Research Profile - Mapping your inner habitat

A Canadian researcher studies the microbial communities that help keep our bodies healthy.

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We tend to think of our bodies as single entities, but they are actually home to many other living things. We are walking ecosystems that can change depending on our state of health.

Dr. Josh Neufeld, an environmental microbiologist at the University of Waterloo, and his colleagues are exploring these ecosystems, and trying to determine what the bacterial populations in different parts of the body look like in a healthy person.

"Our bodies are just another type of environment," explains Dr. Neufeld. "It's important for us to understand how the organisms living in that environment influence our health."

Researchers have understood for a long time that bacteria play an important role in maintaining – and sometimes threatening – our health. But available methodology limited their ability to identify the species present in the body and what role they played in preventing or causing disease.

"The problem with microbiology has been that for so long, probably close to about 100 years, we relied exclusively on the ability to culture (grow) organisms, and that is fraught with problems and biases," explains Dr. Neufeld. "Only a small proportion of organisms, like those found in our bodies, respond to cultivation in most cases."

Now, with the explosion in molecular techniques such as genome sequencing, researchers like Dr. Neufeld can get a nearly complete picture of the bacterial communities that live in locations throughout the digestive system in healthy bodies. Dr. Neufeld and his team are actively developing and applying new technologies that will allow researchers to describe the bacterial populations at various sites in people's bodies based on specific DNA sequences found within all bacteria.

"For this project, we decided to take advantage of a technique we'd developed which profiles communities to great depth – even the rare organisms are sampled with this technique," says Dr. Neufeld.

With the help of funding from the Canadian Institutes of Health Research, the researchers are sampling bacteria from the mouth, stomach, small and large intestines, and feces. According to Dr. Neufeld, the number of profiles they will collect and sequences they will generate will be unprecedented. Through this study, he hopes to show that the technology his team has developed is a cutting-edge method for profiling bacterial communities in the body.

"Once we've demonstrated that this is an affordable, comprehensive way of studying bacterial communities, we want to describe the communities that are characteristic of our bodies under normal, healthy circumstances," says Neufeld. "Our next step is to look at how these communities shift in various disease states."

Researchers have already identified some conditions, such as ulcers, Crohn's disease, and obesity, in which the bacterial populations at certain sites of the body change in dramatic and distinctive ways. But little is understood about why these changes take place, or what role these changes play in the disease process.

Dr. Neufeld's team is also trying to identify less common species of bacteria in our bodies, some of which may have never been detected by researchers before.

"There are organisms in every environment, including our own bodies, that are adapted to life at low relative abundance, even though they may actually play an important community function. As a result, it's quite possible that these have never been detected before," says Dr. Neufeld. "There may be some benefit to having a high diversity of organisms in our bodies, offering some form of stability to communities. These are some of the questions we are hoping to address."

"Our bodies are just another type of environment. It's important for us to understand how the organisms living in that environment influence our health."
-- Dr. Josh Neufeld.