Fermented Good = Antibiotic Bad?

If our bodies need a constant supply of bacteria-rich food to be healthy, as I have argued here many times, antibiotics — which kill the bacteria we already have — should be bad for us. Maybe so:

A team of researchers at the University of Michigan Medical School gave mice allergies by pretreating the animals with an antibiotic. The experiment provides support to studies hinting at a connection between antibiotic use and asthma. These epidemiological studies show increased rates of asthma wherever antibiotic use is common.

Asthma cases in the United States climbed 75 percent from 1980 to 1994.

So ignored are fermented foods (the easy way to get bacteria-rich foods), that an author of the study does not mention them:

To avoid the role that antibiotics may play in allergy and asthma, Mr. Huffnagle suggests people watch what they eat in the weeks following a course of antibiotics.

Avoid junk food, he said. Earlier studies on rats showed that animals fed a kind of junk-food diet had far different gut flora than animals fed well-balanced meals of rat chow. [This doesn’t make his point, since it isn’t clear that different = worse.]

He suggests the Mediterranean diet — with lots of fruits, vegetables, whole grains, nuts, beans, seeds, and olive oil, and low to moderate amounts of wine — may be protective of your gut flora. Countries where this heart-healthy diet is consumed also have lower levels of asthma and allergies, he said.

The Mediterranean-diet advice makes more sense than the junk-food advice. But again, we should ask: Have we properly described “the Mediterranean diet”? That is, what people in “countries where this heart-healthy diet is consumed” actually eat? As with the Inuit Paradox, I suspect the fermented foods they eat, such as yogurt, are ignored. If high consumption of fermented foods does reduce asthma and allergies then asthma and allergies should be low in Japan because of miso and natto.

Thanks to Oskar Pearson.

14 thoughts on “Fermented Good = Antibiotic Bad?

  1. This isn’t strictly related to the post, but I consume ridiculous amounts of wine and have felt much healthier since I started doing that. I grow the grapes and make the wine myself so I know it’s very natural.

    My dad drinks a lot of this wine too. He has not gotten a noticeable cold since we started drinking our own wine. I have had less allergy problems and I have only gotten two colds in the past four years, both on occasions when I was traveling (and didn’t have access to my wine). I think this is probably coincidence or a placebo or willful ignorance or something. But I thought I’d share.

    I should probably mention that my mom also drinks a reasonable amount of the wine, but she is still constantly sick.

  2. That’s closely connected! I don’t think anyone expects wine to prevent colds so I don’t see how it could be a placebo effect. As for your mom being sick, I’d bet she drinks a lot less wine than you and your father. I think wine is a good source of bacteria but not a great one.

  3. @seth

    What makes you think that wine has any bacteria?

    As I noted here: https://sethroberts.org/2009/03/30/natto-shopping-continued/#comment-286176

    Taking wine for example, generally, you kill off everything living in the must via addition of sulfur, after which you add your desired yeast. The yeast then ferment by digesting the sugars in the must thereby generating alcohol, which ironically kills them off. As we used to joke when making wine, in a sense, the yeast are killed by their own shit, which we consume. :)

  4. Patrik, wine has lots of dead bacteria. I don’t think the immune system cares if the bacteria are alive or dead, so long as they are whole.

  5. Additionally, some wines are made with natural yeasts (although most of what I drink has yeast added). I also use very minimal levels of sulfites. The yeasts I do add tend to just beat the crap out of the naturally occurring fermenting agents. There’s a certain point where one yeast population will explode and decimate competing yeasts. And then yes, they choke themselves out.

    But a small amount of bacteria are still around and kicking which is one way wine can go bad. I think that one of the reasons to complete a malolactic fermentation (and also one reason to fine and filter) is to prevent the few remaining bacteria from starting up again after bottling. I’m under the impression that wine that goes vinegary is almost always the result of bacteria coming back from the brink and producing volatile acids as a byproduct. But I’m really fuzzy on a lot of the science.

    And it’s interesting that dead bacteria might protect gut flora as well or better than live bacteria. Like an inoculation?

  6. Four weeks into my Latin American backpacking trip, I’ve enjoyed perfect digestive health, even while sampling all manner of street food. That’s got to be some kind of record – it definitely is a record for me. And I attribute it to the (Trader Joe’s brand) probiotic-acidophilus pills I started taking just a few weeks before departing the US, upon the advice of this blog.

    Thanks, Seth!

  7. My 5 year-old son has had mild to moderate asthma and eczema since he was an infant. The asthma presents as a night-time cough. We completely eliminated both the asthma and eczema symptoms by giving him a daily probiotic drink. Our pediatrician dismissed this by saying he had likely “grown out of it.” However, whenever he has taken a course of antibiotics, the symptoms immediately reappear.

    I have always been curious if his condition was precipitated by the I.V. antibiotics his mother had to take late in her pregnancy with him. This study https://ajrccm.atsjournals.org/cgi/content/abstract/166/6/827?ijkey=d8be8904020279b8ebff11e0e6e8bce2a9e39cdd&keytype2=tf_ipsecsha suggests there is a link.

