A sophisticated system

Jane Norgren was suffering terribly. A pernicious bacterium, Clostridium difficile, had taken up residence in her colon and refused to leave—no matter what antibiotics she took. As a result, she had bouts of uncontrollable diarrhea on and off for nearly four years. It was a miserable situation. She always had to be near a bathroom. “I felt like I was untouchable,” she says.

Then Norgren’s agony was over. That’s because she was one of the first people in Connecticut to benefit from fecal microbiota transplantation (FMT). Most of the existing bacteria in her digestive tract were killed by a heavy dose of antibiotics and replaced by healthy bacteria from a fecal donor (her daughter). “I have been fine ever since,” she says.

The procedure was performed by Paul Feuerstadt, MD, an assistant clinical professor of medicine at Yale School of Medicine. He says that more than 95 percent of the patients he has treated in this way through the Gastroenterology Center of Connecticut have recovered.

FMT is the first treatment that has emerged from a wave of research on the role of the microbiome in health. For years, most medical researchers treated microbes as a sideshow to the main event—the role of genetics in illness and medicine. Now, many are turning their attention to the impact on health of the trillions of bacteria, fungi, and other tiny organisms that colonize human digestive systems, lungs, nasal passages, skin, vaginas, and many other body parts and surfaces.

“For medical science, this is our next frontier. The better we understand our microbiome, the better we’ll be able to potentially avoid diseases or treat them more successfully,” says Feuerstadt.

Researchers believe that the microbiome plays a role in a wide variety of human diseases and conditions, including inflammatory bowel disease, irritable bowel syndrome, Crohn’s disease, lupus, chronic fatigue syndrome, fibromyalgia, cardiovascular disease, cancer, Parkinson’s, diabetes, cystic fibrosis, asthma, autism, and some forms of mental illness.

At Yale School of Medicine, researchers from more than a dozen academic departments are studying the microbiome. Some focus on understanding the fundamental mechanisms whereby bacteria interact with each other and with our bodies. Others develop tools for sequencing and editing genes in bacteria. Still others are focusing on the effects of the microbiome on specific diseases.

While these are early days, it’s already clear that Yale researchers are playing a key role in the microbiome revolution. For instance, Loren Laine, MD, professor of medicine and interim chief of the Section of Digestive Diseases, was instrumental in establishing the American Gastroenterological Association’s Fecal Microbiota Transplantation National Registry, which helps researchers assess short- and long-term outcomes associated with FMT.

This wave of microbiome research has been gathering strength for about a decade. However, the history of such research began in the 1860s when the French chemist Louis Pasteur showed that microbes are present all around us and in our bodies, and that some are responsible for diseases. Ever since, medical scientists have been studying the microbiota in the environment, animals, and humans so that physicians can better combat infection. With the emergence of antibiotics in the 1930s and 1940s, many believed that infectious diseases would swiftly be eliminated. Sadly, it didn’t happen. Now, resistance to antibiotics is a major concern.

Until a little over a decade ago, most research on the microbiome focused on which microbes played a role in causing infectious diseases, and how. Then came the Human Genome Project (HGP), launched in 1990 and completed in 2003, which provided the foundation of a better understanding of the genetic basis of such diseases as cancer. It was discovered that genes alone were often not sufficient to fully explain why complex diseases occur or how therapies work. So researchers began to look more deeply into the genetic makeup of microbes and their interactions with each other and with human cells—both negative and positive.

In an effort reminiscent of the HGP, the U.S. National Institutes of Health in 2007 launched the Human Microbiome Project. The goal was to fund research and collect data about the genomes and interactions of all the microorganisms in or on our bodies. Research funded by the project provides today’s scientists with a trove of data upon which to base their new inquiries.

One factor that makes this research so complex is that no two people have the same microbiome. While broad commonalities exist, each human has his or her own stew of bacteria and other organisms. In addition, while our personal microbiomes tend to be relatively stable, they change with the introduction of new organisms from the environment. So my microbes interact with my body differently than yours do with your body; and they interact differently today than they did six months ago.

And consider this: There are 150 times more genes in our microbiome than in our genome.

Yale faculty members say this complexity must be overcome. The ability to sequence and map human genomes has raised hopes that physicians will be able to understand an individual’s body so well that they can deliver truly personalized medicine—custom-designed therapies and treatments that will work especially well for that individual. Yet it’s becoming clear that understanding human genes and cells won’t be enough. “To truly understand the signals that regulate the expression of both healthy and diseased genes, you need to understand the microbiome. Precision medicine will be fairly imprecise without this,” says Gary Desir, MD, the Paul B. Beeson Professor of Medicine and chair of Internal Medicine.

Scientists admit they are still at the beginning stages of understanding the role of the microbiome in health. “We aren’t yet at the point where we can look at what is there in a microbiome and tell you much about what it can do. It’s hard to identify a diseased microbiome if you don’t know what a healthy one is,” says Andrew Goodman, PhD, an associate professor of microbial pathogenesis.

Goodman is determined to change that. His lab on Yale West Campus focuses on deepening understanding of how microbes in our digestive systems, the so-called gut microbiome, interact with each other and us. He and his colleagues have seen situations in which one microbe species uses a vitamin produced by another to survive in the gut; and others in which microbes fight each other to the death. On the microbe-to-host axis, the team is learning how gut microbes could affect how particular individuals respond to particular drugs.

