IRA FLATOW, host:

For the rest of the hour, the real scoop on baby poop. The world of a human gut is mysterious. I know this may - it's lunchtime now in California. And scientists think that the thousands of bacteria living in our intestines protect us from disease as well as keeping our body healthy. But how this microscopic ecosystem works is really unknown.

To answer the question, our researchers decided to go to the source. Researchers at Stanford University thought that they should start right at the beginning by looking at instant poop. Here to tell us about the study, which was published in the July issue of the Public Library of Science Biology is Chana Palmer, who used to work for PhD thesis. She's now program director at the Canary Foundation, helping to bring scientists together for cancer research.

Welcome to the program, Dr. Palmer.

Dr. CHANA PALMER (Program Director, Canary Foundation): Yeah.

FLATOW: Hi. Welcome to SCIENCE FRIDAY. Can you hear me? We're having trouble. Can she hear me? Chana Palmer, are you there? Hello?

Dr. PALMER: Hello.

FLATOW: Hi, there. Can you hear me, doctor...

Dr. PALMER: Yes, I can.

FLATOW: Ah, good. Thanks for taking time to be with us. How did you - tell us exactly what you're doing? What is this about the baby poop that is so interesting to you?

Dr. PALMER: Well, it's our first window into the bacteria that live with us for our entire life. So we are born without bacteria and we develop, eventually, a population that outnumbers our human cells by a factor of 10. And we know very little about what these bacteria do, and we figured the first step was to figure out which ones are there.

FLATOW: You mean each of us have our own unique flora and fauna in our guts so to speak?

Dr. PALMER: Exactly, yeah. In fact, one of the messages of the story is how unique our different bacterial populations are or the ecosystems or communities that live within us. Each baby - we had 14 babies in the study. Each of them had a unique mixture of bacteria living within them.

FLATOW: Well, and so how did you go about collecting these samples?

Dr. PALMER: Well, we had a lot of help from their parents actually. We recruited 13 parents around the Stanford area, which was remarkably easy. And we asked them actually to collect the stool samples at home, to scoop them immediately out of the diaper using these little vials we provided that have little spoons in the lid. And they stored them temporarily in their home freezers. Then at periodic intervals, I would come over their house and collect them and bring them back to the lab.

FLATOW: Oh my goodness.

Dr. PALMER: Yes.

FLATOW: They had no problem with storing these frozen poop samples in the...

Dr. PALMER: Yeah. Well...

FLATOW: Some are next to these frozen milk samples there.

Dr. PALMER: Yeah, we had them do some breast milk for us as well. We also obtain vaginal swabs from the mom, which involves me meeting them at the doctor's office right afterwards and running home to the freezer. So it was a little bit logistically complicated but we managed to pull it off.

FLATOW: Hmm. And for how long did you study? Did they have to collect these samples?

Dr. PALMER: These babies were followed for an entire year. And they collected much more frequently at the beginning of the year and then less frequently throughout the year.

FLATOW: Mm-hmm. And did you find the difference in different kinds of, let's say, delivery? Were babies who were naturally delivered different than caesarian sections?

Dr. PALMER: I don't think we have enough babies to answer that question really yet. We had - we did have five babies with C-sections and the remainder were naturally delivery. One interesting thing we did notice is that there were two babies that were delivered by planned C-sections, and these happened to be a pair of twins. The interesting story there was that those twins - since it's planned C-section, those were the only babies where the baby never actually encountered the mother's vaginal canal. And it so happens that those babies were the latest to actually acquire a substantial bacterial population in their guts.

FLATOW: If they're born with sterile guts, so to speak, where do they get their seed population of bacteria?

Dr. PALMER: Yeah, that's a very interesting question. And when - we can start to, you know, hinted answers to that based on the samples we had here. We found that they come from a variety of different sources. We found some babies where there would seem to be a lot of similarity between the baby's early samples and the mom's vaginal sample. And another baby is that would be similar to the milk or to actually, the mom's stool sample.

FLATOW: Wow. Was it hard to find moms to participate in this study?

Dr. PALMER: It was remarkably easy. I think, maybe, having it in the Stanford community helped. We had a number of physicians enroll in the study, and people who are interested in science.

FLATOW: Well, you know, let me just put it gently. If you're involved with moms, you have to help swab out different parts of their bodies, you're going to get pretty, you're going to bond with them, aren't you after a while?

Dr. PALMER: Yeah. I definitely consider all of the families to be friends of mine now.

(Soundbite of laughter)

Dr. PALMER: I hope they feel the same way.

FLATOW: Well, what about the father? Did you test fathers or the people who come in contact with the babies, changing diapers or whatever?

Dr. PALMER: Yeah, we did end up deciding, near the end of the study, to ask the fathers to provide samples. Not so much because we thought they're still would be in direct contact, but we thought we could maybe try and look at whether there was fathers who are more similar to their own baby than other babies for example. And the fathers were very obliging as well. So we had wonderful volunteers for this study.

FLATOW: Mm-hmm. So did you determine if the micro-ecosystems of our gut are determined by genetics or by the environment, did they got this from the environment, you know?

Dr. PALMER: Yeah, well, this study wasn't designed to specifically answer that. What I can say the study told us is that the process of colonization does seem to have rules that govern it. And it would be some combination of environment and genetics. And we can say that because we had one pair of twins in the study and they were by far the most similar pair of babies. It's hard at this point to tease apart how much of that was environment and how much of it was genetics. But previous study tell us - and there are mechanistic reasons I think there could be a genetic basis. But I think we'll have to some further family studies to really tease that apart.

