How can I rebuild my gut biome?

November 12, 2015 10:11 AM

While living overseas for the past two years I went through two different rounds of antibiotics, which were generally handed out like candy. After reading this article about the damage antibiotics can cause to the gut biome, I'm wondering how I can rebuild my gut.

I've been suffering from mild stomach acid problems for almost a year, but am hesitant to keep taking string antacids because of the potential for chronic liver disease.

posted by mecran01 to Health & Fitness (14 answers total)

The current conventional wisdom is prebiotics and probiotics.

But the actual medical theories and research behind that are still fairly early-days, and the probiotic market is still mostly in the "nutritional supplement" phase.

But you can do some reading and maybe make your own decisions about if and how to proceed. There are, of course, all kinds of semi-cults and woo-vendors deeply invested in the topic.
posted by Lyn Never at 10:27 AM on November 12, 2015 [1 favorite]

You may want to get tested for H. pylori infection at your PCP. This is a very common bacteria that is more commonly found in more developing nations and is one of the leading causes for acid reflux and ulcers worldwide. Treatment would be another round of antibiotics, but letting this infection go without treatment is even worse, and can put you at risk for bad ulcers and even cancer if left for years.

Regarding your gut microbiome, you can get over-the-counter probiotic pills that contain some of the most common "good" gut bacteria that may help to bring that back to balance.
posted by i less than three nsima at 10:28 AM on November 12, 2015

I take the VSL#3 probiotic daily at the recommendation of my primary care physician to assist in the control of ulcerative colitis. (I also take Lialda and 6-MP.) My local Costco carries it; it must be kept refrigerated. She recommended it because it has been subjected to double-blind, placebo-controlled studies.
posted by apartment dweller at 10:41 AM on November 12, 2015 [5 favorites]

Here's a list of microbiome-friendly foods. They are high in prebiotics - inulin and polyphenols.
posted by lizbunny at 11:07 AM on November 12, 2015 [1 favorite]

Coming from the Ancestral Health camp (see Chris Kresser, Stephan Guyenet, Robb Wolf, Sally Fallon, Mat Lalonde), you would hear various recommendations to avoid gut irritants such as grains, legumes, dairy, sugar, plus eschew grain-fed meats and low quality oils high in Omega-6 in favor of Fish, Olive, Avocado & Coconut/Palm Oils. Bone broths, fermented foods and grass-fed meats are applauded (and nutrient density is king). Everyone's gut health mileage varies in response to these different additions/eliminations to/from the diet.

In addition to prebiotics and probiotics (I use Jarrow products because they're affordable), I am hearing a lot of buzz around RS - Resistant Starch - commonly found in cooled rice and potatoes.

As they say above, you can do your own reading and tinker around with various recommendations to see what works for you. Different programs like the Whole 30, and Chris Kresser's "Personal Paleo Code" could give some structure to your tinkering. Good luck!
posted by phreckles at 11:26 AM on November 12, 2015 [2 favorites]

Personal speculation from a biomedical researcher (I don't work on this topic but I submitted fecal samples to uBiome and sometimes read about it for fun): the measure being studied and discussed in that article is microbiome diversity. Your mouth rebounds better than your gut because it's easy to introduce many new types of bacteria to your mouth after a course of antibiotics. Most of bacteria you put in your mouth don't survive the trip to your colon, and/or aren't suited to live in your colon anyway. This is part of why fecal transplants are a method of choice for trying to restore flora in the colon after C. Diff infection, as opposed to just taking some probiotics orally. The other reason is that a poop slurry has a ton of different bacteria - hundreds or thousands of different kinds - whereas a commercial probiotic might have 12 different strains at best.

Maybe it's because they give me terrible gas cramps, but I don't buy the whole prebiotics thing. If you've killed off 90% of your flora (by headcount) and now you have fewer bacterial strains in your gut (by # of species), adding more Microbe Chow isn't going to do a damn thing to increase species diversity - it'll just feed the species of microbes you've already got. If you're hoping to increase diversity (and the evidence for diversity having a direct positive improvement on your health is... highly speculative, at the moment, but fascinating to talk about), you have to add more species into your GI tract. From one end or the other.

