The Microbiome is the New Buzz Word


The word Microbiome is the new market trend - hardly a day goes by without a research study or article being published about the gut microbiome.

When it comes to cutting-edge innovations in medicine, all signs point to the microbiome. I’ve been saying it for years, but Hippocrates beats me hands down as he said it first. “All disease begins in the gut”, and how.

So, with all the latest buzz going on about getting the microbiome tested, I've done just that via a company called AtlasBioMed. Not to bore you with the details, my gut system's always been a bit 'iffy' - colitis in my teens and just a general inability to digest properly, despite a decent non-junk diet - I've always been a salad and healthy-stuff lover with little meat, low carbs and a daily probiotic going on. So to have the chance to now ask my gut directly what it needs for me to be the best me, well, sign me up for that.

The central location of our microbiome is in our gut system, which contains trillions of trillions of microbes. If we want to optimise our health, we need to bio-hack our body, prevent chronic disease, and eat the foods are right for us. Simples, you’d think, but what foods are the right ones for us? And does one size fit all? It's turns out that the answer to this is a big Non.

Every week there’s a new health-food fad, from paleo to vegan to keto, and each one is the new best way to eat for all of us – understandably it’s all too easy to be sucked into trying each one to get the healthiest us that we can be. But here’s a thing – we can bypass the trying-every-food-fad by asking our microbiome directly, because all the information we need on what we should – and shouldn’t – eat, is right there in our microbiome - we just need to know how to read it.

Understanding the microbiome is changing the understanding of who we are and how our body functions. In essence it’s the Mission Control Centre for body and mind, part best friend, part power converter, part engine and part pharmacist; lots of internal complex machines needing a finely tuned balance.

As new insights keep emerging about microbiome research, we’re changing the perception of what keeps us healthy and makes us sick. It’s all good news – the more we understand about our own personal Mission Control, the more we can put an end to conflicting food advice and kick food fad diets into touch.

Here are some of those insights:

1. ‘Health Food’ isn’t necessarily healthy

A health fad shouldn’t necessarily be followed by everyone, i.e. we’ve been told to eat our greens, and that greens and nuts are anti-inflammatory – I’ve followed this theory for decades. But – it’s not always true. Spinach, bran, rhubarb, beets, nuts, and nut butters all contain oxalate, and oxalate-containing food can be harmful, unless we have the microbes present that can metabolise it into a non-harmful substance.

Current stats from one of the microbiome testing companies, Viome, shows that 30% of their tested clients don’t have the microbes to metabolise oxalates properly, which means that for these people, healthy foods like spinach are actually not healthy for them at all.

2. Foods containing antioxidants aren’t good for everyone

Polyphenol antioxidants in foods are usually considered very healthy, but unless you have microbes that utilise specific polyphenols, you may not get their full benefit. One example is a polyphenol called ellagic acid. Tests can detect if your microbiome is metabolising ellagic acid and converting it into urolithin A, as it’s only the urolithin A that has anti-inflammatory and antioxidant effects. Without the microbes to do this conversion, we won’t benefit from the ellagic acid in foods such as walnuts, raspberries, pomegranate, blackberries, pecans, and cranberries.

Viome’s stats show only about 50% of their clients (and we’re talking tens of thousands) actually receive the anti-inflammatory and antioxidant benefits from eating foods containing ellagic acid.

3. We’re probably eating too much protein, and it may be causing inflammation

We know protein’s good for us; it helps build muscle and provide us with energy, but if we eat too much, it can cause inflammation and decrease longevity. Our microbiome can determine if we’re eating too much protein that feeds protein-fermenting bacteria like Alistipes putredinis and Tannerella forsythia, and if these organisms are producing harmful substances such as ammonia, hydrogen sulfide, p-cresol, or putrescine. These substances can damage the gut lining and lead to health issues like leaky gut.

4. Some ‘Health’ foods may cause heart disease

Choline in certain foods can get converted by bacteria into a substance called trimethylamine (TMA). When TMA gets absorbed into the body and is converted to trimethylamine N-oxide (TMAO), it’s associated with heart disease. However, TMA conversion doesn’t happen if we don’t have the right types of bacteria in our microbiome.

