How yogurt can alter gene expression

Scientists don't actually know how the bacteria in yogurt and other fermented foods help humans digest food easier. But a recent study hit on a possible explanation. Turns out, some probiotics seem to be capable of altering gene expression in our native gut flora.

Jeffrey Gordon, a microbiologist at Washington University in St. Louis, and his team gave a commercially-available probiotic yogurt containing five strains of bacteria to healthy adult volunteers and administered the same five strains to mice that harbored a subset of genetically-characterized human gut microbes. The yogurt bacteria did not significantly alter population structure in any of the entrenched gut microbes, in humans or mice—a result that is not surprising, according to Mills. “To assume that you could eat a yogurt and numerically challenge what’s in your gut is kind of like dumping a gallon of Kool-Aid in your swimming pool and expecting it to change color,” he said.

But RNA sequencing of the human gut microbes in the mice revealed that the probiotic bacteria changed the expression of gut microbe genes encoding key metabolic enzymes, such as those involved in the catabolism of sugars called xylooligosaccharides, which are found in many fruits and vegetables. Mass spectrometry of metabolites in urine, which result from the ramped up metabolic processes in the probiotic-fed mice, confirmed the alterations, and when the researchers ran similar analyses on gut microbes from the human yogurt eaters, they found upregulation of the same genes.

This study won't be the final word on the subject of how probiotics work. It needs to be replicated and, even then, there are still a lot of questions that need answering. But it does represent an interesting peek inside an interaction between our bodies and other life forms. Cool stuff!


  1. i believe there have been at least two studies where the subjects had their guts “sterilized” (by administration of pulses of broad spectrum antibiotics until the fecal material didn’t culture anything).  the older study result was: “no significant effect [shrug]”.  whereas the more recent study found: “subjects suffered significant nutritional deficiency”.  (do i have references for these? alas, no.  but i don’t think i dreamed it…hn.  i’m sure Ms Koerth-Baker knows all about ’em [wink] ).  I sure wish someone would do the definitive study:  “Given a well-balanced, (but sterile), diet, do we have any absolute need of our gut flora?”  NASA should be willing to fund that.

  2. Usually a Maggie article is dumbed down enough for the likes of little ol’ dumb me, but I just don’t understand why this is cool stuff. The first sentence of the second embedded paragraph seems to be the exciting part, but is completely over muh leetle head. Should I be preparing for probiotic bacteria overlords or something?

    1. Well, yes and no. While over the past decade it has been made increasingly clear that the microbes in our guts (and elsewhere on and in our bodies) are a major influence on our health, it isn’t entirely clear on what is going on. Lately, there have been a lot of foods that claim to be “probiotic” (containing helpful microbes) or “prebiotic” (containing compounds encouraging the growth of helpful microbes), but in general this is just marketing at this point. That being said, in the not too distant future one could imagine foods with actual scientifically supported probiotic and prebiotic effects.

    2. wawb, the lead researcher spoke about the work during the second hour of last week’s Science Friday; transcript and mp3 are here. John Dankosky (taking over the host’s mic for Ira) and Dr. Gordon worked well together, and the two had a good informative chat about the paper. (Digesting the transcript is easier than the mp3, unless you really crave the experience of fantasizing how weird it must be to host a radio guest who’s capable of 20 “ums” per minute ;-)

  3. For quite awhile I got locked into antacids, PPI’s and most every other form of pharma gut fun.
    Thankfully I didn’t wait until someone figured out how probiotics work. I ‘fixed’ my gut and health issues by making and eating probiotic foods. But I’m just a marketing tool, an extension of the multinational viral empire of heretical home based health experimenters. We’re taking over! Occupy Your Gut!

      1. Myself personally? I would put my money on anecdotal evidence, way before I would your bought & paid for (think: Merck & Co., Pfizer, Johnson & Johnson…just to name a couple) science. Follow the money stupid! << (aimed at nobody in particular)

        I could give plenty of personal anecdotal evidence myself, that would be totally meaningless to you. Bottom line: prove ALL things, hold fast to that which is good. In other words, take responsibility for your own-self.

        It's a no-brainer.

        1. Unfortunately, anecdotal evidence is not science. If you believe that all studies are financed by Big Pharma, you are A) mistaken, B) free to die of whatever disease you get because you wouldn’t take any pharmaceuticals, and C) free to waste money on whatever hokum you read on the internet because of anecdotal “evidence”.