I am not your biomedical researcher, and I am not advising to stick stuff up your butt.
posted by deludingmyself at 12:18 PM on November 12, 2015 [15 favorites]

Best answer: Probiotics are interesting, and there's a lot of clinical research supporting their potential, but that doesn't translate into a trustworthy market. They're considered supplements, which aren't regulated as medicines and therefore can make wildly unsubstantiated label claims and/or not contain what they profess to contain. You should know, up front, that advocates pushing a particular product or food solution are toeing the line where questionable capitalism ethics, consumer fraud, and light quackery meet. I work on this subject as a part of my day job from the scientific side of things, but this is also a very current issue being sorted out in the courts (example). The US FDA is also revising its approach to the kind of data that companies must provide to substantiate the safety of food additives and the relevance of supplement label claims, so expect the market to change significantly once that process translates into new formal FDA guidance on probiotics (this revision only started in 2014 so it'll be 2017 or later before the regulatory system even pretends to have caught up).

The simplest way to get regionally-relevant gut flora back into your system is to consume regional produce (e.g. go to the farmer's market in your town, get some carrots or whatever, scrub and eat; repeat). The list of microbiome foods linked above is reasonable and interesting place to start, but by no means complete or even necessarily relevant to your diet/region.

The tough answer here is that gut flora can take a very, very long time to repopulate and stabilize with appropriate representatives from the appropriate bacterial superkingdoms. We've understood this for some time, but we're still getting into the details in a clinical sense just now. You can read (much) more about that through the NIH Human Microbiome Project.

All that said, commercial probiotics most likely won't do you any harm so you can feel reasonably safe trying a couple kinds. I mean, I've tried a few myself.
posted by late afternoon dreaming hotel at 12:22 PM on November 12, 2015 [3 favorites]

Prebiotics are aerobic bacteria and the bacteria in your gut is anaerobic.

Infants get colonized within short days after birth and I'll be darned if I can figure out where they get it from. They get colonized long before they are old enough to crawl around and eat mud.

I tentatively theorize that it would be a good idea to cut back on simple starches and all sugars to reduce the yeast in your system, since the yeast is probably providing competition for bacteria that is a better steward to their home planet than the yeast. I have been perplexing over the same question you asked about, as I have a family member with Crohn's disease, without coming up with any more information that this, and the unlovely suggestion of a fecal transplant or eating dirt?
posted by Jane the Brown at 1:43 PM on November 12, 2015 [1 favorite]

yogurt, real fermented sour kraut, real fermented kim chee.
lots of veggies, good fats, nuts. help good things find you and stick around.
posted by acm at 3:49 PM on November 12, 2015 [3 favorites]

Eating lots of fermented food, as acm recommends, is a great idea. So is avoiding eating a lot of processed food and sugar.

I had a doctor once recommend me a product called Bio-K when I was going through some bad times with my own gut. It's sold in the refrigerated section at health food stores, and resembles runny yogurt. It's a cultured milk product and you drink a little bit each day. It's kind of like yogurt on steroids, so to speak. Full of probiotic microorganisms.

If you try it, I've found the strawberry flavor to be pretty palatable, whereas the plain flavor tastes to me like an old gym shoe.

It's pretty expensive (four or five dollars for a little container), but you can make one container last a few days.

As others have noted, the scientific jury is out on whether or how much these things can help, but at the very least, I don't think it will hurt you. It never hurt me.
posted by toomuchkatherine at 4:04 PM on November 12, 2015

Rite Aid has a house blend in blister packs. It is advertised as just like product x, your doctor prescribes. I had similar two rounds of antibiotics. I have not been ill since and I tolerate dairy better, so I am happy with it. Take a thirty day run and see if you feel better. Best to you and your gut.
posted by Oyéah at 5:37 PM on November 12, 2015 [1 favorite]

You may want to get tested for H. pylori infection at your PCP.

Yea, this. I had perpetual low level weird gut problems until i had to take different antibiotics for something unrelated... and then suddenly it all just kind of rebooted. I had also started eating lots of kimchi and yoghurt because my partner loves those things. After that i finally had a eureka moment and talked to a doctor about it, but i can't prove it definitively was or wasn't the case because whatever had been ailing me was gone.

But still, yea. Doctor. Tests. It might seem counterintuitive that the answer is more antibiotics, but for me it was.
posted by emptythought at 5:57 PM on November 12, 2015 [1 favorite]

Stop taking antacids, which can change how you digest your food. If the food isn't being properly broken down, all sorts of stupid things begin to happen. Commit to a few weeks of no booze or processed foods. Don't eat anything with yeast in it for the first several days and then sparingly after that, if at all. Eat every single fruit and vegetable that you can. And do take probiotics. My brother and I use Garden of Life Raw Probiotics (Whole Foods, $50) and it has made a huge difference.
posted by myselfasme at 5:42 AM on November 13, 2015

Local raw honey is supposed to have wonderful properties to help your digestion. I put it in the camp of "might help; can't hurt".
posted by CathyG at 12:52 PM on November 13, 2015 [2 favorites]