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Clean Freak: Is our Fear of Bacteria Making us Sick?

We disinfect, we sterilize, we pasteurize. We’ve made bacteria Enemy No. 1, but playing it safe might be what’s making us sick. 

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Illustrations: Takeshi. colagene.com

The gaggle of reporters waiting inside Queen’s Park in Toronto on Friday, November 4, 2011, no doubt expected a feeble, exhausted radical when dairy farmer Michael Schmidt emerged. It was the 37th day of the hunger strike he started after being convicted of endangering public health by the Court of Appeal for Ontario; he claimed to have lost 50 pounds. But the reporters encountered someone alert, emphatic and entirely undeterred.

Schmidt’s hunger strike, which he ended after Premier Dalton McGuinty agreed to meet with him, was the latest chapter in an 18-year legal battle that began in 1994 when local police and health units raided his Durham, Ont., farm. He pleaded guilty to the charges and was forced to sell three quarters of his farm to pay legal fees and fines. Since then, he’s been in court numerous times in Ontario and has faced contempt-of-court charges in British Columbia. The issue? Selling unpasteurized milk to willing customers. Schmidt believes pasteurization (heating milk to a microbe-killing temperature) destroys beneficial bacteria, making it less healthy than raw milk.

Schmidt’s problem is that every health agency in the country disagrees, insisting that pasteurizing milk is essential for preventing acute illnesses caused by E. coli, listeria and salmonella bacteria. Pasteurization laws were first introduced in Canada in 1991 in response to dozens of major cases of illness linked to raw-milk consumption. According to Health Canada, the number of outbreaks has since plummeted – between 1998 and 2007, only seven were reported. “Given the clear health and safety benefits of pasteurization,” says Health Canada spokesperson Christelle Legault, “we aren’t considering any changes to the rules.”

Canada isn’t alone: Australia and Scotland both keep bans on raw milk. In the United States, where raw milk is legally available in many states, the issue is intensely debated. A recent study by the U.S. Centers for Disease Control and Prevention (CDC), which reviewed dairy-product outbreaks from 1993 to 2006 in all 50 states, found that people were 150 times more likely to become sick from raw milk, and products made from it, than pasteurized milk. “Some people think raw milk has more health benefits,” says study co-author Barbara Mahon, a deputy chief at CDC. “But this study shows that raw milk has great risks, especially for children.”

Nevertheless, Schmidt is resolute. Eating almost anything, he says, carries some risk of food poisoning (and, indeed, the U.S. Food and Drug Administration estimates that every year an average of 1,600 American citizens become ill with listeriosis from eating deli meat, compared to an average of three cases from unpasteurized milk). Schmidt argues, moreover, that we can’t fully predict the consequences of wiping out the naturally occurring bacteria in milk, which have evolved alongside us for thousands of years. Raw milk, for instance, contains the bacterium lactobacillus, which pasteurization destroys. Lactobacillus helps break lactose down into simple sugars that can be easily digested. Given dairy’s ubiquity in the average North American diet, it’s no surprise lactose intolerance has become a minor crisis – some estimates peg the number of Canadian cases at more than seven million. Sufferers, however, have reported drinking raw milk without problem. “To destroy the ecosystem of bacteria in milk,” says Schmidt, “is to tamper with some unknown, essential balance.” 

Next: How our relationship with bacteria became
less of a balance and more of a war.

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Illustrations: Takeshi. colagene.com

Schmidt isn’t a medical doctor. His master’s degree in agriculture doesn’t qualify him as a bacteria expert. Nonetheless, new research suggests his theories may be dead-on. Scientists are now focusing their attention on the “microbiome” – the menagerie of microbes that reside inside, and on, our bodies. Research has already linked microbiome breakdowns to ailments as varied as mental illness, obesity and cancer. At the moment, the concept of the microbiome isn’t taught with any depth in medical schools. In fact, Western medicine considers the relationship between bacteria and humans to be less a balancing act than a war. In the past century, the study of pathogenic bacteria led to huge breakthroughs, most notably the invention of antibiotics. Such accomplishments created the conventional image of “bad bacteria.” Danger, we’re warned, lurks everywhere: on poorly washed salad, in undercooked hamburgers, in public bathrooms, on doorknobs, on a co-worker’s hands. Our rinsing, boiling, grilling, scrubbing and disinfecting have thwarted countless illnesses – but also reinforced a view of bacteria that is grossly oversimplified.