          Science is not black and white. Things change all the time. People must rely on their critical thinking, however — something which is sorely lacking in so many…I blame the education system. (But that’s another can of worms…)

          I would rather be a skeptic than a gullible believer, and that’s true in both directions: both the pharmaceutical side of the spectrum, and the naturopathic side.

  4. What a strange coincidence, just had a lecture on probiotics in my Immunology class on Friday. What I took out of the class: probiotics is nonsense, the host can select for its intestinal flora, there may be a slight influence of intestinal flora on risk for obesity (investigated with some sterile mice), and that intestinal flora certainly plays a role in inflammatory bowel diseases (well, the immune response to it anyway).

    PS, theophrastvs: that study would be pretty useless, as you also swallow nasal secretions, spit, lung secretions that you cough up, etc etc. (and therefore your “diet” could not be completely sterile). The mice in the aforementioned study were raised sterile, as in had completely sterile mothers, live in a completely sterile bubble with sterile air, autoclaved food, autoclaved water…pretty much impossible for humans.

    1. “What I took out of the class: probiotics is nonsense”

      Ah, medical school, no doubt; The same institutes that train our medical doctors to go forth, with license in hand, and murder, ‘admittedly’, 130,000 people a year, through the abusive use of antibiotics and other drugs/poisons….pure genius!

      1. Who said anything about antibiotics? Though I agree most doctors are a little heavy handed with them, that is not the subject of this post. In my class we were presented the scientific evidence for probiotics, and they have yet to be proven useful.

        I believe in science, not conspiracies.

    2. ‘probiotics is nonsense’
       Wonderful, just wonderful. And the bacteria that will drop you dead in a matter of hours? Do those bacteria work? I bet they wouldn’t even change the color of the pool water, and yet, death ensues.  I wish you success in your studies. Hopefully you’ll never encounter deadly bacteria while you further your knowledge into the meaningless ‘pro’biotics. Fearing for our future- My burden.

      1. Again, check the science. Probiotics is marketing for now, nothing more. Further research will give us more to go on. Also, your normal intestinal flora protect against those “bacteria that will drop you dead in a matter of hours” (um, what?). That has nothing to do with “probiotics”. Or do you believe you have no bacteria in your gut without yogurt? How do you believe the human gastrointestinal system deals with such bacteria? You know, because we don’t have immune systems, right?

        1. And antibiotics don’t affect those “good bacteria” in the gut at all do they?? No, they just selectively go around and slay the bad ones. Modern medicine pretty much created the need for probiotics. I have nothing against antibiotics when used only when *really* needed, but I have personally seen antibiotics given to elderly people for things like a dental cleaning, the result was that all the gut bacteria is killed off, the person then immediately gets some kind of horrible infection that their body cannot even begin to deal with and then the antibiotic circus begins in the local ICU. Probiotics can really help in situations like these, I hope to see more research in the future to support the use of probiotics. 

          1. They do, and there is antibiotic-associated diarrhea. I am not disputing that. In fact, I was not talking about antibiotics at all. Though there have been studies done in children with so-called “probiotics” to reduce antibiotic-associated diarrhea, I wouldn’t go so far as to say that it is completely conclusive and therefore our diet should be completely composed of yogurt. Claims that probiotics improve conditions like arthritis and such are to be taken with a large grain of salt, as there simply has not been enough research done.

  5. I just skimmed through the full paper, and although slightly interesting, this is nothing groundbreaking. Basically, they found that when you introduce new strains of bacteria to an existing population, the existing bacteria change their expression of a few genes, specifically those involved in breaking down some types of carbohydrates. What does this mean? Certainly nothing directly related to human health.

    The authors start with a vague hypothesis, then collect a massive amount of data, dredge through it with a lot of high level statistics, and come out with a few patterns. They then wildly speculate about what those patterns might mean. Overall, this seems to fit with a disturbing trend in molecular biology: instead of carefully formulating a question, and then carefully designing an experiment to test that _specific_ question, researchers are taking the approach of ‘Let’s use this shiny new machine to collect ALL the datas! We can sort out what it all means later.’ If a scientific paper can’t explain something succinctly, it’s probably because the authors are as confused as you are.

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