Do bacteria control your brain?


A new study has found evidence suggesting that you are not what you eat, so much as you are what's living in your gut. In mice, at least, the presence of normal gut bacteria has a significant impact on how an individual mouse behaves, and how its brain develops.

this new study is the first to extensively evaluate the influence of gut bacteria on the biochemistry and development of the brain. The scientists raised mice lacking normal gut microflora, then compared their behavior, brain chemistry and brain development to mice having normal gut bacteria. The microbe-free animals were more active and, in specific behavioral tests, were less anxious than microbe-colonized mice.

In one test of anxiety, animals were given the choice of staying in the relative safety of a dark box, or of venturing into a lighted box. Bacteria-free animals spent significantly more time in the light box than their bacterially colonized littermates. Similarly, in another test of anxiety, animals were given the choice of venturing out on an elevated and unprotected bar to explore their environment, or remain in the relative safety of a similar bar protected by enclosing walls. Once again, the microbe-free animals proved themselves bolder than their colonized kin ...

Consistent with these behavioral findings, two genes implicated in anxiety -- nerve growth factor-inducible clone A (NGF1-A) and brain-derived neurotrophic factor (BDNF) -- were found to be down-regulated in multiple brain regions in the germ-free animals ...

When Pettersson's team performed a comprehensive gene expression analysis of five different brain regions, they found nearly 40 genes that were affected by the presence of gut bacteria. Not only were these primitive microbes able to influence signaling between nerve cells while sequestered far away in the gut, they had the astonishing ability to influence whether brain cells turn on or off specific genes.

Personally, I'd like to see more analysis on what these findings mean. The Scientific American story quoted above makes it sound like normal gut bacteria are, on the whole, kind of cramping the brain's style. Given the evidence that exists about healthy gut bacteria's importance to maintaining other aspects of physical health, I'm curious whether this study implies that we humans have accepted a bit of a trade off. We get gut bacteria that help us digest food and train our immune systems—but we loose some control over how our brains function, possibly to our detriment, but possibly not, depending on the circumstances.

Oh, and, before the rest of you get a chance, I'm going to jump in here and make the obvious comment: "I, for one, welcome our new E. coli overlords."

Scientific American: The Neuroscience of the Gut

Via Matt Feltz


  1. It’s not like we have any choice in the matter so I wouldn’t characterize it as accepting anything so much as dealing with the reality that is available.

  2. I find this interesting as there have been links between gut bacteria and Autism as well. This would explain only some of the links between gut illnesses like IBS, Crones and Colitis and Autism as well.

    1. Primarily, the tinfoil hat keeps the neurobacteria (Escherichia Synapti) from maintaining a carrier wave signal to the greater hive mind. As a result, E. Synapti don’t contribute as much to your overall intellect, leading in fact to a reduction in IQ for those that continually wear tinfoil hats.

      1. Actually, most studies indicate that tinfoil hats actually act as amplifiers to the wave lengths they are supposed to protect against, unless you go far enough to make a true Faraday cage out of the foil.

        A copper foil hat is supposed to be a better choice, but really, who wants to be so tacky as to wear copper foil? It’s so … tacky.

        1. “A copper foil hat is supposed to be a better choice, but really, who wants to be so tacky as to wear copper foil? It’s so … tacky.”

          gold foil then?

        2. Actually, most studies indicate that tinfoil hats actually act as amplifiers to the wave lengths they are supposed to protect against, unless you go far enough to make a true Faraday cage out of the foil.

          Two words: Ground cable.

  3. This has interesting, if slightly paranoid, implications. Imagine if big agri-business, at the behest of the government, could introduce specially enginnered bacteria into our food, to make us fearful, easily cowed, and more easily controlled. Imagine a smaller subset of this population, people who ate organic food, say, and thus not as easily intimidated, rising up against an unsuspecting government.

    1. Thanks, submitting my grant to DARPA for weapons grade probiotics now in handy crop duster format.

  4. it’s not necessarily a trade-off. those bold, free-thinking, creative mice probably get eaten a lot faster than the colonized ones. One man’s anxiety is another man’s caution…

    1. I think this is exactly the right perspective. These bacteria are seeing to their own survival by enhancing their host’s danger-avoidance instinct. This is a lot like previous research ( that discovered that the parasite Toxoplasmosis causes rat hosts to almost seek out cats, who would then eat them and move the parasite into it’s next stage of life in the cat.

      In short, none of this is surprising except in the details. As Dr. Malcolm says in Jurassic Park, “life, uh… finds a way.”

      1. Why not the opposite? Enteric bacteria are useful. If you notice you don’t have any from current foods, you are more likely to take risks, since there’s a chance those will get you food that does.

