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Microbiome: Buzzword in Gut Health — But What Is it?


The advances in gene sequencing have created an enthusiasm for research linking gut bacteria to diseases.

Have acne? Could be your gut. Crohn’s disease? PTSD? Obesity? Could be your gut.

The gut microbiome — trillions of bacteria in your gastrointestinal tract — has everyone from immunologists to gut health nuts excited about what problems it could explain, or solve, about their health. Researchers are pumping out new studies linking the gut bacteria makeup to everything from asthma to irritable bowel syndrome, and lay people obsessed with their guts eagerly await the next study explaining all that ails them.

Experts, however, caution that a larger body of research is needed before the extent of the significance is known.

On the verge of discoveries

Dr. Ken Croitoru, professor of medicine and immunology at the University of Toronto and gastroenterology at Mount Sinai Hospital said advances in gene sequencing have created the enthusiasm for future discoveries. This sequencing “revolution” allows researchers to understand the community of bacteria within a DNA sample, he said.

“We can catalogue what’s in there and. . . see how the makeup of the bacteria in a given sample from someone who’s got a disease is different from someone who’s healthy,” said Croitoru. “This is where all the excitement starts.”
“It’s hugely exciting whenever you’re at the forefront of things,” said Croitoru. “Hopefully we’ll get some discoveries that will be paradigm shifting.”

For the past decade researchers have been trying to pinpoint the specific roles the microbiome play in preventing disease and boosting immune systems. Once more is known, experts say the implications for illness prevention and treatment are boundless.

But they aren’t there yet.

Researchers have yet to discover what makes up a “normal” gut microbiome. They’re overwhelmed by the amount of microbiome data collected and by how to best analyze it, said Croitoru.

“We’re still not sure what it’s trying to tell us,” he said. “The real question is . . . if we’ll be able to take this information at some point down the road and say, ‘Aha, this abnormality in this community describes someone who is at risk for developing inflammatory bowel disease, for example, and . . . develop a strategy that would change that abnormal microbial makeup.’”

Croitoru estimates researchers are five to 10 years away from establishing scientifically supported methods of how to change the microbiome to fight or prevent disease.

Good for your gut

In the last 15 years, researchers have discovered a diverse and richer gut microbiome is better than one with less bacterial diversity.

“What’s shifted is our understanding that not all bacteria are harmful,” said Dr. Vincent Pedre, a New-York based medical doctor and functional medicine specialist and the author of the book Happy Gut. “(Good gut health) is about promoting the growth and presence of good bacteria.”

A study released last year examining the microbiome of an “uncontacted” Amazonian indigenous tribe that ate a high-fibre diet, found the community had the most diverse microbiomes researchers had ever seen. They appeared to be healthy without obesity or metabolic diseases, though some experts caution it’s too early to read much into those findings.

Good bacteria promotion can come from eating fibre, probiotics, such as yogurt and kefir, or even from exposure to dogs and dirt, say experts.

So step away from the hand sanitizer.

“Dirt does not equal disease,” said Marie-Claire Arrieta, a postdoctoral fellow at the Michael Smith Lab at the University of British Columbia and co-author of the book Let them Eat Dirt, out in September. “That does not mean that I should be licking surfaces of a mall or of a subway. . . but that does mean that we shouldn’t be . . . disinfecting everything that a kid touches early on in life.”

Microbiome composition changes throughout life but the first 100 days of life are most important for microbiome development, said Arrieta.


In the womb, babies are “sterile,” so they first accumulate bacteria when travelling through the birth canal — accessing rich bacteria caesarean-born babies miss out on — and continue to build their microbiome “ecosystem” through contact with surfaces, people, animals and other environments, she said. Babies putting their hands and feet in their mouths may even be an evolutionary function that helps get environmental bacteria into their guts, she said.

It takes about three years for the microbiome foundation to be established, she said.

Building a diverse microbiome

Antibiotics, while potentially life-saving, can be problematic for the microbiome.

“When you take an antibiotic, it’s not that it’s like a targeted missile, going in to shoot the (bacteria causing an infection), it’s more like a carpet bomb that is going to kill that one and a whole bunch of others,” said Arrieta, who supports use of antibiotics to treat illnesses but said use can detrimentally affect microbiome diversity.

