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Gut Microbiome & the Impact on your Health


Gut Microbiome & the Impact on your Health


The microbiome is an ecosystem of trillions of microorganisms (bacteria, viruses, fungi, and protozoa) that live in and on an environment called ‘you’.

While most internal organs are sterile, the skin, nose, mouth, gastrointestinal tract and the urogenital tract is teeming with microscopic life. With up to 10,000 unique species and 100 trillion individual organisms.

More than 90% of these microbes are found in the gut, primarily in the colon.


These microorganisms have evolved with humans since Paleolithic times and are native to the body.

You mostly get it from your mother, generation to generation, as people are born through the vaginal canal, breastfed, snuggled and kissed, mothers provide their babies with her bacteria which then colonizes their bodies.


There are periods of our lives where the microbes go through larger changes, like puberty.

In adults, the microbiome is described as relatively stable. But what is changeable is the relative abundance of those types of bacteria.
As we get older, we also get our microbiome changes from our environment and from the food we eat.

People with a Western lifestyle and diet (lots of sugary, fatty foods and indiscriminate use of antibiotics) harms microbial diversity, which degrades generationally.

As an adult, your diet is one of the leading drivers of microbiome shifts you may go through week to week or day by day. If you spent a week eating South Asian food, and then a week eating Irish pub food, you would see changes in the abundance of certain microbes between those two weeks.

There are other factors like exercise, which can affect your immune system. That can change which microbes can survive and thrive. Also, alcohol consumption and medications can impact the proportions of how many bacteria in each species are present.


The majority of these microorganisms are beneficial and essential. Native to the body, these microorganisms produce enzymes we don’t have that are critical for proper processing and maximising the nutrition we get from food to prevent deficiencies.

Numerous studies show that microorganisms play a role far beyond the GI tract, affecting everything from brain function to the immune system. Cancer, depression, obesity and diabetes, skin diseases, Parkinson’s, multiple sclerosis and even autism leave microbial footprints.

People with certain diseases have different microbiomes but the Holy Grail question is:

Does their microbiome cause the disease? Or does the disease change their microbiome?

Researchers are finding that microbes found in people’s poop can be reliable biomarkers for disease, which could help predict and diagnose what disorders people have. This has the potential for treatment before symptoms take hold.

There are many studies on bacteria that are present in disease but scientists still don’t know what a good or bad microbiome is.

Researchers now believe diet and other external factors can switch harmless gut bugs into harmful ones.

Certain bacteria species are acutely responsive to the presence or absence of food. The effects of fasting are being investigated in mice. The microbial community quickly rebounds when the normal diet is restored, but some positive changes can persist.


Studies show that if you take the microbiome from an individual who has been diagnosed with a certain disease and transplants their microbiomes into mice, you also see symptoms of their disease in the mice.

This is compelling evidence that doing the opposite might help people one day. Putting the microbes of healthy individuals into those with the disease through their poop, called a fecal transplant.

There’s also evidence that there are differences between people’s microbiomes with mental health issues and healthy controls.


The bacteria in our guts stimulate nerve endings which send signals to the brain. They also release a chemical into your bloodstream, which can also interact with brain functions.

Frequent consumption leads to cravings which diminish with diminished consumption, suggestive of a relationship.


The short answer is Fiber. Only 5% of Americans meet daily fibre requirements and it is thought to be leading to changes in our microbiomes. Try to get your fibre intake up to at least 25 grams a day by eating more salads, vegetables, and fruits or by taking a fibre supplement. Fibre is powerful for feeding the bacteria which produce beneficial chemicals in your gut.

Eating a wide diversity of healthy foods to make sure you’re giving all the diversity of bugs in your body enough to eat. Try to count more than five natural colours on your plate.


Prebiotic is the stuff you eat that feeds the good bacteria you already have in your gut. This is mostly fibre.

Probiotic is consuming “live” bacteria in pill or food form (like yogurt). A highly controversial topic in the microbiome field right now. Two papers came out last year in the journal cell that turned the probiotic field on its head. Major issues are that many probiotics don’t have the bacteria or amounts of bacteria they say they do. And, whether or not a probiotic does anything for you depends on the native microbiome you already have. So you need to know your starting microbiome to determine if the probiotic will even work.

Usually, probiotics are bacteria that are just visitors. They don’t end up living permanently in our bodies. But after antibiotics, some of the probiotics stuck around. Scientists are not sure yet if that colonisation is a good or a bad thing. But in some cases, it ended up slowing the recovery of a person’s natural microbiome.

Post-biotic is a newer concept. These are the beneficial byproducts that bacteria make. In the current form, there’s no good post-biotic pill to take, you’re just trying to leverage the good bugs in your gut by feeding them prebiotics so they can make post-biotic (like short-chain fatty acids, amino acids, even serotonin) for you.

Post-biotic or ‘bacterial waste products’ (one organism’s trash is another’s treasure) for example: Hydrogen Peroxide is produced. This may protect us from salmonella and other pathogenic bacteria or yeasts that may be hanging around.

Short-chain fatty acids are one of this acetic acid helps regulate blood sugar and gives the metabolism a boost. While Butyric Acid helps promote colon health by providing an energy source for colon cells.

What’s the one type of food that has it all? Fermented foods! These are prebiotic, probiotic, and post-biotic rolled into one! Good stuff.


We should recognise the importance of beneficial bacteria and bacterial diversity. They’re part of us, the microbes. And we need to be very mindful and take care of them.

There are at least 500 different species of bacteria inhabiting our guts and for a total of 300 trillion microorganisms. Even concentrated probiotic capsules contain only about five species and 50 billion bugs. And kombucha serves up even smaller quantities. That’s far from enough to make any real difference in health.

So the take-away message on prebiotics! Eat lots of salads, vegetables and fruit. Fibre is the food of choice for our gut microbiome.


Suzanne Devkota: Instagram
·      A rising star researcher and assistant professor at Cedars-Sinai LA
·      A microbiome specialist and disease generalist

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