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Gut Wars: One Man's Adventure with Antibiotics and Ulcerative Colitis (ubiomeblog.com)
60 points by accarmichael on May 1, 2015 | hide | past | favorite | 32 comments



Looks like a candidate for a fecal transplant:

http://www.mayoclinic.org/medical-professionals/clinical-upd...

Most facilities do it the fancy way (use a tube down the nose or up the rear), run tests and, as usual, charge you and your donor out the a! But I've read of DIY'ers who simply spun out the solids, held their nose and swilled the goods(I suppose a real man would use a spoon) or took them in an enema:

http://blogs.plos.org/publichealth/2013/05/29/why-diy-fecal-...

http://www.bbc.com/news/magazine-27503660

Either way it works.

"Compatible" donor? Healthy family member(s).

As the author of the article notes, probiotics can't possibly match the variety of organisms that a typical human has in their gut.

Business proposal: a repository where people deposit feces prior to taking strong antibiotics, so that, should they find themselves consequently absent intestinal flora and fauna, those could easily be restored. Kind of a new twist on the old curse "Eat shit and die!"


Talk about making a "back up". The possible vowel deficient start-up names for this alone are amusing me greatly.


I can sympathize with him. While my issues didn't get as far as his, my issue resulted from taking Cipro which killed all the good bacteria in my gut making room for something else to move in. Sadly what moved in was related to dogs feces as I have a pair and you don't have to see it to get contaminated.

End result, new drugs to wipe out the bad then a few months with specific medications and kefir and related food products to rebuild the bacteria in my gut. It is no fun planning any drive, even to work, where the primary issue is knowing who is open and has public bathrooms


Reading this makes me feel really fortunate. I had a bout with colitis, but the doctor prescribed me Cipro and it went away with no other side effects.

As an aside, even talking to the doctor made me immediately feel better. Being a pessimist, I assumed the worst and was already planning out my will. This doctor, who looked like Gene Simmons, asked me how many days off I wanted from work, and told me "You gotta take it easy, bro" with a jerky boys accent, he completely snapped me out of whatever I was going through with his amazing personality.


I think a key component often missing in these discussions is creating a habitat where good gut bacteria can thrive. This article identifies having fiber a critical to maintaining good gut bacteria. http://www.scientificamerican.com/article/fiber-famished-gut...


I'm always happy to read this kind of articles. I have a history with C. ulcerosa myself (now under control) and since it begun my gut just hasn't been the same. I am pretty sure my microbiota was left in a very bad shape after some hard periods, and since then I have tried to bring it back to balance... but it seems a hard task. I haven't tried probiotic supplements, like described in the article, but just tried to include probiotic-rich food in my diet, like yogurt and sauerkraut, and also prebiotics like bananas and honey. So it would be just great to get exactly the combination of probiotics-supplements that one needs, based on this kind of uBiome test, and then just wait until you have a balanced microbiota again. But for what the article describes, we would have to wait a bit until the real effects of each particular probiotics-combination are understood.


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

David frequents HN (which is how I found it) and he even took the time to personally answer questions for me via email.

There is no probiotic on the market like it and it is based on real science.


Wow, thanks! It looks very interesting. I had never heard of it :)


Any recommendations for probiotics? I've tried a couple with no luck myself.


I think you are better concentrating on natural prebiotics, by eating lots of fruit and vegetables. Apples in particular are meant to have very good prebiotic properties.


Thanks, and I do love apples. Any good literature that you have read on the topic? I'm interested in changing to a more probiotic friendly diet.


There is this study:

http://www.sciencedaily.com/releases/2014/09/140929181156.ht...

Although it is looking into obesity, they did find that apples restored abnormal microbiota.

I suffer from mild IBS myself, and find that eating an apple a day seems to help (although it's impossible to know for sure without doing a double-blind trial on myself).


I like General Biotics[1]. It has 115 strains which is an order of magnitude more than any other supplement. One of the founders is a researcher in the field published in all the big name journals. They don't make claims that can't be scientifically supported, unlike most health supplement companies. Highly recommended.

1: http://www.generalbiotics.com/


I had good experience with the Trader Joe's Milk Kefir.


Sauerkraut is a good option if you like actual food.


And if you've never made, and eaten, homemade sauerkraut, then let me tell you: you're missing out.


I love Sauerkraut on a good sausage. Do you actually eat it on it's own?


A beet/cabbage mixture sauerkraut is DELICIOUS to eat on it's own.


Pretty good as a side dish.


I've used this in the past:

http://www.amazon.com/dp/B00SXBWDOY

Seems to work. My wife uses it regularly. Just a couple of data points for what it's worth.


I would first do some research on probiotics. From what I've seen, the only proven benefit came using them ina very certain situation which I forget completely (it was something like it helped clear up diarrhea after an antibiotic quicker or something like that). My point is they aren't cheap and you could simply be wasting money. I'm honestly not informed enough either way, but when I looked into them a few years ago, there was little to no proven benefits of using them.