The idea that purging ourselves of bugs might be making us sick is hardly new. In 1989, scientist David Strachan proposed his “hygiene hypothesis” in the BMJ (British Medical Journal). He had been curious about the low rate of hay fever in children from large families, and attributed it to the fact that more siblings means more exposure to germs. Strachan’s hypothesis inspired epidemiologists to explore the link between the explosion of autoimmune disorders in developed countries and our obsession with cleanliness. One U.S. study, published in 2007, found that kids who were exposed to animals and drank farm milk had lower rates of asthma and allergies than kids who mostly drank pasteurized milk and weren’t raised on farms.

Schmidt wonders how much longer we can afford to ignore such evidence. “When you’re not exposed to bacteria at the start of your life, you have no proper immune system to deal with other diseases later in life,” says Schmidt. The fear of food poisoning, while justifiable, is short-sighted. Our concern, he argues, “should be about laying a nutritional foundation in early childhood.”

Schmidt isn’t alone in his thinking. Sandor Katz, a self-described “fermentation revivalist,” is also trying to spread the pro-bacteria message. Katz believes that fermentation, a millennia-old culinary art, not only draws out new tastes and textures in vegetables (as when cabbage becomes sauerkraut), but also transforms food into a powerful cocktail of enzymes, vitamins and probiotics – or beneficial bacteria. “Fermentation is a part of everybody’s traditions, but because we’re severed from food production, people no longer feel connected to it,” he says. In his book Wild Fermentation, Katz argues that because we’re constantly depleting the bacteria in our bodies (owing, in large part, to antibacterial soaps and antibiotics), bacteria-replenishing fermented foods are vital for a strong immune system. “When factors in people’s lives continually assault their microflora, they become more vulnerable to bacterial infection, not less,” he says. 

Next: “We aren’t at war with
bacteria-we are bacteria.”

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Illustrations: Takeshi. colagene.com

The theory behind Schmidt and Katz’s ideas is simple: We aren’t at war with bacteria – we are bacteria. Nearly 1,500 varieties inhabit our bodies, outnumbering our cells ten to one. Five years ago, biologists launched the Human Microbiome Project: an effort to name every bacterium associated with humans in order to learn about their impact on our health. Since then, we’ve discovered these micro-organisms help us digest nutrients, regulate perspiration, convert glucose to muscle, overrun pathogens and repair cells. Collectively, bacteria are our single most important – if unheralded – organ. “You can survive with an artificial heart or a lung machine,” says Gregor Reid, a microbiologist at Ontario’s Western Uni-versity and a leading probiotics researcher, “but you can’t survive without bacteria.”

The project has already started yielding results, giving doctors a tantalizing glimpse at alternative options for treating serious illness. One group of French scientists, for example, believes that agonizing, hard-to-manage inflammatory bowel diseases – which afflict 200,000 Canadians, with thousands of new cases every year – could be dealt with simply by making changes in a patient’s gut microbial content. A recent article from the journal Reproductive Sciences, which linked women’s urogenital cancers (such as cervical cancer) to out-of-whack bacterial counts, reports that researchers are experimenting with various probiotics to rally the patients’ own antipathogenic defences.

Given that we carry hundreds of varieties of bacteria, with many more yet to be identified, these discoveries only scratch the surface of what’s possible. For instance, research has shown that obese bodies have a significantly different bacterial ecosystem than thinner bodies. Scientists are unsure whether that means obesity may be triggered by a glitch in the microflora or if weight problems cause the bacterial change. In any case, they are looking into the possibility of curing obesity by rejigging the bacterial ecosystem. Because no two people have exactly the same microbiome, Reid envisions a time when doctors might personalize probiotic treatments for patients. “Microbes are the future of health,” he says, “and we’re only getting the tools to explore them now.”

In the beginning, there were bacteria. Three billion years before the first multicellular organism emerged – and four billion years before Homo habilis walked the Earth – bacteria thrived. They can survive in the most inhospitable settings: volcanic vents, Antarctic ice, toxic waste. Some scientists even argue that when humans entered the microbial world, they became useful to certain bacteria that adopted our body as a home – bacteria that would have died if not for the environment we provided. “To a certain extent,” says Bruce German, a food chemist at the University of California, Davis, “we exist at their pleasure. We’re a trivial biological afterthought.”

Over 15 years ago, German began a quest to decode nutrition. If he could study a food that evolved specifically to feed humans, he believed he could unlock the secrets of dietary well-being and eradicate illnesses such as heart disease and diabetes. Natural selection usually favours plants and animals that succeed in avoiding being eaten. But human breast milk has one purpose: to be baby food.

Next: How milk drove human evolution.

