For Justin and Erica Sonnenburg, overhauling their family’s diet was an easy decision. Their toddler was painfully constipated, and the couple run a Stanford University lab devoted to studying how dietary and other changes effect the community of microbes that live in our guts, known as the microbiome.

“We, of all people, should not have a child with gastrointestinal issues,” they write in The Good Gut, their new book. The family began religiously consuming fibre-filled and probiotic foods, and altered other aspects of their lifestyle, from handwashing to antibiotic use.

Their daughter hasn’t had a problem since.

The Good Gut is one of a burst of new books that advise how to nourish the microbiome and explain how doing so may lead to better health. But as the Sonnenburgs know well, findings from the field of microbiome research are exciting, but unsettled. What are the ethics of broadcasting lifestyle changes based on immature science to a broad and impressionable public?

“This is something we debated at great length,” Justin Sonnenburg told the Star. Others in the field are debating it, too: overselling the research could backfire directly onto scientists.

“I’ve seen congressional hearings where they basically say, ‘You promised the Genome Project was going to cure all these diseases and you’re wrong, and we’re going to take away all your money now,’ ” says Jonathan Eisen, who researches microbiome diversity at the University of California Davis. “I think we run that risk . . . People are saying we can cure everything.”

For the Sonnenburgs, the decision to publish came after realizing that fellow scientists were making some of the same choices they were.

“The people that we knew who were changing their lifestyles know how to read a Nature paper . . . The general public has no idea about that and most press articles don’t do it very well,” says Sonnenburg. “We just felt like it was a huge disservice to the general public to not have some resource available.”

Eisen called the Sonnenburg’s approach and that of Martin Blaser, an NYU microbiologist who wrote the book Missing Microbes, “reasonably responsible.” He does not feel the same about other books. “Most of them are ridiculous — just completely outlandish claims with no basis in science.”

Eisen took particular exception to claims made by David Perlmutter, author of the microbiome book Brain Maker, calling them “at best horribly misleading.” Brain Maker uses much stronger language than the Sonnenburgs when it comes to the brain-gut link, an area of research that has implications for disorders such as autism; the diet Perlmutter recommends bans gluten and advises lighter legume consumption.

Perlmutter welcomes criticism. “For someone to say the book is overstated, I don’t have any problem with that. I can absolutely see where that would come from.” But generally those critics “are locked into an institutional framework where they can’t make statements like I make, for fear of retribution, lack of continued funding, on and on. I’m, fortunately, not in that situation.” As a neurologist, he says, he deals with illnesses for which mainstream medicine offers very few answers; his patients have seen improvements after diet alterations.

Rob Knight, a microbiome researcher at the University of California San Diego, says he sees a benefit in maintaining public interest in the research, but a larger risk “that people will be disappointed with recommendations that are inconsistent or turn out not to be true, and that some people will have major adverse outcomes for reasons we don’t understand yet.”

The only lifestyle changes he feels comfortable backing are those backed up by other fields, like the benefits of eating more vegetables, fibre, yogurt and nuts. “Keep tracking the research — there’s an enormous amount of potential — but be careful of making major changes that aren’t well supported by data.”

The Sonnenburgs were reassured for similar reasons. The “microbiome diet” looks an awful lot like the Mediterranean diet, which reams of research have shown to promote health. Their other recommendations, including avoiding unnecessary antibiotics and promoting breastfeeding, also square with public health policies.

Justin Sonnenburg admits to being frustrated that the general public may not have the science literacy to differentiate between solid science and showmanship, and that provocative books may attract more attention.

Still, that left the same choice. “One option is to not write a book, and to just kind of watch it happen. The other is to put something out there that will both serve as a good example and try to educate people.”

Sickness and the microbiome

Asthma. Allergies. Alzheimer’s.

Obesity. Autism. Eczema.

Depression. Cancer. Colitis.

Pick a sickness, any sickness. Chances are good that it has been linked to alterations in the microbiome — the trillions of bacteria, viruses, and other micro-organisms that peacefully coexist in and on our bodies.

This week, a study in Nature Communications described a diet swap between 20 African-Americans and 20 rural South Africans. The switch quadrupled the Americans’ fibre consumption while raising fat intake for the Africans. After just two weeks, the researchers saw remarkable changes to the microbiomes of both groups and metabolites those bugs produce: the Americans saw increases in anti-inflammatory compounds and other biomarkers linked to lower colon cancer risk, while the Africans saw the reverse.

But research into the microbiome is still in its infancy. “There’s lots of evidence that diet affects health, that the microbiome affects health, and that diet affects the microbiome,” says researcher Rob Knight. “The microbiome has tremendous potential,” he adds, “but we don’t yet know the links.”

Is it too soon to make over your life for the microbiome — or not soon enough?

Where your microbiota comes from

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Most of the one to two kilograms of microbes that live inside us reside in the gut, but our skin, mouths and noses are also colonized, as are women’s vaginas.

Childbirth: Our first influx of microbes comes from the birth canal — so babies born by caesarean section have very different microbiomes than those born vaginally.

Breastfeeding: Breast milk provides complex carbohydrates that microbiota thrive on, as well as more living bacteria.

Food: Hunter-gatherer tribes like the Hadza and the Amazon’s Yanomami, who eat vastly more fibre than westerners, boast much more diverse microbiomes.

Probiotics: The beneficial bacteria found in foods like yogurt, kimchi and sauerkraut and in commercial supplements fortify our own bodily systems.

Environment: Microbes are all around us — in our homes and offices, on our families and pets — and evidence suggests that aggressively eradicating them works against us.

AT HOME WITH THE SONNENBURGS

In the fridge: Lots of vegetables and fruit, which are full of fibre — food for your microbiota, which feast on what you cannot digest and produce health-promoting metabolites.

Not in the fridge: The family also limits their consumption of meat: red meat and fatty foods, especially when eaten in large amounts, trigger the synthesis of a microbiotic byproduct linked to higher risk of stroke and heart attack. They also cut down on saturated fats.

In the pantry: Whole grains like wild rice and wheat berries (which they grind themselves into a rougher flour than the store-bought kind, the better to pass down to the lower intestine intact), and plenty of beans and legumes, both fantastic sources of fibre.

Underneath the sink: Cleaners that are not advertised as antimicrobial, such as Castile soap. The emerging “hygiene hypothesis” suggests that overly sterile homes are contributing to the rise of immune-linked illnesses such as asthma and eczema.

At the sink: Handwashing is mandatory after a visit to a hospital, mall, zoo, or during cold season, when pathogenic (disease-causing) microbes are more likely to be picked up. After gardening, petting the dog or playing in the yard, they skip it.

In the medicine cabinet: Probiotic supplements, but only after a course of diarrheal illness — the family prefers to get their probiotic kick from food like yogurt, kefir and sauerkraut.

Not in the medicine cabinet: Antibiotics. When illness strikes, the family discusses with their doctor whether a “wait and see” approach will work, avoiding microbiota-wasting antibiotics unless necessary.

In the backyard: Fresh-grown vegetables covered in dirt, another source of microbes. Farms are more microbiotically diverse than urban dwellings, a condition the Sonnenburgs try to imitate.

On the couch: A dog. Pet owners have more diverse microbiomes than non-pet owners, a situation the Sonnenburgs began to understand after seeing their dog come in from the yard and lick their daughters’ faces.