'm looking at them now and there are a LOT more options than when I got into it a few years ago.

3. Cover the top with cheesecloth so it can breathe. Make sure mold stays out. If you get mold toss the batch and start over. As the scobys grow and break apart and you drink (using the spigot at the bottom) they float to the top, with the bottom spigot you can easily pour without having to move the scoby out of the way.


How do you tell the difference between mold and scoby? Is the mold black or dark?


I haven't brewed it in a few years, but my first batch ever wound up getting mold in it. I'm not really sure why, or how, the rest of my batches were fine.

It was very obvious, it looks like just the white/green mold that will grow on top of a drink if you leave it out.

edit: Oh, the scoby is always obvious, it's basically a gelationous alien looking thing that should star in Xfiles. Every few weeks the scoby will split off and you'll have multiples, you take out the second one and can give it to someone else or make a new batch.

https://www.kombuchakamp.com/wp-content/uploads/2012/04/5-Si... -- the white thing on top with "laywers" is the scoby. The layers detach every so often and become independent.


Smell is supposed to be a big clue as well. Kombucha generally does not smell nasty (sulphurous): http://www.naturalkombucha.com/how-to-tell-if-kombucha-is-sp... .


Realistically, what are the chances of bad bacteria being generated with these made at home ?

I understand the benefits, but when cultivating any bacteria, how do you know what you've made without lab testing ?


It's relatively low. The fermentation process tends to increase acidity and lactobacilli then out-compete other bacteria in that environment. That said, the advantage of fermentation in terms of food safety is that in general if you have a batch turn on you, you will know it. Anything that would make you sick you would not want to put in your mouth in the first place. (Unlike, say, meat, where you can have a perfectly tasty piece of meat that will still make you violently ill.)


the wiki on kombucha is rather scathing indicating that its therapeutic benefits do not outweigh its potential risks.


Made me wary of it being mostly a blind trend.


oh nice. Saw the kefit suggestion above by someone else but don't get along with dairy so will give the other two a try. Will shop bought sauerkraut work? e.g. In a glass.


Some people make kefir with milk substitutes like coconut.


Interesting. Pure coconut juice is reasonably easy to obtain here so that might be feasible.


Wow, kefir made with coconut? That sounds wonderful, I'll have to read more on that.


Just wait till the same damn companies who have been piping out antibiotics start patenting bacteria.


I don't see why people blame companies for this. Don't hate the player, hate the game. If you give the government the power to provide people with monopolies of ideas companies will fight for that power. If they don't, someone else will.


My comment was bitter, but it wasn't so much about blame or hate as it was about deep frustration.

While I acknowledge that this is a systemic issue, it's an individual ethical issue too. There are individuals lobbying for the power to own entire species. That powerful people seriously think this way, let alone act on these beliefs, leaves me bewildered and upset.

Beyond that, the player and the game are inseparable. The player you talk about, playing "the" game... they are playing a game. There is not one game. In the game I aspire to play, his rules are cheating. Now, I can't blame him on a human level for doing what his life has led him to do, for believing what his experiences have led him to believe. But I have extremely serious doubts about the consequences of this sort of belief system. In my worldview, this is a kind of fascism extended into the microbiological scale. That might seem far away, be we are entirely composed of microscopic ecosystems such as the ones that this "player" wants to insert his or her manipulative, magical control mechanisms into.


"To therapeutically influence the microbiome long-term in humans is a big hurdle," said Sander van Deventer, managing partner at venture-capital firm Forbion Capital Partners. "The microbiome is very stubborn. Everything we’ve done so far has only had a temporary effect."

I am guessing they are looking at one shot drug therapies. This is totally doable if you make dietary and lifestyle changes and are persistent. Yes, actually moving the numbers (so to speak) is tough going, but it can be done.


Obligatory xkcd comic: https://xkcd.com/1471/




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