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German, who later founded a research group called the International Milk Genomics Consortium, began looking at every element of breast milk in order to learn what made it such an effective food for humans. But he discovered something puzzling: In addition to the immunity-strengthening vitamins, minerals and proteins that nourish infants, breast milk is also full of complex sugars babies are unable to digest.

When German’s research group finished their work, they had a surprising realization: The presence of these sugars was connected to the growth of a powerful probiotic called Bifidobacterium infantis. Breast milk’s job, in other words, doesn’t simply feed the baby; it educates its digestive system. “Mothers are guiding their babies’ microflora with these complex sugars,” says German. Just as a mother orangutan spends years teaching her child which foods in the vast jungle are safe to eat, human breast milk tells a child’s gut which bacteria are beneficial.

But that’s not all the scientists discovered. They also found that, to date, there is only one industrially viable food source able to replicate many of breast milk’s functions: bovine milk. When humans first domesticated cattle for their milk 8,000 years ago, the effect on our genetics was huge; people who descended from regions where milk was a major source of nutrition developed a genetic mutation that helped them digest lactose. Milk kept those lactose-eating mutants alive while everyone around them died – and we know this because their DNA is now part of our biological record. “That means milk was pretty important to the survival of humans,” says German. “It drove our evolution.” 

On a crisp afternoon on June 2012, Michael Schmidt hosted an open house at a farm in Chilliwack, B.C. The modest farmhouse was surrounded by fields where cows and goats leisurely grazed. In the background, mountains rose from the lush valley floor. In front of the house, a local cheese maker offered visitors samples made from the farm’s milk. The guests were members of a cow-share co-operative housed here. More than 300 families participate in the co-op, which is based on a model Schmidt pioneered in Ontario to circumvent pasteurization laws. Since it’s not illegal for farmers to drink their own raw milk, Schmidt argued any owner of a cow should have the same privilege.

Schmidt was inside the barn, drumming on overturned buckets in accompaniment to a visitor’s young son, who played a saxophone. The cows, their coats shining, poked their noses through the railing, curious about the racket. Two blue-eyed teenagers prepared to demonstrate how the cows are milked. It was difficult to think of these giggling girls as criminals.

Schmidt doesn’t believe all milk should be sold unpasteurized. He acknowledges that milk produced at conventional, large-scale dairies – which turn out an increasing percentage of Canada’s milk – needs to be treated because standard production processes increase the likelihood that dangerous bacteria will be present. After all, pasteurization was introduced in the late 1800s to solve a public-health crisis: As the industrial revolution progressed and dairies grew, milk-borne outbreaks skyrocketed. The reasons were twofold. First, instead of letting cows graze on grass, industrial dairies fed them whatever was cheap – at the time, spent distillers’ grains – and the cows became disease ridden. Second, crowded pens led to unsanitary conditions that increased the chances of fecal matter entering the milk.

Next: “Pasteurization worked but allowed dairies to
ignore the root causes of milk-linked illnesses.”

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Illustrations: Takeshi. colagene.com

When Louis Pasteur invented a heat-based method for killing bacteria in wine in 1863, it was soon applied to milk. Pasteurization worked but allowed dairies to ignore the root causes of milk-linked illnesses. Today most commercial dairies continue to prioritize production over the health of their animals. Dairy farmers can’t turn a profit without the high yields largely possible because of antibiotics that help cows digest corn-based feed.

Schmidt argues that the milk from small-scale organic dairies, which usually maintain better conditions for cattle, doesn’t need to be pasteurized to be safe. He claims that in 38 years as a dairy farmer, he’s never had a problem with food-borne illness, and he points out that Canada is the only G8 country that doesn’t allow citizens access to raw milk. France has twice the population of Canada and produces three times the amount of raw milk we do, but its last dairy-related listeriosis outbreak was in 1997 (ours was in 2008). In Italy, Poland, the U.K. and Germany, raw milk is even sold in vending machines. “Canadians,” he says, “ought to be given the choice.”

A couple of years ago, Karen Kamon exercised that choice. She and her family are members of a cow-share co-operative in Vancouver, along with hundreds of others. Every week, they pick up fresh milk from a dairy farmer who’s hired to tend and milk the co-op’s small herd of cows. After reading widely and weighing the risks, Kamon had come to believe that raw milk might ease her youngest son’s allergies. Friends questioned her judgement. One person told her husband, Paul, “If your children get sick, our health-care system shouldn’t have to pay for it.”

