How Microbes Make Malnutrition Worse

Feb 23, 2016

Photo credit: Mike Hutchings/Reuters

By Ed Yong

Several years ago, a group of gut microbes went on a 14,000 kilometer-long trip. Having freshly emerged from an infant in southern Malawi, they were scooped up by eager scientists, frozen, stored in cold boxes, exchanged from one courier to another, flown across the Atlantic Ocean, driven to the Washington University in St. Louis, and finally transplanted into the bodies of germ-free mice that had been raised all their lives in a sterile bubble. Their epic voyage was part of a study by Jeffrey Gordon, showing how the microbes of our gut contribute to the problems of malnutrition—and how they might help to fix them.

Gordon is a leader in the study of the human microbiome—the trillions of microbes that share our bodies and influence our health. A few years ago, his team showed that malnourished children grow up with different gut microbiomes. These communities change during early life. Waves of species replace each other in predictable steps, much like new landscapes get colonized by lichens, then shrubs, then trees. Normally, it takes three years for the communities to reach an adult state. But this pattern of succession slows and stagnates in malnourished children, leaving them with a microbiological age that lags behind their biological one.

This hidden immaturity matters because our microbes help us to harvest energy from our diet. If they’re not doing that effectively, their hosts might suffer, especially when their diet offers very little energy to begin with. “Most people think about development from the perspective of our human cells and organs, but there’s another facet to it–our gut microbiota, an organ composed of microbes,” says Gordon. “It gives us a more transcendent view of human developmental biology.”

Now, following similar work in Bangladesh, Gordon’s graduate student Laura Blanton studied the changing microbiomes of 60 healthy Malawian infants, and devised an algorithm that calculated their microbiological age based on the species in their guts. She then applied the algorithm to another group of 259 babies, and found that their microbiological age scores at 12 months predicted how much weight they had put on by 18 months. That’s a sign that the microbes are influencing the babies’ growth, rather than merely reacting to them.

The team found another such sign by transplanting stool samples from Malawian infants into sterile baby mice. Even though all the rodents ate the same food, those that received microbes from an underweight infant put on less weight and developed weaker bones than those which received a healthy baby’s microbiome.

So, if certain gut microbes can stymie a baby’s growth, perhaps others can speed things up? To find out, Blanton simply implanted mice with microbes from either a healthy infant or an underweight one, and housed them together in the same cages. Mice willingly eat each other’s poop, and so regularly bombard their own microbiomes with those of cage-mates. And in these “Battles of the Microbiomes”, the healthy communities came out on top, invading and displacing the immature ones.

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