FLATOW: Though you had those paternal twins, right?

Dr. PALMER: Mm-hmm. Yeah.

FLATOW: And they...

Dr. PALMER: Yeah. That was very fortunate for us.

FLATOW: Yeah. Why do we care about the microscopic organisms in our intestines? Why is this something you want to study?

Dr. PALMER: Well, for one thing, there are a number of diseases where we know that the microbes in our gut are contributing. And we imagine that as we better understand these communities, we'll be able to track down bacterial causes of more and more diseases.

So we need to understand in the study we're trying to contribute to the what? A healthy bacterial mixture looks like and so that eventually, you can compare different disease states and see, you know, what's going wrong.

FLATOW: We're talking about baby poop this hour on TALK OF THE NATION: SCIENCE FRIDAY from NPR News. I'm talking with Dr. Chana Palmer, director of the Canary Foundation. Our number 1-800-989-8255. Let's go to Devin(ph) in Salt Lake. Hi Devin.

DEVIN (Caller): Hello.

FLATOW: Hi there.

DEVIN: Hi. I'm actually calling about the previous guest but this guest is, it's a direct relation at this one. My question deals with probiotics and how the relationship between microorganisms in our gut affects the regulation of body weight and also the immune system development.

Dr. PALMER: Well, yeah, there are some very interesting studies of mice that are raised with no bacterial flora, and their immune systems do not develop properly so they're currently important in that capacity. I think we don't really know yet exactly how to manipulate those populations, and if you were to give a probiotic, how long it would actually, how long that bacteria would live in the gut.

We saw in our study that they actually reorganize and change considerably at fairly regular intervals, so it maybe that they would persist for awhile but not even...

FLATOW: Right.

Dr. PALMER: ...stick around.

FLATOW: You know, when you take medication, take specifically antibiotics, the doctors say you watch out, you'll get a stomachache. These antibiotics may kill the bacteria in your gut. Did you see that with these babies?

Dr. PALMER: Yes. In fact, we did have one very dramatic example of a baby that got, you know, typical antibiotics, Augmentin, and there are bacteria were entirely wiped out. That baby...

FLATOW: Wow.

Dr. PALMER: ...you know, it rebounded fairly quickly and ended up looking, you know, not distinguished, distinguishably different from the rest of them by the end of the year. But we saw that at least in some cases that it can be very dramatic and, but not in every case, though. It's varied for baby to baby about how - what the effect of the antibiotics was.

FLATOW: Do you see the possibility of finding out what the best mixture of bacteria in your gut might be when you, you know.

Dr. PALMER: Yeah, I think there is - there's definitely a hope for that. We'll need to develop some new tools; of some new ways to measure what a good community is so that's very interesting. We don't know what should we strive for.

FLATOW: How many different kinds are there?

Dr. PALMER: Well, there - so far are been at least 400 species identified living in our guts not in an single individual, but...

FLATOW: Right.

Dr. PALMER: ...we're definitely in the hundreds.

FLATOW: Right. So you might, there might be some day where they'll take a stool sample and say, you know, you don't have enough of this kind. Because we know that to be a good bacteria, we'll just give you some of that?

Dr. PALMER: I think it's conceivable that we could that. As I say, it's not for sure that we can make sure it would stick around, but perhaps if we know what combination of bacteria works well together, we can make it so that it'll stick.

FLATOW: Mm-hmm. At what time, you know, at what point you actually start seeing the bacteria growing in the gut?

Dr. PALMER: That varies from baby to baby but it was, as early as 24 hours and for the twins who I said were the latest, it wasn't until about seven days that we had a large population.

FLATOW: Mm-hmm. Is there anybody else collecting baby poop besides you guys?

Dr. PALMER: Yes. There are other people collecting baby poop, but they just haven't used the same tool that we've been using.

FLATOW: What tool is that?

Dr. PALMER: It's a microarray-based tool, which uses DNA to identify the bacteria.

FLATOW: And you could do a lot of them at once then?

Dr. PALMER: Yeah. The great thing about this tool is that it allows you to look at a lot of samples and then that data that you gather is both - it gets a very detailed picture of the population.

FLATOW: So how do you take your research further here now that you've gotten to start? What would you - how would you like to expand it?

Dr. PALMER: Yeah. Well, I think one study that's already underway in the lab is a study of antibiotics' effects, of having healthy people voluntarily take courses on antibiotics and to see how their populations change before, during and after.

That's an important one. Ones that we don't have explicitly planned but we'd like to do would be more twin studies to see the, you know, to understand the contribution of genetics and environment.

FLATOW: But what about we adults? Does anybody know what's going on there?

Dr. PALMER: Yeah. Adults have actually been studied more than babies in this respect. And we know that adults each have a unique population and that their bacterial mixtures are quite stable over long terms and maybe even, you know, over a year, you can see not - doesn't change that much usually.

FLATOW: Mm-hmm, because we know that some people take bacteria pills to increase their - the bacteria in their stomachs and intestines.

Dr. PALMER: Yes, so I'm not too familiar with the probiotics area and, you know, what effects you would have, were you to take bacteria.

FLATOW: All right. Well, I'm not going to ask you to speak about something you don't know about.

(Soundbite of laughter)

FLATOW: But we certainly learned a lot. This certainly has been very interesting today.

Dr. PALMER: Thank you.

FLATOW: Thank you for taking time to talk with us and good luck to you.

Dr. PALMER: Thank you. You're very welcome.

FLATOW: Chana Palmer, director of the Canary Foundation and her efforts at collecting baby poop and actually seeing what's inside of it. It's a kind of interesting work.

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