Gut Check

Thousands of species of bacteria, viruses and fungi live on and in our bodies. Microorganisms teem in every pore and crevice, from mouth to stomach to intestines to colon.


October 15, 2015

Illustration by Lisa Haney
Illustration by Lisa Haney

We’ve all gone through it and wished we hadn’t: growing discomfort, a stomachache and nausea, maybe vomiting and diarrhea. For most of us, symptoms pass in a day or two. We call it “stomach flu” or “food poisoning.” But for Pat (not her real name), the symptoms did not improve, so she went to her doctor. He concluded that she had picked up a parasite during a recent vacation and prescribed an antibiotic. That might have been the end of it. But the 35-year-old woman’s debilitating struggle with intestinal distress and bacterial infections was just starting. Before it was over, she landed in the hospital twice and lost so much weight and became so weak that she had to walk with a cane. Her hair fell out. Her doctor told her he might have to remove part of her colon.

“He said, ‘It’s not so bad,’” Pat recalls. “‘You wear a little bag. Lots of people live with one.’”

In the late 1990s, when Pat was in the throes of her illness, antibiotics and surgery were the major medical options for people with inflammatory bowel disease, colitis, Crohn’s disease and related illnesses. Scientists and physicians knew that microorganisms played a role in digestion, the immune system and other bodily functions, but there was little understanding of the diversity and ecology of this community — nor of its complex relationship to human health.

At that time, microbiologists needed to grow an organism in the laboratory in order to study it. “No one in the field thought we were doing comprehensive surveys of microbial diversity by culturing microorganisms,” says Thomas Sharpton, assistant professor in the Oregon State departments of Microbiology and Statistics. “We were doing the best that we could.”

It turns out that most of a body’s microbial residents won’t grow in a laboratory culture dish. And the idea that organisms could be identified through genome sequencing was still a dream.

Microbe vs. Human

Microbiome research is poised to transform society: It has captured public imagination, ushered in new industrial opportunities, and potentiated changes in how we manage health and natural resources. The Oregon State University Microbiome Research Faculty in a June 2015 letter to the Office of Science and Technology Policy

In 1907, Élie Metchnikoff, a Russian microbiologist, proposed that microbes in our gut could exert a powerful influence on health (see “Five Facts About the Microbiome”). But it wasn’t until 1972 that a University of Missouri scientist estimated that, based on analysis of a single gram of feces, microbes in the body outnumber human cells 10 to one. That simple ratio has been passed along in scientific papers, lectures and news media and is now considered crude at best. Still, the point remains: When it comes to our health, we may be as much microbe as we are human.

Pat and thousands of people like her learned this lesson the hard way. What if, rather than using radical surgery or broad-spectrum antibiotics, intestinal health could be restored with simplicity and precision, perhaps by getting a vaccination or by following a strict diet? What if physicians could diagnose and treat illnesses in the gut on the basis of a deep understanding of this dynamic system?

microbes-16The new picture that is emerging through research is not for the squeamish. Thousands of species of bacteria, viruses and fungi live on and in our bodies. Microorganisms teem in every pore and crevice, from mouth to stomach to intestines to colon — all along the alimentary canal, which, if removed and stretched end to end, would measure about 30 feet. Microbes deploy chemicals in an ongoing competition for resources, and the full picture is just coming into view.

“It’s a little like being Dr. Livingstone and walking around in the jungle and saying, ‘What’s that?’ and ‘Oooh, what’s that?’” Sharpton says. Researchers are discovering that the biologically active compounds produced by these microbes likely play a role in diabetes, obesity, atherosclerosis (hardening of the arteries), mental function and vulnerability to infections.

In 2001, Joshua Lederberg, a Nobel Prize-winning molecular biologist, proposed a term for these microbial communities: the “microbiome.” The word stuck. The National Institutes of Health launched the Human Microbiome Project. A new nonprofit research organization opened its doors: the American Microbiome Institute. In the grocery store or online, you can buy products — probiotics and prebiotics — that claim to boost your microbiome. You can send stool samples to at least two organizations — American Gut and µBiome — to have your personal microbiome analyzed.

microbes-14Through growing collaborations at Oregon State, Sharpton and his colleagues are delving into connections between the microbiome and human health (see “More Microbiome Studies at Oregon State“). They are looking for clues in large datasets of microbial DNA and conducting experiments in a lab that maintains — ironically — a colony of germfree mice. Natalia Shulzhenko (College of Veterinary Medicine) and Andriy Morgun (College of Pharmacy) established the facility in 2014 to study the role of microbes in disease and what happens when they are buffeted by antibiotics and dietary changes.

At the Sinnhuber Aquatic Research Lab and in the Department of Microbiology, teams of scientists are studying the microbiomes of zebrafish (Danio rerio). “What we’re really interested in using zebrafish for is understanding changes in the environment of the host (be it a fish, a mouse or a human) — whether they’re due to exposure to drugs, toxicants or diet. How do they alter the established communication with the host and how do they affect the physiology of the host?” says Sharpton.

It’s a Microbial World

As an undergraduate at Oregon State, Sharpton studied microbes in sea anemones with OSU zoologist Virginia Weiss. Later, as a Ph.D. student at the University of California, Berkeley, he delved into the field of bioinformatics — the analysis of DNA sequences with computers. As he came to understand the potential of this new field, he got hooked.

Thomas Sharpton
Thomas Sharpton

“I had never done anything like this before,” Sharpton says. “I thought it was the coolest thing in the world. This guy (John Taylor, fungal biologist at Cal) turned me toward this field that I didn’t even know existed.”

At the same time, the emerging technology of rapid DNA sequencing (led in part by OSU scientist Steve Giovannoni) was revealing the presence of a microbial universe in seawater, soils and plants.

