What’s in a baby poop?

What’s this? An invitation to discuss poop? And I have a baby? Do you not know moms of infants? I can hardly spend a day without talking about poop. And familiarity has not bred contempt for the poopy diaper. They say that diapers are not as gross when it’s your own child, but I have to break the news here – that’s complete crap. As it were. All poopy diapers are gross. Do not fail to respect the poopy diaper.

Surprisingly, the lowly feces may be the window to the most complex organ in the human body. I’m not talking about the intestines, but actually the bacteria that live inside them – what’s known as the human normal flora. Not merely the source of “ick,” the gut intestinal flora helps digestion, modulates the immune system, and protects the cells of the gut.

How does a baby, coming from a sterile womb, develop its intestinal flora? I contacted a friend of mine, Dr. Emma Allen-Vercoe, Assistant Professor of Molecular and Cellular Biology at Guelph University, to ask her. Emma, a delightful British expatriate with a quirky sense of humor, studies intestinal ecology in humans. Which means that she spends an inordinate amount of time dealing with poop. And she’s a mother of two girls. So that’s like a double whammy – poop at home and at work.

Emma sent me a couple papers dealing with the development of the microflora in babies and what I learned really surprised me. Traditionally it was thought that infants were inoculated with the flora of their mothers as they passed through the birth canal. However, babies born by c-section are not delayed in the development of their intestinal communities. Instead what seems to be the determining factor in the development of early microbial communities is whether or not the infants breastfeed. And it seems that the bacteria that colonize the infant gut comes directly from the breast milk (Martin et al. 2007. Research in Microbiology. 158:31).

It’s long been known that you can cultivate Lactobacilli, a very friendly and common intestinal resident and component of many probiotic mixes, from breast milk, but it was assumed that the original inoculum came from the birth canal to the baby’s mouth, then baby’s mouth to the breast. However, the finding that c-section babies and their mothers show similar levels of Lactobacilli in babies’ stools and breast milk contradicts that theory. It’s unclear how Lactobacilli are getting in breast milk, but Emma suggests that evidence is pointing to translocation from the gut.

The story gets more interesting yet: it turns out that breast milk also contains milk oligosaccharides that the infant is incapable of digesting. They can be eaten, however, by Bifidobacteria, specifically a subspecies of B. longum that colonizes the infant gut. While it’s chemically possible to generate hundreds of oligosaccharides, only those that are potential food for important microflora are produced in the breast (Sela and Mills, 2010, Trends in Microbiology, 18:298).

That breast milk supplies both beneficial bacteria and food for these bacteria suggests that intestinal microbiota is far more important and sophisticated than we typically think. The time from birth to when an infant is weaned is the time when this microbiota is established, and once established, is largely stable throughout an individual’s life. In fact, a person’s microbial community may be as distinct as a fingerprint. It’s a poo print.

And that brings us back to poo. Unglamorous, maybe, but an invaluable research tool? Definitely. Emma has developed sophisticated chemostats for the culturing of gut microflora to mimic the ecology of the distal gut. These chemostats are computer monitored to maintain proper flow rates, retention times, and feeding rates, and are affectionately called “roboguts.” “They stink,” says Emma, “and I love them.” Using paired roboguts seeded with feces, Emma and her students are able to mimic challenges to the gut microflora to see what happens to the community. For example, the hormone norepinephrine mediates the stress response. When added to a robogut with a stable microbial community, the community is immediately disrupted and the populations exhibit chaotic dynamics.

The intestinal microflora probably plays a large role in the development of the gut and immune system. Mice raised in sterile environments posses intestines that fail to fully develop. In babies, the intestinal microflora is dynamic over the first two years, but largely approximates an adult community by the time they are eating adult food (Martin et al 2007). Emma and her colleagues are involved in front line research that suggests that challenges to the normal flora within these years may be implicated in regressive autism. Children with regressive autism develop normally until about two years, then suddenly become autistic. They are also plagued with gastrointestinal upsets: diarrhea, constipation, pain, even distended bellies. While traditionally, it was assumed that the GI complaints were secondary to the autism, Emma and her colleagues are investigating whether the GI disorder is causative.