        It seems the assumption is that the bacteria are manipulating the host for their own benefit. This does happen, but in this case I don’t see why you would rule out an evolutionary benefit to the host as the reason it reacts to them.

  5. Why do so many people incorrectly spell “lose” with two O’s? Or did you actually mean that we might be setting “loose” the control of our brain functions?

  6. I want to see the definitive research on the necessity of human gut flora. I swear i’ve read distinct “we took this (too small sample) of grad students and subjected them to a course of intensive antibiotics until their stool samples cultured nothing and as a result they were”:

    (a) pretty much ok.

    (b) seemed to be a bit anemic and weak (possibly because of all the antibiotics)

    (c) became dangerously vitamin deficient so we had to immediately re-infect them with an egg-salad sandwich from a truck-stop

    which is it? what really happens? are they necessary necessary, or just facultative?

    1. Hi Anon, Here are a few articles on the importance of healthy gut flora. I think the first one is pretty convincing that it was of life and deathimportance for at least one person.

      On a side note, everyone seems to be in agreement that science is of particular interest to BB readers and yet we also seemed compelled to attack it when it, it, it what? Is presented here? We are a pretty fickle bunch.

      1. That’s what you do with science: attack it, and see what stands up to criticism. Doubly so with this kind science reporting, which sometimes slants the result, and quadruply so with mainstream science reporting, which often misses the result entirely.

  7. To the extent that psychology could, on a theoretical level, be explained using biology, which could explained using chemistry->physics->mathematics, I suppose that it’s unsurprising. Still, applied research in this area is incredibly fascinating, and could lead to some exciting new anti-depressants/mental health treatments

  8. TL;DR, but I’m bothered by the quote “…these primitive microbes able to influence signaling between nerve cells while sequestered far away in the gut” Did they at some point repopulate the mice with gut bacteria and see if they became more anxious? Or is it that the bacteria influenced development but now no longer have that direct of an influence?

    Likewise, could they have killed off the gut bacteria in the (former) control group and then tested them?

    Maybe this does give new meaning to having a gut feeling.

  9. There’s always been a strong connection between autism and some kind of digestive system oddity.

  10. Not only were these primitive microbes able to influence signaling between nerve cells while sequestered far away in the gut, they had the astonishing ability to influence whether brain cells turn on or off specific genes.

    Wouldn’t it seem more reasonable to phrase this that the mouse, in making decisions, takes into account the microbes it has sequestered? It’s only astonishing if you assume the bacteria are forcing themselves on the brain, as opposed to there being an evolutionary advantage to listening to them.

  11. I was hoping someone would point this out, but isn’t the behaviour of the “paranoid” mice MORE conducive to survival than the behaviour of the “bold” mice? Obviously the value of such behaviour is context dependent, but the negative values we associate with this paranoid behaviour could actually be a positive adaptation in wild mice.

  12. Without Knowig their methods, I am extremely suspicious. Seems more likey to me that the no-bug group was probably handled different (procedures etc) and it is the difference in experience that is drivig the anxiety rather than simply the gut microflora population.

  13. I want to know how they managed to ensure that the “microbe-free” mice were actually microbe free? maybe I overlooked the part of the story that explained how they set-up and qualified the control group of this experiment.

    1. It’s standard—the colonies get established and maintained that way—the pregnant mice get a C-section, babies get dipped in something to kill external microbes(bleach) then they get moved into germ-free housing a la bubble boy. Looking for colonization is just plating or rich media, which is done routinely because there can be accidental colonization—since everything everywhere is coated in germs.

      Still I would not worry about this we evolved in the presence of these microbes, the neural trends in the colonized mice are the norm and not those in the uncolonized mice. They make it sound bad but if you’re a prey item you need to have a certain amount of anxiety to live to reproduce.

      1. Thanks for the explanation. I work with marine microbes and used to work in pathogens, so I understand the ubiquity and necessity for microbes. I just didn’t understand how they were able to TOTALLY sterilize a living organism. Good to know. :)

  14. No.

    This is absurd.

    Continue living as normal. Do not stop eating.

    Post more articles about going soap-free.

  15. pretty much all organisms are simply habitat for smaller organisms. in the fungal endophyte symbioses my lab studies, fungi turn various genes on and off (we’re interested in stress response) in inoculated plants compared to sterilized plants. considering that the “normal gut microflora” are not pathogenic but form a positive symbiosis with animal hosts, it is unlikely that any changes they are making to our gene expression are harmful. it is more likely that without “normal” (whatever that means; i’m pretty sure we can’t define it yet) microbial symbionts, “normal” gene expression is less likely resulting in negative health effects.

  16. Is there any chance that the mice without bacteria are less-able to digest nutrients, and so it would be to their advantage to be bolder in searching for food, as they’ll need more?

