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For anyone who doubts the importance of eating for your microbiome, look no further than the panda exhibit at the zoo. Giant pandas have unfairly been cast as lazy animals who sit around eating all day, but they have little choice — their ancestors switched to a vegetarian diet more than two million years ago, but they still have the gut microbiome of a carnivore. The species of bacteria that break down cellulose in most herbivore guts are extremely scarce in the panda, so most of that bamboo comes out the other end more or less undigested.

Humans also suffer when the things we put in our mouths don’t work well with our microbiomes. The trouble is, no two people have identical microbiomes. The Figeys Lab at the University of Ottawa’s Faculty of Medicine is working toward a future where both nutrition and medication can be tailored to the individual’s unique blend of gut microbes.

Ask your gut which drug is right for you

“Drugs should have two labels — one label for its effect on the host, and another for its effect on the microbiome,” says Dr. Daniel Figeys, a professor in the Department of Biochemistry, Microbiology, and Immunology at the University of Ottawa’s Faculty of Medicine. “Drugs would never make it on the market without doing a liver function test, for example, and there should also be a microbiome function test.”

Dr. Figeys’ team at the uOttawa Faculty of Medicine has developed a technology to keep a patient’s gut microbiome alive in fine-tuned culture conditions and then test it against various substances — whether that’s a battery of 300 medications or an array of dietary fibres.

“We prepare a culture medium and put in microbiomes collected from human stool samples. We have a procedure to filter it and obtain the microbiome alive and then we put it into 96 well plates with a different drug in each well, so it’s high throughput,” says microbiologist Dr. Leyuan Li of the Figeys lab.

Measuring the changes to the microbiome could tell doctors in the future which among a number of otherwise equivalent drugs would be better for their patient from a microbiome standpoint.

Clinical trials for children

The lab, in collaboration with Dr. Alain Stintzi and Dr. David Mack, is currently involved in three clinical trials for pediatric inflammatory bowel disease. Research has established that dietary fibre is important for nurturing organisms like faecalibacterium that boost the immune system and seem to be protective against everything from obesity and Crohn’s disease to asthma and depression. However, nutritionists’ one-size-fits-all advice to increase fibre intake doesn’t capture the whole story.

“Overall, they have a beneficial effect, but from one individual to another they may not have the same effect. One type of fibre may have zero effect for that person — or worse, a detrimental effect,” says Dr. Figeys.

After the children are treated to bring down their inflammation, the clinical trials will test each child’s microbiome against different resistant starches (fibres) and will then prescribe a certain type of fibre (whichever led to more butyrate production) to be added to their diet for six months.

While a completely personalized medicine may still be out of reach of most health systems’ budgets, it’s not an all-or-nothing choice, but a spectrum of personalization. Stratifying our treatments and nutrition to cater to categories of microbiome composition would go a long way to improving gut health.

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