CLEAN LIVING VERSUS HEALTHY LIFE
The consequences of our antibacterial obsessions
GUELPH, Ont. Emma Allen-Vercoe and her graduate students have come to appreciate the unmistakable odour that hits when you enter their laboratory.
“When we walk in and don’t smell anything, that’s when we begin to worry,” says Allen-Vercoe, a microbial ecologist who has spent almost a decade at the University of Guelph studying what most people can’t wait to flush down the toilet.
Feces provide a window on the vast community of bacteria, fungi and viruses living in the human gut, an ecosystem Allen-Vercoe finds more intriguing than anything in the tropical rainforests or world’s oceans. “It’s the most diverse and densely populated ecosystem on Earth,” she says.
The human “microbiota” or “microbiome,” as the trillions of organisms are collectively known, is critical to good health. And the microbes do a lot more than help digest food. Mounting evidence indicates they also offer protection against asthma, pathogens, allergies, diabetes and perhaps even certain forms of autism and cancer.
“You mess with it at your peril,” says Allen-Vercoe, who makes a strong case for treating microbes as an ally, not an enemy.
Allen-Vercoe is so intrigued by the internal ecosystem, she eavesdrops on it with the “roboguts” she designed to mimic conditions in the intestines. “You can listen in on how microbes are speaking to each other, and behaving and interacting.”
At the heart of the contraptions are glass bottles, anchored in stainless-steel housing and kept at a toasty 37 C. They are seeded with fecal donations from volunteers.
Allen-Vercoe is quick to joke about her work, which gets lots of attention from the “pooparazzi” — her lab’s name for the news media.
But she is very serious about the way modern life, with its focus on cleanliness, refined foods and reliance on antimicrobial drugs, is damaging the invisible organisms that live in and on the human body.
The notion that the best microbe is a dead microbe is so pervasive that modern store shelves are lined with cleaners, equipment and toys infused with compounds said to be “antibacterial.” There are even “antimicrobial” staplers and file folders for the office.
“The worry is that being brought up in an average clean household, children are just not getting the exposure to microbes that they should at critical points in development,” says Allen-Vercoe.
More concerning than the antimicrobial consumer products are antibiotic drugs.
While antibiotics can be life saving, public-health officials are calling for much more prudent use of them in medicine and agriculture.
Allen-Vercoe recently asked the 300 students in one of her microbiology classes how many had made it to university without ever being treated with an antibiotic. “Not one person raised their hand,” she says.
Antibiotics kill off both good and bad bacteria. This can leave people susceptible to weedy microbes such as antibiotic resistant Clostridium difficile, which can cause relentless diarrhea that can be fatal, particularly in older individuals.
“C. diff is very much the poster child for how we’ve messed things up by interfering with the microbiota,” says Allen-Vercoe.
Scientists are concerned the microbiota is becoming more impoverished with each successive generation.
Work in several labs suggests decades of antibiotics use have altered the microbiota in ways that may be fuelling epidemics of obesity, diabetes, allergies and asthma.
The tiny bacterium Helicobacter pylori, one the few microbes that can live in the harsh acidic environment in the stomach, is one casualty. A century ago, it was the dominant microbe in people’s stomachs, but studies have found less than six per cent of children in the United States, Sweden and Germany now carry the tiny corkscrew-shaped bacterium.
Doctors initially thought it was good to be rid of H. pylori, as it increases the risk of ulcers and stomach cancer. But recent studies show people without the microbe are more likely to have hay fever and allergies. Dr. Martin Blaser at New York University has reported that eradicating H. pylori also affects two key hormones that regulate appetite, which could be helping drive the obesity epidemic.
Antibiotic treatment early in life can also take a toll on microbes that help stimulate development of the infant immune system to differentiate between friendly and harmful organisms, according to research on mice in Brett Finlay’s lab at the University of British Columbia. This might explain why children given antibiotics in their first year tend to have higher rates of allergic asthma. The wheezing and shortness of breath is due to an overactive immune response to things such as harmless microbes, pollen and pet dander.
Allen-Vercoe decided to explore the internal microbial ecosystem after years of studying pathogens in Britain and Calgary. “It had been largely ignored,” she says.
Rather than taking the traditional approach and looking at the organisms individually, she cultures microbial communities as they exist in the body. “Microbes are like teenagers, they like to be with their friends,” says Allen-Vercoe.
Conditions in her “roboguts” mimic those of the lower intestine, with plastic tubing and clamps controlling what goes in and out. They keep out oxygen, which is toxic to many of the microbes, deliver food that comes as an amber mixture, and divert the gassy “farts” to a vent in the ceiling — with limited success.
The odour in the lab simply means the microbes are “healthy and happy,” says Allen-Vercoe.
The “liquid gold” that drips out of roboguts provides insight into what the communities are up to, and what kind of compounds and metabolites they are producing.
Humans’ microbial ecosystems hum along in ways scientists are just beginning to understand. And they can shift dramatically when people develop disorders such as inflammatory bowel disease. The Guelph team is trying to identify the microbes involved and assess the impact of different drugs, hormones and foods.
Allen-Vercoe is also working with researchers at Western University in Ontario on regressive autism, which is associated with gut inflammation and proliferation of certain types of bacteria. These children appear to develop normally as infants, but their social and behavioural skills regress by the time they are about three years old.
There might be a “narrow window” when it might be possible to restore a healthy gut microbiota in the children, but Allen-Vercoe says “it might not necessarily fix the cognitive issue.”
While scientists are linking more and more disorders to the microbiota, Allen-Vercoe cautions against thinking there will be easy solutions.
“To have this idea that we just can carry on as we are and just fix our microbiota every now and again is very short-sighted,” she says, stressing the need to curb use of antimicrobials and better protect our resident microbes.
“They really are vital,” she says.
Next: The C. difficile detectives Research for this story was funded in part by a journalism award from the Canadian Institutes of Health Research.