Well, since TFA is specifically about post-antibiotics gut problems, the commenter is in a good place to be asking for information.


Since this isn't the first time UC has come up on HN (are programmers more prevalent maybe?), may I ask for a quick show of hands of people that have UC or had UC and if you've managed to beat it then how?

Me, I've had UC since 2012. I take Pentasa 2mg granulated mesalazine per day. I am an ex-smoker and internalize stress. My UC is definitely exacerbated by poor sleep and high stress. Antibiotics were also what started me off on this horrible disease. I'd love to get rid of it.


Wouldn't this be a great case for fecal transplant? I have to wonder how effective oral probiotics can really be, give that the oral route includes an acid bath on the way to the intestines. Seems that a fecal transplant would get the desired results near-instantly.


The obvious importance of gut bacteria is the health-news flavor of the month, but I don't know. There are definitely two sides to this debate. On the other side some very smart people with nothing to sell (probiotics/prebiotics/tests) argue for a relatively sterile gut. They say feeding gut bacteria with fermentable fibers/starches in general generates LPS and other stressful toxins.

Some lab experiments definitely bear out this idea. Animals with sterilized guts fed sterile diets live way longer, and are stronger/healthier.

Like I said I don't know, but I advise extreme caution on this stuff where there's any tangential connection to probiotics/prebiotics/tests.


Disclosure: I work for a microbiome biotech company. I have no connection to ubiome.

I'm sure this commenter means well but this person is severely misinformed. Any person with even a minimal understanding of our gut microbiome would never argue for a relatively sterile gut. We rely on out gut bacteria to digest foods and there is a healthy, normal exchange of metabolites between the microbes and our bodies. Microbes digest foods such as fiber and starches into (for example) short-chain fatty acids that have been shown to have beneficial effects on our bodies. They also prime our immune system so that we are better prepared to combat invasion of potential pathogens. LPS is a necessary component of all gram negative bacteria. Many of our commensal bacteria are gram negatives. The problem with LPS is when it gets to places where it shouldn't be (e.g. crossing our gut epithelial barrier).

Some labs utilize germ-free mice to investigate the causative role of the microbiome on the host. While these animal models can serve as great systems in which to investigate certain hypotheses, every germ-free model researcher would no doubt agree that the immune system of germ-free animals is completely different and severely compromised compared to a normal, conventional animal. They, in fact, do NOT live longer and are NOT stronger/healthier.

I felt that the above comment needed to be rectified before people starting actually believing it.


Let me boil down your essential claims:

1) Bacteria in the gut make stuff you need and helpfully digest things for you.

2) Endotoxin is only a problem when it crosses the gut.

3) By various magic bacteria in the gut strengthen the immune system.

Well #1 just isn't really true. There aren't any identified compounds that are at all hard to get from food that you need gut bacteria to make for you. Maybe some vitamin K and that's about it, but a serving of liver or some other foods will more than cover your vitamin K dose.

#2 is a silly argument because endotoxin is constantly crossing the gut barrier. LPS endotoxin is a continuous stress on the liver to detoxify. Whether it's a real problem in an otherwise healthy individual or not is a separate question, but the argument presented here is totally specious. It is quite plainly a continuous stream of toxic material the organs work to clear.

As for #3, that's the big totally open question I guess. You see the claim made but nobody ever really breaks it down in detail in terms the experimental physiology proving the idea. It's usually some eye-roll-worthy trials.

The fact that the sterile rats can't survive outside the lab environment is not the point. No kidding they have under-trained immune systems. The point is that absent the chronic stress of bacteria load they do in fact live longer and are in fact stronger in the literal definition of strong. This guy is being deliberately hand-wavy.


Look you're being just as hand wavy, and your sterile gut idea is a bit of spherical cow. We will never be able to sterilize our environment to the point where we can easily maintain a sterile gut. No one fully understands the human microbiome, including you.

Are there any case studies of people maintaining a sterilized gut and living healthier lives? Therapies like fecal transplant or helimintic therapy actively introduce third parties into your gut with positive outcomes. Which at least suggests that bacterial balance in the gut is important for some people.


Sterile/non-sterile is a bit of a false dichotomy. The practical choice is between species you can live with... and thing's you can't.

This also applies to larger biomes.


Can you point to any of those smart people who argue for a sterile gut? I have honestly never heard that, and I've been following news / research (on a surface level) for a couple years.


I would also like to know what that was in reference to. Talk about vague, unspecified "toxins" tends to trigger skepticism on my part (but I suppose "LPS" is something specific I know nothing about)...


I agree with you that there probably are a lot of non-scientific arguments coming from probiotics/tests vendors but your statements about sterile guts is weird and is in direct conflict with the information taught at universities world wide. Care to elaborate?




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