Musings on “good” bacteria, antibiotics, and brain function

The growing trend recognising that gut bacteria affect all other body systems, the brain, of course, included, is often accompanied by what I think is a faulty assumption. That assumption is that there are healthy strains of bacteria that are difficult to cultivate that we should specifically insert into the gut (through pills, yogurt, or transplants, for example) and then keep alive by feeding with high fiber plants in order to maintain health.

The main reason I find this implausible is that it’s not evolutionarily supported. There is just no strong evidence that evolving humans ate fibrous plants with any regularity. Moreover, any gut bacteria that we can’t easily keep living inside us seem unlikely to have evolved there. It makes no sense that regularly eating something we didn’t evolve to eat regularly, to keep alive something that doesn’t appear to have evolved a strong penchant to stay alive in us, would be the only, let alone best way to maintain an inner environment conducive to health.

There do seem to be positive effects from taking probiotics, but I question the interpretation of that. One hypothesis I have is that the main benefit of probiotics is that they in turn displace worse strains of bacteria. If this is correct, then another, possibly better solution may be to minimise the worse bacteria by not feeding them. One way to not feed them would be to avoid fibrous plants.

(Please see my related post on germ-free mice, where I show that mice with no gut bacteria, contrary to common interpretation, are healthier than those with bacteria.)

Another possible explanation, is that these bacteria we are pushing mainly help people digest fibrous plants. So in people who eat fibrous plants, it is better to work to maintain these bacteria, than not to. However, this, too has the obvious alternative solution.

Antibiotics and the brain

I just learned about the potential benefits of antibiotics in autism. The author of the linked article has found evidence that negative symptoms of autism may be mitigated by taking antibiotics. His own son, for example, had improved eye contact, speech, energy, and motor control. This prompted him to look for clinical evidence, and he did find some preliminary such.

Some antibiotics appear to improve brain function. Animal studies have shown cognitive improvements in, for example, mouse models of schizophrenia, and Alzheimer’s. The mechanisms are unclear.

Often researchers suppose that such properties of antibiotics are coincidental, and unrelated to the antibiotic effects. For example, minocycline, the antibiotic used in the latter study, has been shown to have antioxidant properties that are neuroprotective. The mechanism is unknown, and I am not aware of people testing the hypothesis that the antioxidant property is a downstream effect of bacterial modulation.

I did find one nice exception to this. Antibiotics are known to improve cognition in hepatic encephalopathy. In this study, the researchers tried to discover a plausible mechanism for that. What they found was that there was a shift in the activity of different gut bacteria, resulting in an increase of many types of fatty acids in the blood. They speculated that these fatty acids, which brains like to use, were reponsible for the cognitive improvements.

Antibiotics often get a bad rap, because some conditions appear to get worse after you take them. People explain this with the story that after you’ve taken them, your gut is now prey to the “bad” bacteria, which for some reason never explained, naturally takes over in place of the “good” bacteria that “should” be there. This all appears rather backwards to me. I would think that if we were feeding our guts naturally, we wouldn’t have to go out of our way to ensure this didn’t happen.

What is salient to me is that supressing our gut bacteria, or changing the way they function from the default, is often having a positive effect that goes away when we go back to our normal way of treating those bacteria — feeding them our Western diets. The common wisdom for dealing with that is to force in bacteria optimised for an onslaught of plant fiber. One wonders what would happen if instead, we just stopped the onslaught.

22 replies
  1. Brian Stretch
    Brian Stretch says:

    Best guess is that when antibiotics are beneficial it's because they killed chronic pathogens like mycoplasmas, Lyme, Bartonella, etc. Zero carb seems like the best way to make the body inhospitable for said pathogens which use inflammation to break down tissue for food. Plants have chemical defenses that cause inflammation, sugar is both inflammatory and feeds many pathogens directly, etc. Buhner's "Healing Lyme, 2nd Edition" ought to be a good place to start. His other books are excellent. I've been meaning to watch this workshop of his:

  2. Michael Frederik
    Michael Frederik says:

    Hi Amber. Nice to see you publishing a few blog posts again. Hope you are doing well.
    I agree with your assessment. I any case, I'm still doing fine. Carnivory FTW. And I want to thank you for that, because although others wrote about it too, it were your posts that somehow resonated with me and actually made me want to try Carnivory as opposed to just LC. Cheers, Michael

  3. Larcana
    Larcana says:

    Great post. I agree we need to more investigation into decreasing gut microbes rather than proliferating them. Just this weekend I had guests at my house, both morbidly obese and both heavy sugar eaters. Both with allergenic symptoms… When I suggested that their lives would improve with no sugar no gluten eating, I of course got the " I can't do that" answer. They mean I won't do that. The female ate every thing in sight of the holiday deserts except my no sugar pumpkin pie. I made it with Swerve and I used a gluten free crust. I thought it was quite sweet!
    Sadly, no amount of my gentle coaxing helped. Yet, she swore she wanted to lose about 150 pounds. Sigh.