So far, most of this experimentation involves mice—but not just any mice: germ-free mice. Only by using mice with no bacteria present can researchers introduce individual species or consortia of microbes and study the effects of their absence or presence. Although Goodman has a dedicated team of experts in these techniques, the med school also has a central germ-free mouse facility that all the scientists can access.

Another essential element of microbiome research is the tools that are used to read and analyze the genetic code within microbes and then to edit or even recode their DNA so that they interact with each other and our bodies in different ways.

Scientists employ the same tools for microbes that are used for human genetics research. The CRISPR/Cas9 technology has democratized gene editing by enabling scientists to cut and paste snippets of DNA code relatively easily. But researchers at Yale are some of the leaders in developing new approaches that don’t involve breaking the double strands of DNA and killing cells.

One effort is led by Farren Isaacs, PhD, an associate professor of molecular, cellular and developmental biology. His lab produces and uses high-throughput gene engineering technologies. With these tools, the researchers can rewrite the genomes of human cells and bacteria on a large scale—introducing scores of precise edits without creating double-stranded breaks in the strings of genes. His team developed a technique called eukaryotic multiplex genome engineering (eMAGE) and used it to alter the genetic information in yeast. The team members hope this technique will be used eventually to alter disease-causing genes in human cells and microbes.

Earlier this year, Isaacs’ lab pitched in on an effort aimed at engineering communities of gut microbes to help humans digest cellobiose, one of the most abundant disaccharides present in vegetables, which our digestive systems don’t have the means to metabolize. If efforts like this pay off, we will be able to harvest more energy from the food we eat.

Across the spectrum of Yale academic departments, researchers are using germ-free mice and gene sequencing and editing tools to advance research on the role of the microbiome in a wide variety of diseases and body functions. Laypeople tend to think that bacteria in the digestive system stays put, but in fact, microbes migrate via the blood to a host of other body organs and systems, including the liver, the lymph nodes, and even the brain. Much of the research focus at Yale is on infectious diseases, the immune system, and autoimmune diseases.

Martin Kriegel, MD, PhD, FW ’06, adjunct assistant professor of immunobiology, and of medicine (rheumatology), has been focusing on Enterococcus gallinarum, a bacterium that his team discovered can migrate from the gut into the lymph nodes, liver, and spleen in predisposed hosts—thereby producing an autoimmune response. Kriegel’s research team found that they could suppress the response caused by E. gallinarum in mice with an antibiotic or vaccine. Research like this could help pharmaceutical companies produce antibiotics and vaccines that are particularly good at attacking specific bacteria.

“This may become personalized medicine,” says Kriegel. “We need to look at the host predisposition such as the human genes, and at the microbiome in the patient’s gut and tissues. Based on these analyses, we should be able to decide on the best treatment for a particular patient in the future.”

Other labs are focusing on prevention in addition to cures. Li Wen, MD, PhD, FW ’97, associate professor of medicine (endocrinology), is looking into the causes of type 1 and type 2 diabetes. Her team’s research has shown that certain types of gut bacteria cause intestinal inflammation, which in turn promotes the development of type 1 diabetes. At the same time, the research shows that obesity and other factors associated with type 2 diabetes are more prevalent in patients with low diversity in the gut microbiome. Down the road, she believes, people with a genetic predisposition to diabetes may be able to fend off the disease by consuming customized probiotic cocktails.

“I think prevention is most important,” she says. “It’s the most effective and economical way to deal with diabetes.”

While most of the research at Yale concerns the gut microbiome, a handful of faculty members are focusing on other body parts or systems. For instance, Barbara Kazmierczak, MD, PhD, a professor of medicine and of microbial pathogenesis, specializes in the lung microbiome—specifically the effects of bacteria on cystic fibrosis.

Much of the research being done at Yale, while promising, is not expected to deliver new treatments or drugs for many years. But some projects might be closer to the marketplace. For instance, two professors—Noah Palm, PhD, assistant professor of immunobiology, and Richard Flavell, PhD, Sterling Professor of Immunobiology—are co-founders of a startup company Artizan Biosciences, aimed at identifying harmful bacteria in the gut and targeting them for destruction. One of their first targets: inflammatory bowel disease.

“We found that when we take a healthy microbiota and add one microbe to the mixture, the mouse gets sick. On the flip side, if you’re able to block the pathologic effects of that bug or eliminate it entirely, the mouse does not get sick,” says Palm. The next step is figuring out how to attack the bad bug—with targeted antibiotics, small molecules, or perhaps even phages.

Elsewhere around the country, a number of medical schools are establishing major research initiatives focused on the microbiome. Among them are Harvard, University of Chicago, Stanford, University of Pittsburgh, University of Michigan, and New York University.

Several Yale researchers say they’d like to see a larger and more coordinated effort to foster and support microbiome research. Such an initiative might make it easier for them to secure funding and develop more multidisciplinary collaborations. Moreover, there would likely be benefits from expanding the variety of research done at Yale. Right now, most of the focus is on experimental science and the gut microbiome. They’d like to see more done in data analysis and in other microbiomes.

Goodman, who on his own keeps a web page (medicine.yale.edu/microbiomeresearch) tracking microbiome research at Yale, says, “I’d like to see it happen. There’s such a great base of people here. There’s a lot of opportunity for really exciting things with more coordination and resources.”

Meanwhile, local people who suffer from diseases related to the microbiome are cheering Yale researchers on. One of them, Shari Hoffman of New Haven, says, “This makes me optimistic that patients may one day receive better care and have better overall well-being.”