    If this made sense, then it might be equally likely that evolution would select for mice whose boldness-genes are switched on if they have a lack of bacteria during development, as they might otherwise be at a disadvantage during their lives.

  17. ‘You could argue, for example, that the brain is a gadget evolved by the stomach, in order to serve the stomach for the purposes of getting food. Or you can argue that the stomach is a gadget evolved by the brain to feed it and keep it alive. Whose game is this? Is it the brain’s game, or the stomach’s game? They’re mutual. The brain implies the stomach and the stomach implies the brain, and neither of them is the boss.’ – Alan Watts, the Nature of Consciousness, 1960

  18. Similar research has noted that gut critters of obese people may be different – either cause or effect or simply correlation. Anyway, what about vegetarians, vegans, etc vs omnivores of various styles (classic american diet, people who like meat but eat rarely, etc)? If these gut critters do have an effect on our minds, perhaps we should investigate the populations that occur with different diets. Do diets correlate with critter types? Do diets/critter-types correlate with higher level thinking or lower level behavior?

    Sounds like a great project for DIY Bio folks. A lot better than gen engineering new characteristics into bacteria, etc. Or perhaps those go hand in hand…

    What genetic traits in gut bacteria cause the brain/behavior? Can those be xfered to other bactiera from other diets? Does that change thinking so people change their diet?

    Maybe this is how the hive mind gets extended? Maybe we get a bacteria-computer interface to push along The Singularity?

  19. This is not surprising! The gut plays an extremely important role in how our brain works and has been studied extensively by Gershon.

    He even talks about a “second brain”: “nerve cells in the gut that act as a brain. This “second brain” can control our gut all by itself.” Dr. Gershon’s work has led to radical new understandings about a wide range of gastrointestinal problems including gastroenteritis, nervous stomach, and irritable bowel syndrome.

    “Our two brains — the one in our head and the one in our bowel — must cooperate. If they do not, then there is chaos in the gut and misery in the head — everything from “butterflies” to cramps, from diarrhea to constipation.”

    CHECK OUT his ground breaking book:

    “The Second Brain: A Groundbreaking New Understanding of Nervous Disorders of the Stomach and Intestine”

  20. I’m reminded of the parasite that invades ants’ brains and makes them stand on the top of grass stalks so that sheep will eat them and the parasite can reach the next stage of life in a sheep’s gut (similar to the mouse->cat example above). But that involved a direct invasion of the ant’s brain if I remember correctly.

  21. I seem to recall reading that in the 18th and 19th century, pre-freud’s “talking” cure, some physicians treated mental illness by focusing on the digestive system and intestines.

  22. what i beleive this really implies is that lack of gut bacteria after birth (usually transferd in the mothers milk) creates a specimen that does more “risky” behavior which means that it is more likely to die but also more likely if it doesn’t to pass those genes on to its offspring however on the flip side of the coin with the natural bacteria in the gut of said animals causes them to seek less risky behavior and more protective behavior.. what this means evolutionarily is unknown to me but is quite interesting

  23. Reminds me of the story where they were testing telekinesis in mice, (mentally turn the dial) so they never found the telepathic hypnosis (make the scientist turn up the dial)

    Best argument on correlation and causation *evar*. (sic)

  24. There was a recent Freakonomics podcast on “transpoosions”, fecal transplants. So we could find someone with the optimal microbial organ, and harvest their feces. Offer everyone an enema of said feces, and… voila!
    Wonder who that would be…

  25. Actually what it is saying is the “sterile” (free of fauna) mice are acting like self destructive mice that would rapidly be selected out naturally (wild mice loathe the light, they are anxious because it helps them avoid predators). While cortisol levels may be different there are good reasons the colonized mice are acting normally while the non-colonized are acting bizarrely, the non-colonized mice need a very special diet in order to get the nutrients they need and are probably even then malnourished in certain ways. And yes, Antonio Damsio argues that the sensory data from the gut/torso helps us interpret emotions/feelings and this would imply that gut information tells us about the environment in ways that we don’t get from our other sense organs, I would venture to say that the non-colonized mice are gut blind.

  26. reminds me of that Futurama episode where Fry becomes smarter with intestinal parasites, but kills them off to preserve his original personality.

  27. And what of the claims that GMO plant DNA can migrate to human gut bacteria?

    This is your brain on Monsanto….

  28. In answer to those claiming a connection between autism and gut bacteria, this is not the scientific consensus but rather an idea promulgated by Jenny McCarthy and her ilk.

    The existence of a gastrointestinal disturbance specific to persons with ASDs (eg, “autistic enterocolitis”) has not been established.


    In summary, published reports have not established the presence of a unique gastrointestinal pathophysiology specific to ASDs.

  29. I agree that there is a reason for this, which can be explained by evolution. The mice with the gut flora were a bit “apprehensive” because this optimizes their chances of survival.

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