The Kamons finally decided to take the leap after visiting a friend who had raw milk in her fridge. The Kamon boys, who had never been fans of conventional milk, finished their cups of raw milk and asked for more. Then they asked for even more and polished off a litre. “Sometimes you have to listen to your instincts,” says Karen, “to what your body is telling you.”

Our bugs can also change our moods. John Bienenstock, a professor at McMaster University’s Brain-Body Institute at St. Joseph’s Healthcare in Hamilton, has pioneered research into the connection between bacteria and mental health, also known as the “gut-brain axis.” The largest community of bacteria, and 80 percent of our immune system, lives in our intestines – an estimated 100 trillion microbes, weighing up to two kilograms. Our gut is also our second largest “brain,” lined with millions of nervous cells. And those nerves are constantly picking up signals from bacteria.

Bienenstock is fascinated not only by this crosstalk between brain and gut, but also by the things that can interrupt the conversation. He explains that illnesses depend not only on the presence of pathogenic microbes, but also on the absence of beneficial bacteria. “For example, some vitamins can only be synthesized by certain bacteria in the intestine,” he explains. “Therefore, if you’re missing those bacteria, you could be without a vitamin.”

Knowing that the absence of certain bacteria could have such an effect, Bienenstock wondered what happened when a person’s entire microflora was disturbed by a major shock. To explore this question, a research group at McMaster looked to the 3,000 survivors of the Walkerton, Ont., E. coli outbreak. In May 2000, E. coli was found in the small Ontario town’s drinking water; it killed seven and caused half the population to fall ill. Researchers found that eight years after the illness, many residents continued to suffer from irritable bowel syndrome (IBS), suggesting that the effects of unsettling the bacterial balance persisted long after the source of disruption was gone. The study, however, also raised the possibility that prior history of anxiety and depression might be triggers of IBS. The disorder has long been suspected of coexisting with mental-health problems, and scientists around the world continue to find fresh evidence linking the two.

Next: Why the probiotic craze
might be missing the point.

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Illustrations: Takeshi. colagene.com

Such questions won’t remain unsolved for long. During the 1990s, only a few hundred academic papers a year addressed the impact of beneficial bacteria; last year, well over 7,000 articles were published. They hint at a health-care approach where mood disorders can be controlled by fine-tuning microbial levels. One study found that introducing certain pathogenic microbes into a mouse’s gastrointestinal tract triggered anxious behaviour. In another experiment, researchers used a probiotic to inhibit visceral pain in mice. “The question my team is asking is this: By feeding some of these bugs, can you influence brain and behaviour?” says Bienenstock. “The short answer is yes. It appears possible.”

Probiotics have not gone unnoticed by food manufacturers eager to cash in on what’s been called the “functional food” trend, a nearly $5 billion industry in Canada. French company Danone, which owns the yogourt brand Dannon, has been a leader in this trend. Its research wing has rolled out products such as Activia yogourt, which uses a trademarked version of Bifidobacterium lactis, a bacterium well-known for its digestion-boosting abilities.

The probiotic offerings don’t end in the dairy aisle. You can buy probiotic chocolate, bread, orange juice, pizza and even a chewing gum that claims to help prevent tooth decay. Health Canada maintains a list of approved strains of bacteria, but shows no willingness to investigate a product’s probiotic effectiveness. The department merely recommends that manufacturers use the term “probiotic” only if followed by a statement about the advertised health benefits of the bacteria. Microbiologist Gregor Reid thinks consumers should be aware they’re not always getting what they’re paying for. “Lots of products call themselves probiotic, and are allowed to call themselves probiotic, but they’re not,” he says.

Critics of the industrial food system warn that the fragile balance of gut flora can’t always be achieved in a lab. “People assume that you need a microscope, a Ph.D.,” says fermentation advocate Sandor Katz. “In reality, fermentation is a simple, ancient process people have been doing forever. We need to reclaim these traditions in our kitchens rather than the industrial versions that don’t deliver the benefits they promise. This is what raw-milk farmers have always known.”

For now, the raw-milk debate remains the most visible front line of a deeper shift in our understanding of bacteria’s relationship to our bodies. When it comes to his fight to legalize raw milk, Michael Schmidt believes the tide is finally starting to turn. Last July, he won the chance to appeal his recent conviction in Ontario’s highest court. His contempt-of-court case in British Columbia has also been postponed indefinitely. But Schmidt’s most meaningful victory occurred back in November 2011, when he secured his meeting with Dalton McGuinty and ended his hunger strike. “McGuinty couldn’t say outright he was going to change the law,” Schmidt says, standing among three cows in the Chilliwack barn. “But he listened to what I had to say. That’s all I wanted.”