Giant bug census

When Jessica Grossman was eight years old, she started having painful stomach aches. “I wouldn’t eat dessert after dinner, and my mom thought that was weird,” says Grossman, now 19. One day, she stepped on a scale, and noticed she’d lost five pounds. It was scary, she says, because “eight-year-olds don’t lose weight.” After a series of doctor visits and “really horrible tests” including a barium enema, Grossman got a diagnosis: she had Crohn’s disease. “My parents were really scared,” she says.

In Canada, about 200,000 people suffer from Crohn’s or ulcerative colitis (together called inflammatory bowel disease, or IBD), giving our country one of the highest rates in the world. IBD causes inflammation and bleeding of the digestive system; while Crohn’s can affect any part of the gastrointestinal tract, colitis restricts itself to the large bowel. Symptoms include pain, fatigue and diarrhea. There’s no known cause, and no cure; both conditions are chronic and can be debilitating.

A few years after her diagnosis, Grossman got the stomach flu. This would be fairly normal for most 11-year-olds, but in her case, it was dire. The flu triggered her Crohn’s, and Grossman spent the next two years in and out of hospital. “I’m Jewish, and it was around the time of bar mitzvahs,” she recalls. “I missed most of them, which was really sad.” When drugs failed to help her, the doctors “ran out of ideas,” she says. They surgically removed her colon and some of her intestine. She now has an ileostomy, an opening in her small bowel, and wears an external pouch. “Getting used to a new body function was really hard,” says Grossman, a university student and volunteer speaker for the Crohn’s and Colitis Foundation.

Last month, a global initiative was launched that’s expected to bring major breakthroughs in our understanding of human health, including diseases like Crohn’s and colitis. For the first time, scientists are attempting to take a giant census of the trillions of bacteria that live in and on the human body, which are almost certainly implicated in IBD. The human microbiome, as it’s called, has been completely uncharted, until now.

“Where we expect this project to make the biggest difference, the soonest, is IBD,” says Robert Karp of the U.S. National Institute of Diabetes and Digestive and Kidney Diseases.

We’ve all seen the commercials: a woman douses her toilet with antibacterial cleanser, scrubbing till it sparkles. It’s the very image of cleanliness and good health. Yet according to a new study, this fictional mom could be upping her child’s chances of developing inflammatory bowel disease.

People with modern hygiene in their home (a toilet, running water, or connection to the city sewer) are four times more likely to have Crohn’s or colitis, concluded a recent study in Puerto Rico, “where you can actually find people who grew up without a toilet,” says Kent Taylor, associate professor at the University of California, Los Angeles School of Medicine, who participated in the research. In fact, IBD is rampant across the industrialized world, where antibiotics and a clean water supply have been the norm for years—but in developing countries, it’s almost non-existent. “There’s hardly any IBD in Mexico,” says Dr. Richard Fedorak, president of the Canadian Digestive Health Foundation and director of the division of gastroenterology at the University of Alberta.

It’s one reason experts think bacteria could be a factor in developing the disease. Early exposure to germs gives the immune system a boost, says Kris Chadee, chair of the gastrointestinal research group at the University of Calgary. “To get IBD, you’ve got to be genetically predisposed, and then exposed to an environmental trigger,” he says. That trigger, he notes, could be a foreign germ the body’s not able to deal with; or it could be “your own bacteria, turning against you.”

It’s a terrifying thought. We are literally rife with germs, inside and out. The colon has the highest concentration of bacteria of any known microbial ecosystem on earth, says Dr. Elaine Petrof, a probiotics expert at Queen’s University. Some bacteria are probably common to all of us, but an individual’s microbiome is unique as a fingerprint. Babies are thought to be born sterile, says microbiologist Julian Davies, professor emeritus at the University of British Columbia, but establish their own unique microbiome soon after birth. “We are totally dependent on microbes for survival,” he says. “We cannot live without them.”

They aren’t just freeloaders. Our bacteria interact with us in countless ways: synthesizing vitamins, helping with food digestion, and crowding out bad bugs. Bacteria have been implicated in everything from gastroesophageal reflux disease (GERD) to obesity. A fat person’s gut flora, for example, is different from that of a thin one.

Despite the important role they play, the human body’s microbial populations are a relative mystery. (Until recently, the technology needed to study them simply didn’t exist.) In one study of the colon and feces of three subjects, more than 60 per cent of the microbes discovered were previously unknown, and 80 per cent couldn’t be cultivated in the lab. Why? “If we knew, chances are we could grow them,” says Joseph Petrosino, a microbiologist at Baylor College of Medicine in Texas.

“Everyone talks about going to the Amazon rainforest to look for new species,” Petrof says. “But we’ve got all this stuff inside our own bodies that we don’t know anything about.”

If scientists have their way, that will change before long. Announced last month in Heidelberg, Germany, the International Human Microbiome Consortium aims to chart bacterial populations at various sites of the human body, including the mouth, neurological system and skin. With $10 million in federal funding over the next five years, the Canadian Microbiome Initiative (Canada is one of nine participants, including the European Commission) will start by looking at the gastrointestinal tract. Researchers hope to sequence the genomes of various bacteria. “Once we identify what’s present in normal people, we can find out how [microbial] populations shift with disease,” says Petrosino, who’s involved in the U.S. effort.

For conditions like IBD, where bacteria almost certainly play a role, the project’s impact could be enormous. “If bacteria are initiating Crohn’s, maybe we could change your bacteria and stop the disease. Or maybe we could give you back the good bacteria you need, and help treat the disease,” Fedorak says. In fact, probiotics (beneficial bacteria found in various foods, from sauerkraut to yogourt) have already shown some success in treating IBD in clinical trials, but there’s still a long way to go. Eating yogourt off the grocery store shelf is perfectly fine, Petrof says, but she’s unsure probiotics are ready for widespread clinical use. “I’m not a strong encourager of probiotics in the hospital yet,” Petrof says. “I don’t think we’re ready.”

With the microbiome project under way, we could be soon enough. Karp predicts the effort will have an “enormous impact” on our knowledge of beneficial bugs: “A better understanding of the microbiome will offer the hope of designing probiotic products for the prevention and cure of disease,” he says. “It will offer increased ability to manipulate the microbiome for our own purposes.”

For people like Grossman, answers can’t come fast enough. She’s been symptom-free since the surgery almost six years ago, but her Crohn’s symptoms could return at any time. “I can’t get my ostomy reversed, because that will make me sick again,” she says. “Until there’s a cure, I’ll pretty much have to live with this.”