During a postdoctoral research fellowship at the Gladstone Institute in San Francisco, Sharpton developed new ways to analyze microbiome data. “We take DNA from an entire consortium of cells that comprises the microbial community and sequence them all simultaneously. What we get is an alphabet soup,” he explains. “We use the computer to determine what DNA came from what organism.”

By combining statistical reasoning with hyper-fast computers, he and his colleagues are gradually putting the microbiome puzzle together. However, their work would not be possible without catalogs of genes that scientists have already assembled through DNA sequencing.

Sharpton explains it with an analogy right out of the machine shop. “Imagine you’ve gone to the junkyard and brought me an array of parts from cars, bicycles and skateboards and dumped them on the floor. If I’m a smart mechanic, I can tell you which pieces go to automobiles, which go to skateboards and bicycles.”

Smicrobes-11imilarly, scientists are learning which genes are most likely to work together to make a microbe function. They are creating the molecular equivalent of a parts catalog that can be used to map genes that belong together. And as DNA sequencing labs such as Oregon State’s Center for Genome Research and Biocomputing churn out data by the barrel, Sharpton and his colleagues sort, categorize and annotate their parts lists into a web of microbial life. They are finding surprises.

“Those that we might think of, E. coli for example, are known because they can be cultured in the lab, but in a typical healthy microbiome, they make up less than 0.1 percent of the microbial species present,” says Sharpton. “Thanks to DNA sequencing, we are realizing just how many different types of organisms are out there.”

Three-Way Conversations

As Sharpton was developing his skills, two scientists at the National Institutes of Health were using gene data to explore a three-way chemical conversation between the microbiome, the human immune system and disease-causing organisms. The wife and husband team of Natalia Shulzhenko and Andriy Morgun were investigating the possibility that the balance between health and disease — obesity, diabetes, cancer — could be tipped by the ways in which microbial and human cells communicate. Their goal was to understand who was talking, what they were saying, what could go wrong and how it could be corrected.

Natalia Shulzhenko
Natalia Shulzhenko

“We now know that microbial cells and microbial genes are a central part of our (human) organism,” says Shulzhenko. “We need to understand what they do to us.”

Not surprisingly, there are problems in studying a three-way conversation among thousands of microbial species: Who’s talking to whom? What messages are being received? What do they mean? Now at Oregon State, Shulzhenko and Morgun conduct experiments in a lab equipped with facilities that house germfree mice. Without a microbiome, these animals rely entirely on their innate ability to digest food or develop immunity against infection. By selectively planting specific microbes — or groups of microbes — into the guts of the mice, the researchers can essentially turn down the volume and listen to parts of the conversation.

In addition, like detectives who have developed a new way to track criminals, they are teasing clues out of large genetic datasets through the use of “transkingdom network analysis.” In short, they consider how human and microbial genes affect each other. “The focus is on networks of genes,” says Morgun. “How do different parts of the system talk to each other?”

Andriy Morgun
Andriy Morgun

The scientists are particularly interested in conversations gone wrong. For example, why are some women who have been infected with the human papilloma virus unable to clear it from their systems? And why do some develop cervical cancer?

They also have turned their attention to Type 2 diabetes (also called adult-onset and obesity-related diabetes): How does the immune system interact with the microbiome to affect our blood-sugar levels? Could the conversation between the microbiome and the host affect metabolism in a way that contributes to diabetes and obesity?

And what about broad-spectrum antibiotics? Do these miracles of 20th century medicine disrupt the microbiome or directly affect an animal’s own cells? How do antibiotics pave the way for resistant microbes such as C. difficile, one of the scourges of hospital-acquired infection, which can turn a healthy colon into a painful canker sore?

Diet and the Microbiome

Building evidence toward dietary recommendations. Read more…

With funding from NIH and the Medical Research Foundation of Oregon, Shulzhenko, Morgun and colleagues are starting to find answers to questions about antibiotics. In collaboration with Martin Schuster’s lab at Oregon State, they have found evidence pointing to the effects of antibiotics on whole suites of immune system genes. They have shown that one member of the human microbiome — a microbe known as P. aeruginosa — can be turned into an antibiotic-resistant pathogen that damages the cells of the gut.

Shulzhenko and Morgun continue to work with collaborators at NIH and the University of Sao Paulo in Brazil, where they conducted clinical research before coming to the United States. “We want to identify interactions between the host and the microbiome, to define who are the causal players,” says Shulzhenko. “What genes and microbes are responsible? We are one of the few groups using transkingdom networks to do this.”

Such knowledge — and the medical treatments that could follow from it — might have helped Pat when she was suffering from bacterial infections and severe colitis 20 years ago. Feeling at the end of her rope and facing the possibility of colon surgery, she talked to friends, visited Internet chat rooms and scoured the shelves of local bookstores.

Pat credits her eventual recovery to a diet, The Specific Carbohydrate Diet, described in a self-help book by Elaine Gottschall, Breaking the Vicious Cycle. In the 1950s, the New Jersey mother was struggling with her 4-year-old daughter’s debilitating colitis. Gottschall found a New York physician who had developed a dietary approach to the condition. After her daughter got better, Gottschall went back to college, became a scientist specializing in inflammatory bowel disease and wrote her book to share what she had learned about diet and intestinal flora.

Pat didn’t have her gut microbes analyzed and doesn’t advocate this approach for everyone. Still, based on her own experience, she knows that tending to the microbiome through diet is a key to health. “It saved my life,” she says.

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One thought on “Gut Check

  1. Is anyone looking at the correlation between food poisoning and healthy guts? Are we over sanitizing and reducing our exposure to microbes? If every food is super sanitized or rinsed in bleach solution for instance, are we inhibiting the microbial exchange?

    Do the people with healthy guts get food poisoning as often, or those without a healthy microbiome?

    Yvonne

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