Mysteries of the Microbiome

A U of M associate professor explores the complex world of human microorganisms and the cures they may hold

He's looking to go back in time to a place where the human diet has been unchanged for millions of years. Part of the problem is modern norms that put a premium on baby hygiene — ironically putting kids at greater microbial risk down the line.

"We've started to isolate these kids, and in the process, reduced a lot of the bacteria that they may have taken up," says Leach, skyping from Tanzania via a satellite dish connected to his Land Cruiser's battery. "Kids in the western world — by the time they're 8 to 12 years old, they have a diversity of bacteria that looks very adult-like, but they acquire it very slowly. We think hunter-gatherer groups acquire diversity much faster. So maybe one of the problems with our youth and all these allergies and auto-immune diseases may have to do with delayed acquisition of diversity."

An anthropologist by background before becoming interested in the microbiome, Leach is the founder of the Human Food Project. His group is attempting to crowdsource an idea about what the major bacterial configurations are in our bodies. It's an offspring of the Human Microbiome Project (HMP), which used a $115 million National Institute of Health grant to explore what a healthy microbiome might look like.

Dr. Alexander Khoruts at the U of M is a leading researcher in the new science of the microbiome
E. Katie Holm
Dr. Alexander Khoruts at the U of M is a leading researcher in the new science of the microbiome
Ellen Bolte (left) dedicated herself to helping son Andy (middle) recover from autism-like symptoms
Ellen Bolte (left) dedicated herself to helping son Andy (middle) recover from autism-like symptoms

The Human Food Project's effort, called the American Gut Project, is soliciting samples from everyone and anyone willing to donate $99 to help defray the cost of analysis. They've already received 7,000 samples, and though they've processed only a third, patterns are already starting to emerge.

"We're still finding new types of configurations, although the rate of discovery of these new configurations is starting to level out," says Rob Knight, a fast-talking New Zealander from the University of Colorado whose computer algorithms have helped this revolution in knowledge. "It's interesting because we're all 99.9 percent the same in terms of our human DNA, but if you take two people, their microbial communities can be 80 to 90 percent different."

Though advances in genetic sequencing have led the way, microbiologists were left with massive piles of genetic data. Knight developed computer algorithms to sort the data into phylogenic trees based on the DNA's relationship to a particular RNA molecule.

These family trees offer insight into a bacteria's modus operandi. Recent research also indicates that once one kind of bacteria occupies a niche, it's very hard for a similar family member to dislodge it.

Leach notes how strange our ancestral neighbors would seem to us today. The Hadza breastfeed for two or three years and start eating solid food much later than us. Much of the mother's gut bacteria finds its way into the children through her breast milk.

Because the Hadza have more bacterial variety and less inflammation/auto-immune disease, researchers suspect that their environment or lifestyle may be conferring a bacterial benefit. Children raised on farms have been shown to have more diverse gut bacteria than those from the city.

So Leach is going native. After returning to the states for the holidays, he'll return to Tanzania and start living like a Hadza for four months.

"The question is: If I eat their food, dig their roots, live in their dirt, and drink their water, can I get my bacteria to look like theirs, and how long does it take, if it happens at all?" he asks.

One of Leach's collaborators is Maria G. Dominguez-Bello, who has also examined the gut bacteria of isolated Amazonian tribes. Besides working with the tribes, Dominguez-Bello is looking at the gut bacteria of children born by caesarean section.

Babies born by the traditional method emerge covered with their mother's microbiome after passing through the birth canal. Research has linked C-section to asthma, allergies, obesity, diabetes, and eczema. Dominguez-Bello is looking into whether it's possible to seed C-section babies with their mother's microbiome right after birth.

Between infant formula, C-sections, antimicrobial soap, and widespread and reckless application of antibiotics, we've waged war on ourselves without even knowing it.

"I think how we define self is possibly a bigger idea today than Darwin's idea of natural selection," Leach says. "And it's staring us right in the face."

Whatever useful treatments come out of our discovery of the microbiome, for the moment it's hard not to revel in this strange idea that our bacteria may be as much a part of what makes us human as our heart or brain.

"We are not just human beings. We are an ecosystem. We're not solely a function of our genes, the human genome, but also all those genes provided by bacteria of which we know very little," says Dominguez-Bello. "In order to be healthy we need them. They have co-evolved with us, and if we eliminate them we may pay the consequences."

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