Studies have shown that use of antibiotics, particularly in childhood, may contribute to increased incidences of certain diseases such as Crohn’s disease or inflammatory bowel disease.

“At the same time polio and measles and all these nasty diseases have decreased, there’s been an equal increase in chronic immune-mediated diseases, so diabetes, Crohn’s disease, ulcerative colitis, even autism, asthma — diseases that have only popped up in the last two generations,” she said. “What the evidence is pointing towards is that it’s the microbes within us that is driving that change.”

Researchers also know that babies born by caesarian section face obstacles in building a diverse microbiome as they don’t receive the same rich bacteria vaginally-born babies do. Studies are currently focusing on how to boost the microbiome of C-section babies.

Hope is on the horizon

As the body of evidence grows, researchers will likely learn more scientific-based details about how the microbiome is linked to disease. This could lead to major discoveries in treating and preventing diseases, said Croitoru.

Researchers hope that more physicians will start prescribing probiotics — which help repopulate good bacteria — alongside antibiotics. They’re also optimistic advances in probiotic research will get more effective probiotic supplements and products on the market.

“There needs to be a balance of prevention of infection and promotion of microbes that are associated with health,” said Arrieta.

Arrieta adds that hyper-hygienic practices have to change.

“I do hope that as more information from this field of science reaches the general population, people will begin to understand the overwhelming advantages of not being hyper-hygienic, especially during the childhood years,” she said.

More playing in dirt, less hand sanitizer.

Foods that can boost your microbiome health

  • Fruit, vegetables and legumes that are high in fibre: Sweet potato, yams, raspberries, apples, bananas.
  • Fermented foods: Sauerkraut, kimchi.
  • Whole starches: Brown rice, barley.
  • Probiotics: Yogurt, kefir.

Where to learn about the gut microbiome:

Gut: The Inside Story of Our Body’s Most Underrated Organ by Giulia Enders

Enders, a 26-year-old German scientist, started researching the gut after she developed a skin disease at age 17. She became fascinated with the subject, enrolled in a PhD program in gastroenterology and went on to write Gut in 2014. It’s topped international best seller lists and captivated gut nuts with explorations of communication between the gut and the brain, the gut and gluten intolerance and the gut and your mood.

The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long Term Health by Justin and Erica Sonnenburg

Published in 2015, The Good Gut explores strategies for nourishing the microbiome though lifestyle change-ups in the hopes of achieving better health. The Sonnenburgs, a married couple and Stanford University microbiome researchers, wrote the book after realizing their daughter was suffering from constipation. They changed up the whole family’s diet, solving their daughter’s problem.

Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues by Martin Blaser

In his 2014 book, Missing Microbes, Blaser explores links between the overuse of antibiotics — around since the 1940s — and “modern plagues” such as obesity, asthma, allergies, certain cancers and diabetes. Blaser, a medical doctor and director of the Human Microbiome Program at New York University, also examines the consequences of C-sections, which deprive babies of important bacteria from their mothers, and says antibiotics given to children in early years pose great risks to their long term health.

By KATRINA CLARKE  Staff Reporter   Fri., Aug. 19, 2016
 source: www.thestar.com

4 thoughts on “Microbiome: Buzzword in Gut Health — But What Is it?

  1. The microbiome is a relatively recent concept gaining greater credibility for explaining many disease processes resulting from dysbiosis. As we continue to understand the need to evaluate the body from a perspective of integration rather than treating it as entities of individual function, our ability to understand the factors necessary to improve overall HEALTH will continue to develop. People will slowly come to realize and except nutritional deficiencies are more likely a major missing link in achieving better health than the current belief based on swallowing better and newer drugs to override a pharmaceutical deficiency.

    I believe we share a similar view and approach to achieving better quality health. Our writing approaches these topics from an important OBJECTIVE perspective.

    • Well put Doctor J. As time goes on, I hope that more people can break away from unhealthy routines and start to incorporate healthier choices to enhance better health. Some of the articles I have read indicate probiotics can be greatly effective in this area.
      ~Thanks for your input~

  2. Thank you. Your support is greatly appreciated!

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