microscopic organisms in a petri dish

It’s a Jungle in There

New possibilities are opening up for understanding the impact of microscopic organisms on our health, food and environment.

By Kara Gavin
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Your digestive system, the ocean, the soil where your food grows and your mouth have something in common. They’re all home to teeming communities of microscopic organisms. Trillions of individual bacteria and other wee beasts live in just a few inches of your gut, or your garden.

And without them, not only would your food not grow properly in the first place, but you wouldn’t be able to digest many components of the food. You wouldn’t even be “you” — because more than half the living cells in your body aren’t human. They’re microbes.

The microbiomes of your body — the communities of microscopic creatures and the miniature habitats they occupy — may not seem to have much to do with those in the broader environment.

But new interactions between scientists studying all of them may prove that there’s more in common than we think. And, they’re coming to realize, research on one type of microbiome may boost efforts to study others.

Last month, hundreds of researchers from many different lines of work came together at the University of Michigan for a meeting aimed at searching for those common threads and tools. They also looked at the ethics and potential implications of altering “natural” microbiomes through human action.

Their gathering came just days after the White House Office of Science and Technology Policy announced a major new initiative aimed at understanding microbiomes across the realms of nature and human health.

Part of that announcement was a $3.5 million commitment from U-M to advance microbiome research and education, beyond the $15 million the Medical School has already committed through a multi-year initiative begun in 2013.

Other universities, government agencies, companies and foundations are also pitching in, making the new national initiative worth nearly half a billion dollars in research and innovation.

What led to this convergence of events?

“The national and Michigan initiatives are both aimed at bringing attention to this area of research, and the notion that healthy microbiomes are essential for human health and the health of the planet,” says Thomas Schmidt, Ph.D., a professor of internal medicine, of microbiology and immunology, and of ecology and evolutionary biology who heads the U-M Center for Microbial Systems and was invited to the White House for the announcement. “It’s bringing together money from different federal agencies, all of which have microbiome programs existing, and expanding them.”

That cross-disciplinary push will be vital for progress, says one of Schmidt’s closest U-M colleagues.

“The idea that the findings and principles from one area of microbiome research can impact the others, that you can’t compartmentalize it and that you don’t have to reinvent everything for your field, is growing,” says Vincent Young, M.D., Ph.D., who co-leads the Host Microbiome Initiative and takes his research directly into the hospital halls at the U-M Health System. “The strength comes from people communicating. The medical field can benefit from learning from other fields of microbiome research that bring in their perspectives and tools.”

Scientists have studied microbiomes in the oceans and terrestrial environments for decades. They’ve worked to understand everything from the way microbes help plants interact with the soil surrounding their roots, to how nutrients in the seas help tiny algae generate incredible amounts of oxygen for the rest of us to breathe.

In fact, Schmidt notes, the term “microbiome” was first coined by scientists studying the collection of microbes on the surface of plant leaves.

Research in plant and soil microbiomes has increased crop yields to feed a growing population of humans and livestock, and boosted understanding of the crucial role that microscopic organisms play in keeping our planet humming.

Now, scientists are proposing provocative experiments that would seek to alter microbial ecosystems on a large scale — for instance, adding iron to the ocean at a scale that might boost algae growth and remove greenhouse gases from the atmosphere. And awareness is growing about the unintended impact of the massive manipulation of animal microbiomes in the form of antibiotics used in raising livestock.

In the last decade, those who study human health have awoken to the critical role that microbes play in various areas of our own bodies. In the last handful of years, their findings have grabbed headlines that the microbial ecology research in other environments never did.

Every day, it seems the media trumpets how doctors and medical scientists have made new discoveries about the colonies inside our bodies. Articles abound about how disruptions to the balance of organisms in those colonies might be associated with many diseases and conditions, including diarrhea, depression, tooth decay, pneumonia and sepsis.

Industry has gotten out ahead of scientific knowledge, says Young, as evidenced by advertisements for yogurts, supplements and granola bars containing probiotics — or compounds that allegedly help our natural microbiomes.

None of these products has yet received the kind of scrutiny about their claims that would allow anyone to say for sure whether they do what they say they do. That’s why their ads and packaging tiptoe just up to the line of claiming an effect on health. Some drug companies are now pursuing that kind of evidence for new products through a formal Food and Drug Administration process.

Altering human microbiomes to address disease is also being tested on the other end of our digestive system, through fecal transplants being tried and evaluated at U-M and at a growing number of hospitals. In such transplants, stool samples from healthy patients are transferred to the colons of those with intractable digestive-tract infections, in an effort to rebalance their gut microbiome.

The evidence is growing that this can help patients with the life-threatening infection caused by Clostridium difficile, or C. diff, bacteria. But the jury is still out on how well these work for other conditions says Young, who is also an associate professor of internal medicine and of microbiology and immunology.

Scientists in different microbiome fields can learn from one another, and so it might be possible to apply knowledge across fields. For instance, new understanding of how microbes inside us “scavenge” iron from our food could help the researchers trying to influence algae growth in the ocean by adding iron.

Data-sharing, and pooling of methods for handling, modeling and visualizing the massive amounts of data that come pouring out of microbiome studies, will be vital going forward, Schmidt and Young say. The influx of funding into the human microbiome research world may fuel the development of new knowledge faster than ever.

And even though the applied research grabs the headlines, it’s the quiet, steady work of basic scientists and clinical trial leaders that will have the most impact.

“It’s incredibly important for the medical community to be on notice that the microbiome wasn’t invented to study human health and disease,” Young says.

It’s time, Young says, to do studies that will truly establish which linkages between microbiome disruption and human health are truly causal, and whether manipulating those microbiomes through nutrition, supplements or transplants actually has an impact.

“We still don’t have answers to some of the basic questions,” Schmidt says. “But unifying all these people looking at microbial communities will likely improve our ability to affect the health of the planet and the plants, animals, humans and ecosystems that exist here.”