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On the scientific frontier: the bugs in and on us

By Lorraine Graves

Published 2:51 PDT, Fri November 1, 2019

Last Updated: 4:18 PDT, Fri November 1, 2019

Richmond scientist Dr. Brett Finlay is making the study of the good bugs in our body his life’s work. His two books, the second written with his daughter Dr. Jessica Finlay, are written in lay-persons’ language to help us understand the thousands of different kinds of bacteria, called our microbiome, we need to be healthy.  

Though bacteria were first discovered in 1683 when Van Leuwenhoek peered through the microscope he’d invented, their role in promoting our health is slowly being unraveled by researchers like Dr. Claire M. Fraser of the University of Maryland School of Medicine in Baltimore. 

Fraser is one of the most cited researchers in her field. That means other scientists rely on her work as the bedrock for theirs. 

At the recently sold-out Don Rix Memorial Lecture sponsored by Genome BC, Fraser was clear that we are on the verge of understanding the vital role played by all the bugs our bodies need to be healthy and how we get sick when they are out of whack.

Citing the work of Finlay, Fraser pointed out that when healthy mice or humans are raised without bacteria, they become very sickly. 

Humans are a collection of microbial ecosystems. 

Fraser said, “This collection of bugs, that keep us healthy, live in balance with each other and with the individual human they inhabit. Each person has different collections of bacteria on their skin, in their colon, in their reproductive tracts, and elsewhere. Microbiomes are dynamic.” 

No two people have the same microbiome and it changes over time for each person, both in the short and long term. 

Fraser said researchers are studying the deterioration of the microbiome as one of the possible sources of inflammation that leads to age-related diseases, inflammatory conditions and autoimmune diseases. 

Speaking of the different bacteria, she warned, “Looking at who’s there is probably not the right thing to be measuring.”  

Rather, she said, we should be studying the function of different combinations of organisms like bacteria, that can carry out the same function as others. (Much like there are many tools that can peel a potato. Some look remarkably different but all still get the job done.) 

In answering an audience question about hand washing from a father of two toddlers, Fraser said people should be more like a one-year-old, exposing themselves to natural bacteria in the environment, not washing their hands when they come in from outdoors. 

The one caveat she pointed out was, “It’s different if you have been with a bunch of people who are sick. Then a little bit of hygiene is good.” 

Fraser went on to mention that hand sanitizer negatively affects the composition of our skin’s microbiome. The bugs that live in harmony on us to keep worse bugs at bay, much the way the fuzzy white mould on the outside of Camembert cheese keep nasty organisms, that could make us sick, from growing. 

Speaking of food, Fraser said there is an abundance of medical evidence that diet influences health.

“But,” she said, “What advice should I believe?”

One family of bacteria in our lower gut (the colon) can digest the plant roughage we eat. In doing so they actually produce a family of chemicals that help us. In fact, there are receptors in our gut that look for these chemicals so they can be absorbed by our body to reduce inflammation.  

Our diet determines the health of these organisms that we, in turn, need to stay healthy. 

Fraser said, “You will pay the price for a meal high in protein and high in fat. The metabolic effects extend beyond the gut.” 

She said the best diet is one high in fresh fruits and vegetables, low in processed foods. She suggested a healthy diet has less fat and red meat as well. 

She suggested “Better than the Keto diet, the Mediterranean diet is closer to what is good for more people.”

She cautioned that even the Mediterranean diet may not be best absolutely everyone. 

A person's unique mix of gut bugs even affects which diet is best for an individual with diabetes. 

Fraser also mentioned that while the Inuit thrived on a traditional diet high fat and protein diet with almost no fresh fruits and vegetables, they had evolved over millennia to have gut bacteria that served them well. It means that millennia ago, Inuit who couldn’t be healthy on that diet died out. Those who could thrive eating mainly fat and meat were the ones whose bodies and gut microbiome could get the best out of their diet. They survived to have children who had similar abilities to thrive on that diet. Fraser cautioned that that is not the case with most of us. 

Asked about alcohol consumption, Fraser said reasonable alcohol consumption, however an individual defines it, is probably not an issue but excess is a problem. 

She went on to point out that interestingly enough, a few people have bugs in their microbiome that turn some sugars into alcohol that then seeps into the blood stream, making even a teetotaler drunk or causing the liver diseases usually found in alcoholism. 

She said we are moving to a time when we will be able to come up with more healthful diets for each individual through genomics. That day is coming, she said, because we will understand not only a person’s genetic make-up but also the make-up and function of our body's five to seven pounds (2.3 to 3 kg) of bacteria. 

