Episode 3: Bacteria, Butts, and Brains

This week Zach and Kelly discuss why the trillions of bacteria living in and on your body are good, bad, and why sometimes you gotta do gross things to get them back.


Gentlemen’s Single Use Unlubricated Monocle

Not Exactly Rocket Science’s awesome introduction to the microbiome

Gut bacteria & viruses

Popular press article

Paper 1: Intestinal microbiota promote enteric virus replication and systemic pathogenesis

Paper 2: Successful transmission of a retrovirus depends on the microbiota

Gut bacteria, brains and behavior

Popular press article

Paper 1: Normal gut microbiota modulates brain development and behavior

Paths taken by GF (germ free, or mice without bacteria) and SPF (specific pathogen free, or mice with bacteria) during different time periods. Click on image for a link to the original article.








13 thoughts on “Episode 3: Bacteria, Butts, and Brains

  1. Emerson Guitar

    On the topic of the fecal transplant, I would say that the reason they used the husband would be because of the nature of the relationship. The exchange of bodily fluids – namely saliva – causes bacteria to be shared between the couple. I have heard this is one of the theorized purposes of kissing, on top of hormone exchange and pleasure. Also, the close quarters would contribute to exposure to the bacteria of the spouse. If you can trust the ‘science’ of Mythbusters, their experiment with fecal coliform bacteria on toothbrushes exhibited the ubiquitous presence of the bacteria in a shared room such as a washroom. Although you initially gain your bacteria from your mother, I would think that the variety of intestinal flora later in life would have more in common with the person whom you live and regularly swap bacteria, rather than your mother – unless your family practices are out of the ordinary.

  2. Morris Keesan

    My kid would be totally interested in all of the nitty-gritty details, if one of his parents were getting a fecal transplant.

    Regarding C-sections and newborns not getting their normal set of birth-canal bacteria: earlier this year, I was listening to a bit about this on a BBC radio science show (which also talked about fecal transplants), and I remember wondering whether the increase in the rate of C-sections in the last half of the 20th century could be related to the increased incidence of food allergies among young kids. When I was in elementary school, everyone brought peanut butter sandwiches for lunch, and we never heard of nut allergies. (Which may have been because kids with severe allergies like that didn’t survive long enough to go to school.)

    Re treatments to restore your intestinal flora — go to any health food store, and ask about “probiotics”. Or even look in your ordinary supermarket for “active-culture” yogurt. Whether or not any of this works, there’s certainly stuff out there in the consumer marketplace.

    (And I was perversely amused by Zach talking about over-worrying about bacteria, while sounding like he was coughing up a lung. And yes, I know, if it’s really flu, then it’s viral, not bacterial. But still funny, the way other people’s misery often is.)

    1. KWeinersmith Post author

      I was at a lecture on gut bacteria and the guy giving the lecture said he used over the counter probiotic pills as his experimental controls because they have some bacteria, but are pretty much worthless for recolonization. That being said, he might have been using a particular kind of probiotic that was worthless, and so maybe they aren’t all worthless. I imagine if commercially available probiotics actually worked then fecal transplants might not be necessary. Hard to say!

      p.s.-yes, other people’s misery is hilarious.

      1. Morris Keesan

        Over-the-counter stuff being worthless has never seemed to affect sales. Look at how much gets spent annually on homeopathics. (Hey, maybe we could start of line of homeopathic probiotics: tablets with no measurable amount of bacteria in them at all. The more you dilute it, the stronger it gets!)

        1. Morris Keesan

          P.S. Zach, even while laughing, I do hope you’re really feeling better than you sound, because you sound like fecal matter.

  3. Violet Jane

    I find myself wondering now if the root of a few of my developmental issues and my medical problems could be associated with being extracted through C-Section. I guess the world will never know! Unless, of course, science pops up and says “Hi! We brought you some news!” I would definitely like to see more research on this subject!

    Anywhoo. I would really like to thank you Kelly and Zach Weinersmith. You guys really help bring light on subjects that otherwise I would have never heard of! You guys present yourselves in an entertaining manner, and have fantastic chemistry. I honestly look forward to the show each week! Thank you!

  4. Paul Smaldino

    Great show guys. I found the Heijtza et al. paper especially interesting, partly because I’ve been on a neural development kick lately (because I am the coolest). The GF mice showed decreased expression in both the amygdala and hippocampus, regions associated with anxiety and (spatial) memory, respectively. Maybe the GF mice aren’t as good at processing where they have been, and as such don’t form “cognitive maps” as easily, if at all, which would explain the pattern of exploratory behavior in the open field test. Normal rodents loop around when exploring to start, but eventually settle into a pattern of exploratory ventures from and to specific “home bases.” Damage to the hippocampus disrupts this process, forcing them to exaggerate the looping behavior, possibly because they can’t “path integrate” to remember specific routes. Food for thought.

    Relevant papers for those interested in spatial learning, hippocampus, and cognitive maps:
    Patterns of rodent exploratory behavior and learning. Avni et al. 2006

    Grid cells, place cells, and the brain’s cognitive maps. Moser et al. 2008

    Spatial learning, hippocampal lesions, and path integration. Whishaw 1998.

  5. Philosophantry

    I can see it now… “Honey, can you take out the trash please?” “Women, don’t tell me what to do, I GAVE YOU MY POOP!”

  6. Dr. John

    Great show! There’s a lot of interest in the “probiotic” area, lots of it sponsored by Dannon. There’s a really good set of CEU webcasts by the American Gastroenterological Society at


    Where you’ll find a superb presentation done by Dr. Fergus Shanahan,
    University College Cork, Ireland, with the curious title of:

    Clinical Endpoints Using Probiotics & Prebiotics for IBD, IBS, & Infectious Diarrhea

    This is very highly regarded by some leaders in the area. He has a great “rant” from a 100 year old New York Times article slamming worthless OTC probiotics.

    The New York Academy of Science (NYAS) also has an excellent series in the area at
    (click on the “media” tab to see the list of presentations)


    The NYAS also does a fun “Science in the City” public (easier to understand) podcast series, the one called More Than a Yogurt Cup (although I liked the ones on chocolate and beer a bit more 🙂 at


    or check out http://www.scienceandthecity.org

    PNAS rules 🙂

  7. Pingback: Episode 27: Antimicrobial peptides and Truvada | The Weekly Weinersmith

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