  4. wjones3044
    wjones3044 says:


    Good read. I have something to say about antibiotics, but I'm going to save that for last. Also going to take a pot shot at Chris Kresser. So if that offends you or any of your readers, I'll save you the trouble: stop reading now.

    My journey to improved health hinged on two important observations, both related to digestive distress (which plagued me throughout the nineties and up until 2007/2008). First, the only time I had a proper bowel movement as an adult was when I ate nothing but chicken thighs and broth made from chicken thighs. I had just had major shoulder surgery and was on Vicodin for about a month, post-surgery. (It's hard to shop and make decisions while taking such a serious drug, so I'd amble to the supermarket and get the cheapest, easiest-to-prepare item about once a week. Then I'd sit on the couch and watch silly movies. I rarely ate, but when I did I broiled the thighs and then put the bones in a crock pot, strained the juice and added in the choice pieces of remaining meat. Chicken noodle soup without noodles. Comfort food.)

    I knew that opiates could cause constipation but that's not what was happening. For the first time in 15 years I had regular, completely satisfying toilet experiences. Is it fair to say that I saw Jesus there? Or was I just high?

    So I started looking at other explanations. I'd been sick all my adult life. Various physicians described my complaints as "vague and unspecific," while dispensing cortisone creams for the, in fact, very specific rashes. I suffered from almost Parkinsonian hand tremors and ataxia. I had ballooned to almost 250 pounds (I'm 5'9" tall).

    I remembered my research in the 90s about Celiac disease and how it literally screamed my name. Of course, my (now) ex-wife, family, standard dogma…all these things deterred me from doing anything. And now, an accidental experiment suggested that maybe wheat and I didn't get along. Fast forward to post-recovery and a Pizza Hut relapse. The results were ghastly. Cause and effect exemplified

    Which gets us to antibiotics. In pursuing a gluten-free (and, later, Steffanson-inspired carnivory) diet, I endured the common mistakes (restaurant food contamination, mostly) and experimentation with gluten free "replacement foods." Gluten free crackers, for example. And the results, while not always ghastly, set me back on a number of levels but especially digestively. My solution, based on a PubMed abstract, was to mitigate the effects of gluten or grain intake with amoxicillin. I still use amoxicillin as needed to mitigate indigestion caused when I have a moment of weakness, like a gluten free pizza. It's not a perfect solution, but I'm not a perfect person. The other approach I'd tried, based on conventional wisdom, included probiotics.

    For me, probiotics are terrible. About the worst thing for my digestive tract, and I've even bought the Chris Kresser-recommended one. It lacks L acidophilus which is supposed to make it worth $50. It's less bad than the other ones, but I'm still scratching my head wondering why I'd take my health advice from that guy. His shilling and self-promotion increasingly disgust me, as do many of his recent "guest bloggers" who write about their "extensive clinical experience" while boasting head shots of recent university grads. One of these guest bloggers had the audacity to discuss SIBO, Small Intestinal Bacterial Overgrowth, a subject that I am unfortunately well-versed in, with a naivete that flabbergasted me. Her solution? Eat more carbs.

    God help anyone who takes that advice. Or, at least be kind and get them some antibiotics.

    Keep up the good work,

    William Jones

  5. Galina L.
    Galina L. says:

    I can only speculate why many who feel better eating less fiber, don't benefit from probiotics and may even feel better on antibiotics. My guess – some people have gut bacteria so wrong for their health, that anything what diminishes intestinal population improves health in their case. I know, many speculate as well, that the quality of intestinal gut bacteria may be changed with the use of a probiotic , but I suspect that the degree of such change is limited. The Wooo even experimented with digesting a capsules filled with a hydrogen peroxide (while discouraging others to follow her example) She recently had her intestinal population tested, and the result was good and healthy bacteria. Her microbiote bounced back in no time.