Describing antibiotics as a nuclear bomb on the microbiome, she stressed that not all treatments need to be antibiotics but when they are needed they can be life-saving. 

She reassured, “In most subjects, the microbiome returns to the pre-antibiotic state.”

Like a garden that grows well with the occasional weed scattered about, when plowed under, the fallow soil lets dormant weed seeds flourish because there are no good plants to keep them under control. It’s the same thing that happens when we take antibiotics. 

Speaking of C. difficile, the colon bacteria that can run rampant in people with depressed immune systems like those receiving chemotherapy or in people who have had antibiotics that kill off all the good bacteria, Fraser said, “C. diff is present in all of us but our healthy gut bacteria don’t allow them to overgrow.”

Antibiotics when necessary but not necessarily antibiotics. Fraser also cautioned against depending on milk-based probiotics. The gut microbiome has so many different bugs in it that we still don’t know enough about them. The hope is that someday there will be a custom pill that can restore each individual’s personal collection of gut bacteria. She was clear, we are not there yet. 

In one recent study, taking probiotics actually slowed the recovery of the healthy mix of gut bacteria. 

She said the negative effects of antibiotics are less pronounced in breast-fed babies. 

Discussing babies, Fraser showed graphs showing the abundance of healthy bacteria babies delivered vaginally have in their system. While babies delivered surgically, by C-section, take up to a year to establish this healthy collection of bacteria. The healthy bugs are important to digestion and to their immune system. These good bugs actually stimulate a baby’s gut to grow immune cells. 

One infectious disease physician said that, with sick kids in the hospital, you can tell the babies that are being breast fed. They usually don’t get as sick and they tend to get better sooner. 

But, where the gut biome is concerned, there is much to learn. Fraser kept emphasizing that the data are too early to make strong recommendations but she called the data, “quite compelling.”

She said there is not yet a smoking gun when it comes to whether diseases of aging, inflammation and chronic diseases come from changes in the gut microbiome. “But,” she said, “With enough research, it may be able to reverse losses in the guts’ diversity of bugs.” 

She was clear, one single approach will not work for everyone.  

Nowhere is this more certain than in people receiving chemo for cancer. 

“The gut microbiome plays a role in metabolizing (breaking down) chemotherapy drugs,” she said. 

By genetically analyzing the bouquet of bacteria unique to an individual, and by knowing what compounds they will break down the chemo drugs into, doctors will be able to custom-tailor the mix of cancer-fighting drugs to minimize negative effects and maximize their therapeutic action. To find out which gut bacteria each person has, scientists analyze each bug’s genome. It’s like reading and recording the name tag of everyone at a large conference.

The vital role of genomics, using our knowledge of how everyone is genetically different, was brought home in a GenomeBC video before Fraser’s lecture. A young mom talked of the genetic testing that showed her daughter would likely lose her hearing if the usual mix of chemo drugs were used to treat her cancer. Discovered in time, the little girl’s treatment was tailored to her unique genetic make-up. Today, cancer-free, she is a bouncy child with normal hearing who bops around with her big sister.  

Fraser stressed throughout her talk that we are on the cusp of discovery. She was clear, at this point the data shows correlations only. Just because two things are seen together – like good health and a healthy mix in the microbiome – doesn’t prove that one causes the other. (Just as most people die in beds but beds don’t cause death.) Ever the responsible scientist, Fraser pointed out that correlation is not causation. 

She also cautioned attendees, a good portion who were from the general public, not to get their scientific information from the general press. She said the microbiome has become a trendy topic for authors as she showed a slide littered with books on how to stimulate a healthy microbiome. Of them, she said three were based on solid science, two by Richmond author, beekeeper and scientist Finlay, and one by Justin and Erica Sonnenburg. 

Of the three, Finlay’s Let Them Eat Dirt, written for the lay person, has become a popular book for parents and health enthusiasts. 

Fraser said the next step in microbiome science is to show what bugs actually cause good health and how they do it. 

She said, “Be patient while the science plays out.”

At the close of her talk, Fraser was presented with a hand-carved Coast Salish talking stick. She ended the evening by saying, 

“My greatest hope and expectation is that with a greater understanding of the microbiome this will become a part of mainstream healthcare. I went into science to do good.”

To learn more about GenomeBC go to 

For more on Finlay’s book Let Them Eat Dirt: saving your child from an oversanitized world click on

And to learn more about Fraser and her work as a forensic geneticist for the FBI that led to finding the source of anthrax used to attack people through the mail in the US check out her bio at  

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