As you can imagine, this is a conversation that can induce paranoia in any first time mom; my first reaction was “HOW DO YOU FEED YOUR BABY TO MAKE SURE THIS DOESN’T HAPPEN??!?!” Furthermore, the furor over the now debunked link between vaccines and regressive autism shows how loaded the issue is. (I have done a lot of research on the whole vaccine issue so let me be perfectly clear: THERE IS NO LINK BETWEEN VACCINES AND AUTISM. SO VACCINATE YOUR CHILDREN.) Emma’s advice to me was strongly pragmatic: “quit worrying, and let your baby take the lead. The bugs in your gut control you: what you crave to eat, and to some extent, how you behave. Your baby will let you know when she’s ready for something new, or not ready.” The stability of the intestinal community shows how incredibly resilient it is, and certainly having evolved in a strongly non-sterile environment for most of our evolutionary history would have had to have made our intestinal communities quite tough. So relax. There’s a whole sophisticated army of bacteria in the gut of every infant doing battle to protect their home.


7 Responses to “What’s in a baby poop?”

  1. The Science Goddess August 20, 2010 6:22 am

    So, if breastfeeding is so critical to the establishment of intestinal microbiota…what happens with children who are exclusively formula-fed from birth (e.g. adoptees, children whose mothers die in childbirth)? Are there enough of the Lactobacilli and Bifidobacteria in the immediate environment to compensate?

  2. Lucius Reinhard August 20, 2010 10:22 am

    Cool website Thanks for writing this.

  3. admin August 20, 2010 1:16 pm

    Hey Science Goddess – great question. I’m still looking into it for a more definitive answer, but here are some quick points – inoculation from skin, vagina, and nipple of mother still gives baby most of the same species. Formula fed infants may even have a higher number of bifidobacteria faster (like, by three days instead of four days) than breastfed babies, because it takes a couple days for the milk to come in. Also, newer formulas have probiotics and complex oligosaccharides included. There are some definite differences, but still by a year breastfed babies and formula fed babies have microflorae that converge to the same species.

  4. Emma Allen-Vercoe August 20, 2010 1:35 pm

    Hi, Science Goddess – Carla just alerted me to your post. Great question, and one that is commonly asked. There have been some recent studies that show a difference between the microflora of breast vs. formula-fed infants. Specifically the difference seems to be in the types of initial colonizing bacteria early on following birth, although the Bifidobacteria in particular do colonize formula fed babies in high numbers, just not as high as in breast-fed babies. Perhaps it is also important to realize (as many of us in the field now are) that it is not as much a question of which bugs are colonizing as it is a question of what they are doing there. The gut is a largely oxygen-free environment, and so most of the bacteria that live there carry out fermentation – that is, they convert carbohydrates to alcohols and acids. Mostly, they make short-chain fatty acids, and the profile of these acids that they make is quite distinct between particular bacteria. Now, if you compare the short-chain fatty acid profiles in the guts of formula- and breast-fed infants, you will find that they are very different. As to what that means in terms of health – well, we don’t really understand that yet. One of the confounding factors is that some short chain fatty acids are beneficial to colon health at low to moderate concentrations, but toxic at higher concentrations, and the concentrations are very hard to define because everyone’s tolerance is different.
    Another confounding factor is that when we study bacteria in the guts of infants, we are looking at poop, which reflects what is in the gut but doesn’t tell the whole story. To tell the whole story you would need a sample of the actual gut lining, as believe it or not the microbial population that lives here is different from the one that lives in the gut lumen – the poop. As you can imagine, it is not ethical to suggest that neonates undergo colonoscopy and biopsy removal for the sake of science, and so the question of microflora differences between formula- and breast-fed infants has really gone largely unanswered.
    All that said, the other side of the coin is that our gut microbial community is an extremely resilient thing, with much built-in redundancy to protect us against all that life throws at us. I myself was formula-fed, having been born into an era where this was the norm, and now aged 38 I seem to be doing OK. In fact, I’ve profiled my own gut bugs and they are thriving! I will even stick my neck out and suggest that way above formula-feeding, a far greater danger to our gut microbial passengers is repeated antibiotic use, particularly in childhood. But that’s another story for another blog. Hit it, Carla!

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