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A preference for dark versus milk chocolate, among other things, shows up in the kinds of healthy germs found in the gut microbiome.

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Still unclear what to do about it, but it's clear that the microbiome is an active area of research.

People who like milk chocolate have slightly different microbes in their intestines than those who prefer their chocolate dark, although researchers do not know why. Significant differences in the so-called microbiome are also found in individuals based on whether or not they eat a lot of fiber or take certain medications—such as the diabetes drug metformin, female hormones or antihistamines.

But all these variations account for only a small fraction of the microbial diversity seen in the guts of northern Europeans, according to new research published today in a special section of Science. Of the half-dozen microbiome articles in the journal, two studies stand out as being among the largest ever conducted on the gut microbes that inhabit healthy people’s large intestines and help with digestion and various immune processes—among other things.

In one, researchers identified 14 different microbial genera that form the core microbiomes of nearly 4,000 people—mainly from northern Europe. This list provides unprecedented insights into the basics of microbial inheritance and evolution, says researcher Martin Blaser, director of the Human Microbiome Program at New York University, who was not involved in either study. “These are fundamental characteristics of us humans,” he says.

Jeroen Raes, senior author of the first paper and a contributing author on the second, says he had hoped that the study would be large enough to offer definitive answers to some key questions, particularly how investigators might manipulate the microbiome to promote greater human health. “I thought I would know the answer by now,” says Raes, who eats lots of fiber and—true to Belgian custom—loves chocolate and beer. But he does not take probiotics, microorganisms that are believed to add to or restore a healthy bacterial balance. Nor does he really know what to make of the fact that so many medications appear to affect the makeup of intestinal bacteria. “It’s one of those ‘hmm, interesting,’ moments,” he says, adding that, nonetheless, he thinks variations in the microbiome will eventually be shown to influence the effectiveness of certain drugs as well as the side effects that they can cause. His research, he says, highlights the complexity of the system as well as likely flaws in earlier research.

The Belgian study, for instance, failed to find a benefit for participants who had been nursed or delivered through the birth canal, compared with those who had been fed formula in bottles or brought into the world via Caesarean sections. Previous experiments looking at newborns had, in fact, found a difference. (Healthy germs from moms are thought to coat their babies who are born vaginally, helping the infants establish a robust bacterial baseline. Some studies suggest that babies delivered by C-section are at higher risk for asthma and allergies—possibly because they lack this early protection.)

We are starting to learn to manipulate the microbiome:

Still, scientists are making some progress in learning how to manipulate the microbiome, says Tommi Vatanen, a graduate student researcher at both the Broad Institute in the U.S. and Aalto University in Finland. “There are very small puzzle pieces that we are starting to understand—maybe the corner pieces of the big puzzle,” says Vatanen, who was a co-author on the Dutch study. If he had small children today, he says, he would give them probiotics with Bifidobacterium, a common component of a healthy microbiome, and get them a dog—which apart from being a great companion also has a microbiome that, studies suggest, may help protect toddlers under a year old against developing certain illnesses later in life.

Ley says she’s not ready to encourage people to take certain probiotics or supplements. But she does avoid antibiotics whenever possible. And she eats yogurt as well as the Korean cabbage dish, kimchi—both of which are known to contain a variety of healthy bacteria.

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