  8. @seth

    I definitely enjoy your intellectual curiosity — you have a tendency to be the proverbial bull in the china shop, which is great. However, I think you need to balance, or perhaps, “tune” your hypotheses a bit as you often seem to ignore the underlying mechanisms necessary for your hypotheses to make sense.

    That said, Semmelweiss didn’t know the mechanism (germ theory) for his groundbreaking discovery and perhaps, in your case, pondering the mechanism (how bacteria interact with your immune system) limits intellectual creativity and problem-solving. Interesting. I need to ponder this some more.

    Patrik, wine has lots of dead bacteria.

    I don’t think it does have “lots” of “whole” dead bacteria. My experience and intuition tell me is has very little, since after destroying all life in the must via sulfur and then having the yeast produce alcohol (intentionally) makes for a very harsh environment for bacteria. My guess is that the alcohol physically denatures bacteria ergo why alcohol is used as an antiseptic. BTW Cochrane and Harpending of “10,000 year explosion” posit that we have evolved to drink beer b/c of its bacteria destroying properties. (An excellent book, you should get a copy ASAP, they generate thousands of interesting ideas and hypotheses directly opposed to the conventional anthropological “wisdom”. Seth, you of all people, need to read this book.)

    I don’t think the immune system cares if the bacteria are alive or dead, so long as they are whole.

    No way. Which is more disgusting/malodorous fresh dog shit or dried dog shit?

  9. If we assume that fermented foods are beneficial to our health, my shoot-from-the-hip guess is not that they provide more bacteria (which is for some unknown reason is desirable according to Seth’s hypothesis) than non-fermented, but that they contain less bacteria.

    And not only do they contain less, my guess is that the benefits, if any, stem from mechanisms such as (https://sethroberts.org/2009/01/26/the-inuit-paradox/#comment-264706):

    1. Pre-digestion of food

    2. Elimination of anti-nutrients and toxins such as phytic acid

    3. Lower pH of certain foods making minerals more bioavailable

    4. Probably most important:

    Provides Vitamin K2 — (this is a very interesting post and addresses natto and foie gras https://wholehealthsource.blogspot.com/2008/06/vitamin-k2-menatetrenone-mk-4.html)

    Interesting post on fermenting rice:

    https://wholehealthsource.blogspot.com/2009/04/new-way-to-soak-brown-rice.html

    In the 2008 paper “Effects of soaking, germination and fermentation on phytic acid, total and in vitro soluble zinc in brown rice”, Dr. Robert J. Hamer’s group found that soaking alone didn’t have much of an effect on phytic acid in brown rice. However, fermentation was highly effective at degrading it. What I didn’t realize the first time I read the paper is that they fermented intact brown rice rather than grinding it. This wasn’t clear from the description in the methods section but I confirmed it by e-mail with the lead author Dr. Jianfen Liang. The method they used is very simple:

    1. Soak brown rice in dechlorinated water for 24 hours at room temperature without changing the water. Reserve 10% of the soaking liquid (should keep for a long time in the fridge). Discard the rest of the soaking liquid; cook the rice in fresh water.
    2. The next time you make brown rice, use the same procedure as above, but add the soaking liquid you reserved from the last batch to the rest of the soaking water.
    3. Repeat the cycle. The process will gradually improve until 96% or more of the phytic acid is degraded at 24 hours.

    This process probably depends on two factors: fermentation acidifies the soaking medium, which activates the phytase (phytic acid-degrading enzyme) already present in the rice; and it also cultivates microorganisms that produce their own phytase. I would guess the latter factor is the more important one, because brown rice doesn’t contain much phytase.

  10. Alex, the Mediterranean diet is associated with improved control of asthma. For details, see my healthy lifestyle blog post:
    https://advancedmediterraneandiet.com/blog/?p=59

    Dr. Roberts, most iterations of the traditional Mediterranean diet do mention yogurt, a fermented food. The leading proponent of the Mediterranean diet in the Western world is Oldways Preservation Trust. Here’s their version of the Mediterranean diet:
    https://oldwayspt.org/med_pyramid.html

    -Steve

  11. Japan actually has very high allergy rates and people do go very far to try to combat them. Around this time of year, you’ll see a good percentage of people walking around wearing surgical masks to try to fight against pollen allergies. Incidentally, the popular press/stores recommend eating lots of yogurt during this time of year and plenty of new yogurt brands get launched during allergy season. Natto comes up occasionally but I’ve never seen miso mentioned.

    See:
    https://whatjapanthinks.com/tag/hay-fever/

    and although it’s in japanese you can see an amazing writeup in pictures of how well different recommended remedies act on allergens:
    https://d.hatena.ne.jp/fromdusktildawn/20090406/p1

    The japanese also love cleanliness (think bidet toilets) so that could still satisfy your hypothesis but typical levels of dietary natto/miso aren’t enough.

  12. Incidentally, the popular press/stores recommend eating lots of yogurt during this time of year and plenty of new yogurt brands get launched during allergy season.

    Seems odd and probably ill-advised seeing as Asians in general lack the genetic capacity to metabolize lactose as adults.

  13. actually, most of the lactose is consumed in the fermentation process. those who suffer from intolerance generally can eat yogurt with no ill effects.

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