  6. Galina L.
    Galina L. says:

    I am challenged healthwise since being a child – multiple allergies, a mild neurological disorder, a tendency to be fat. Also, all my life I was trying to find ways to use life-style choices to make myself feel better. I found one thing – no matter what others say, regardless of theories, if you tried something and it worked, use it for your advantage.
    I also feel better eating less plants, and I find quite silly the advice to "eat your rainbow" . I approve the only one aspect of it – it makes LCarbing to be more politically correct for the people who need a social approval. Fortunatelly, I am comfortable to be different, I love my vegetables, but I feel my best on a bland and a monotonous diet with less bulky ingredients. No gluten for me, even though I I have no digestive troubles. My stool gets a consistency of mushed potatoes after eating big quantities of vegetables, but I don't think it could be considered a trouble.

  7. L. Amber O'Hearn
    L. Amber O'Hearn says:

    That's a really interesting story, William! I've never heard of someone mitigating effects of gluten with antibiotics. Fascinating. And I'm glad you discovered it.

    I'm perplexed by some of Chris Kresser's more recent work, but I do still refer people to his posts on blood sugar.

  8. wjones3044
    wjones3044 says:

    I forgot all about the Woo! I read the thing about taking bleach capsules. Two questions, which I will not pursue answering: 1) How the hell do you get bleach inside gelatin capsules? 2) Why not just take food grade hydrogen peroxide?

  9. Galina L.
    Galina L. says:

    I think Wooo wanted a very small amount of hydrogen peroxide to pass into a right place before the capsule gets dissolved. The only way to put some liquid (and to drain the capsule first) into a capsule have to be a needle attached to a syringe.
    Despite her experiments with diminishing her gut microflora, she recently had analysed it in a lab and the result was a numerous population of a good quality. For me it looks like a human can't do much to really harm the system inside him/her, unless it is a major effort. Probably, it is better not to aim for such thing.

  10. wjones3044
    wjones3044 says:

    That would make sense. I've made powder capsules but never liquid.

    Turns out the concept of ingesting H202 is about as polarizing as dietary issues, just from a cursory internet research jaunt.

  11. R Cobb
    R Cobb says:

    Two additional thoughts. The whole purpose for the acidity of the stomach is to kill exogenous bacteria- including all those expensive probiotics and yogurt that people throw down there- I doubt much survives that caustic environment. I agree that perhaps any positive effects gained from probiotics may be a consequent change in macronutrients- more yogurt means perhaps less refined carbohydrates etc. Also, having a personal understanding of SIBO I would say that a person can definitely have an overgrowth of bacteria and in the wrong location – small intestine being one of them. As you know a healthy small intestine should be relatively pristine and free of bacteria since your body produces the enzymes necessary to digest all macronutrients. The bulk of bacteria is located in the large intestine and frees up hard to access micronutrients (at best) from otherwise indigestible fiber, but as you discovered it is completely unnecessary because if you eat a diversity of animal products you can obtain more easily all of these same micronutrients without exposure to the toxins in seed coatings etc. The only thing that solved my SIBO was by going on to an extremely restrictive LCHF eating method. Because it feels best and I have the best outcomes I have naturally been shifting toward almost an all animal food based diet. And a final note having been vegetarian for most of my life 17 of which I was full on vegan I can say that hands down animal foods have been the healthiest, most satisfying and calming method of eating I have ever endeavored on. Thanks for the sciency blog- I love this!

  12. AliB
    AliB says:

    Now here's a thing. What if no microbes were actually 'pathogenic' in their own right…? What if the 'pathogenic' microbes were actually there for a reason? What if the environment does actually dictate the germ….?

    If you put flour and water together, a sourdough will form. Seemingly out of nowhere. As long as you continue to feed and maintain the sourdough it will happily thrive – for decades. But neglect that sourdough and other microbes form to break down the components back into basic structure. The environment dictates the germ.

    What if the wrong gut microbes are generated through wrong, and/or inadequate feeding….? The same microbes do not exist in a fast-flowing river that exist in a stagnant pool. The microbes follow the stagnancy (or the slurry pit), they do not cause it. If microbes associated with disease follow disease then there has to be some other reason for the disease.

    People eating acres of 'non-food' set up a negative imbalance of nutritional elements and toxicity. That creates the disease, which in turn attracts the 'pathogenic' microbes drawn to break down dead and decaying matter or toxic by-products of chemical ingestion. When people, by means of their diet and lifestyle choose, even inadvertently to become slurry-pits, is it any wonder the 'pathogenic' microbes are present?

    Yes, we can be exposed to external unwanted microbes, but the strength of a good digestive system should deal with them. Weak digestions may not. If germs made us sick in general, however, we would all be sick all the time, because they are all around us and are on everything we touch or eat……

  13. Sandy
    Sandy says:

    AliB brilliant post. Microbes for the most part don't fly in from outside but are created in the cell when the nucleus calls for autophagy. But humans just love to revel in their fear of contagion.

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    Userhopes says:

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