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Dr. Brett Finlay had an unusual request for the researchers at McMaster University, who were embarking on a large-scale study on children's susceptibility to asthma. They were following 3,000 children from birth to age five, and Finlay, a microbiologist at the University of British Columbia, wanted to examine the kids' feces – or, more precisely, the bugs in their poop.

Finlay had a curious and compelling hypothesis. Perhaps, he suggested, the trillions of tiny unseen organisms living in the participants' bowels could predict, and even determine, which of them would go on to acquire asthma, a disease that has surged in prevalence over the past few decades.

Six years on, his findings are now being submitted for publication, and Finlay is optimistic that his work could lead to something big. He and his colleagues found several strains of microbes in certain children's feces that seemed to protect them from developing the chronic inflammatory disease. If they are right, it opens the door to the idea of one day preventing the disorder altogether by making sure children's guts are populated with the right microbes.

In recent years, there's been a boom in research on the human microbiome, the universe of microbes that live on and within our bodies, as scientists uncover its importance for our health. An imbalance in the composition of microbes in our guts is now believed to play a role in a staggering array of ailments and disorders, from allergies to autism, obesity and depression. ("The joke in the field now is, 'What isn't affected by the microbiome?'" Finlay says.) It's a paradigm shift that has sparked the hope of thwarting or treating such conditions by zooming in on our microbial inhabitants and figuring out what they do.

The explosion of microbiome science has also fuelled a gold rush among companies and individuals offering dietary advice, self-help books aimed at targeting our gut microbes, and probiotics, which are foods or supplements that contain live bacteria and yeasts. The global market for probiotics is expected to reach more than $52-billion (U.S.) by 2020, according to the California-based market research firm Grand View Research, Inc. Meanwhile, the latest book by U.S. neurologist and author David Perlmutter, Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain – for Life, has quickly found its way onto The New York Times bestseller list, with alluring tips on how to achieve neurological wellness through dietary changes and probiotic enemas.

Yet making sense of the health claims is no easy endeavour. Scientists are still in the early stages of figuring out what bugs exist in our systems, never mind which we need for optimal health. And with few exceptions, the ability to fight or ward off disease with the right mix of microbes – or with the molecular compounds they produce – is still largely out of reach.

"Is there a perfect gut microbiome? … And can you improve it by taking probiotics? Those are questions that are being very definitely asked, and there is no final answer as of yet," says Dr. John Bienenstock, a distinguished professor of pathology and molecular medicine at McMaster University.

Bienenstock is one of the several international scientists who contributed to a recent paper, published in the Annals of Medicine, that suggests our modern, urban lifestyle may be limiting our environmental exposure to an important diversity of micro-organisms. They believe the kinds of microbes we come in contact with, as early as in the womb and into our first years of life, are critical for normal immune development. A variety of factors tied to modernity – including Caesarean births, formula-feeding, a lack of green space in cities, inadequate physical activity and the use of antibiotics – mean many of us aren't coming in contact with the broad spectrum of micro-organisms that previous generations did. This could explain the rise of chronic inflammatory disorders in urbanized parts of the world, the paper says.

The solution, however, is more complicated than simply identifying "beneficial" bugs and re-introducing them into our lives. Researchers are long past viewing micro-organisms as "good guys and bad guys," Bienenstock says. Rather, the microbiome is now understood to be a complex and bustling community, where even potentially disease-causing strains can be useful neighbours and friendly ones can turn against us.

"It's the diversity that counts. The more different types of bugs that live together happily and communicate, the healthier you are," he says.

Moreover, it appears the human microbiome is pretty much set by the age of two or three. That would mean, even though you can temporarily introduce new yeast and bacteria through your diet or reduce your existing microbial population with antibiotics, your microbiome will likely bounce back to its set profile. To achieve long-term benefits for chronic conditions, adults would likely need to constantly replenish their guts with the relevant missing microbes.

And while scientists have made strides in recognizing various strains of gut microbes by identifying their molecular DNA signature, they still have a long way to go to determine what each does and how each functions, Bienenstock says.

That hasn't stopped people from making ambitious promises that leap ahead of the science. Products and advice abound, with claims about how to modify your microbiome for everything from achieving a glowing complexion and losing weight to reducing anxiety and preventing dementia. And people are taking steps beyond popping probiotic pills or eating yogurt and fermented foods. While doctors have found that fecal transplants, a process that introduces feces from a healthy donor into the bowels of an ill recipient, is effective for treating C. difficile infection, there are plenty of do-it-yourself videos on YouTube, showing fecal transplants for other conditions.

For Dr. Gregor Reid at Western University, what's frustrating about the wave of unproven claims about microbial health is they take away from legitimate research. As a pioneer in the field of probiotics, Reid began studying the health impact of microbes in 1982, long before "probiotics" and "microbiome" became buzzwords. His work has led to the development of a probiotic yogurt used in Africa that appears to improve the immune systems of people with HIV and helps those who are wasting gain weight. Reid has also worked with the dairymaker Danone, helping to promote its Activia brand of yogurt, which he credits for popularizing the idea of probiotics.

A lot of research is currently done on animal models, and their findings may not translate to humans, he cautions. But with new findings about our microbial inhabitants emerging every month, major breakthroughs for targeting any number of chronic inflammatory diseases, metabolic and mood disorders may be around the corner.

Reid says unfounded claims do a disservice to the rigorous science in this field, he says, especially since microbiome research isn't just a fad.

"This is, I think, the most exciting area of science and medicine right now," he says.

Love your guts

Giulia Enders thinks her guts are delightful – and she wants to convince others to get acquainted with theirs too.

The 24-year-old German medical student considers herself a "spokesperson" of the human gut. She brings the latest science on the digestive tract to life in her whimsical, highly readable book, originally released in German as Darm Mit Charme (Charming Bowels). Its English version, titled Gut: The Inside Story of Our Body's Most Underrated Organ, is now released in Canada.

During a recent visit to Toronto, Enders offered an introductory lesson on what's actually going on in there:

  • Suppressing the urge to go to the toilet can lead to constipation because it breaks an “unspoken agreement” between brain and gut to go on schedule: “The gut has no eyes, but it has the second largest collection of nerve cells after the brain. So it really relies on the information that is given by the body, and it can also give back. With your whole metabolism and the gut nerve cells, if they feel like they can rely on certain patterns, they can work more effectively.”
  • That growling in your belly isn’t a signal that you’re hungry: “The small intestine loves to clean and it’s very busy all the time, moving things forward. When we haven’t eaten for a while, the small intestine is like, ‘Okay, no need to digest. Everything that’s still here, I’m going to wipe it out,’ so it creates this muscular wave.”
  • Vomiting is a “tour de force performance,” particularly when sparked by powerful emotions: “It’s really your inner digestive tract sacrificing itself because it would like to have this energy from this food. But instead, it will shoot it out to save energy it would otherwise use for digestion.”

This interview has been condensed and edited.

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