So, look out for choline rich food such as liver, salmon, chickpeas, split peas, eggs, navy beans, peanuts, to name just a few.

5. You can see inflammation from too much iron

Minerals like iron in food can, in certain inflammatory microbial environments, promote growth of pathogens like esherichia, shigella, and salmonella. Maybe it wasn’t the raw chicken that gave us food poisoning, but a toxic microbiome that made us sick.

6. Anxiety and stress

The gut and brain are connected via the vagus nerve. A large majority of neurotransmitters are either produced or consumed by the microbiome; in fact, some 90% of all our serotonin, one of our bliss neurotransmitters, is produced by the gut microbiome and not by the brain, as we've long been led to believe.

When we have a toxic microbiome that’s producing large amount of toxins, the lining of the gut starts to deteriorate, resulting in what we know as ‘leaky gut’. When the barrier of the gut breaks down, toxins leak into the bloodstream which starts a chain reaction causing low-grade chronic inflammation. This has been identified as a potential source of depression and higher levels of anxiety, in addition to many other chronic diseases.

7. Ditch the energy drinks - a balanced microbiome is more energizing

Lacking energy? Dump the coffee and get the microbiome into balance.

The microbiome is responsible for calorie extraction, as in creating energy through pathways such as the tricarboxylic acid cycle. The body depends on the energy that the microbiome produces.

How much energy we get from food is dependent on how efficient the microbiome is at converting the food into energy. High-performing microbiomes are excellent at converting food into energy, which is great if we’re an athlete, but if we don’t use up the energy, it may be the source of some of those unwanted pounds.

If the microbes can’t metabolise the glucose (sugar) that we eat, it’ll be stored as fat. If the microbes are extracting too many calories from food or causing metabolic endotoxemia which can lead to insulin resistance, we may end up storing what we eat as fat.

8. We can see joint pain in the microbiome

Got any condition with ‘itis’ in the name? Our microbiome can tell us why. If you have anything with “itis” in it, it’s possible that when you balance your microbiome, the inflammation from your ‘itis’ will be reduced.

Lipopolysaccharide (LPS) is a key pro-inflammatory molecule made by some of our microbes. If the microbes are making too much LPS, it can wreak havoc on the immune system by putting it into overdrive. When the immune system goes on the warpath there is often collateral damage to joints and other parts of the body.

Balancing the microbiome is a better solution than reaching for the glucosamine. The microbiome puts our immune system through basic army training and determines when it goes to war. Ideally, our immune system wins the quick battle and gets some rest, but sometimes if the microbiome keeps it on constant high alert, a long, drawn-out war begins, resulting in chronic inflammation and chronic diseases.

9. The gut is doing the talking

When we have low stomach acid, the mouth bacteria travels to the gastrointestinal tract.

Stomach acid triggers digestion and protects us from the bacteria in the mouth, together with the parasites and fungi that are in food. If we don’t have enough stomach acid, the bacteria in the mouth will invade the gut. This invasion is associated with - and is a risk factor for - autoimmune disease and inflammation in the gut. Low stomach acid is perhaps one of the major causes of chronic disease.

Which means … avoid stress and antacids.

10. Carbs can be protein precursors

This is a biggie for me, as I consciously try to cut my carb intake back, and really notice the difference. However, there’s a rumour that perhaps carbs aren’t as bad as we thought, as long as our microbiome is up to the job. We can see if some of the starches we eat can be made into amino acids by the microbiome.

The microbiome makes 20% of our branched-chain amino acids (BCAAs), and adapts to make these vital BCAAs for us in almost any way it can.

Essentially, the microbiome is hooking up carbons and hydrogens into different formulations of BCAAs, depending on what we feed it. The microbiome is excellent at adapting based on the food we feed it and the environment that it’s in.

So, good news: carbs are protein precursors, as long as we have the right microbiome.

Long and short, look after your microbiome, and it’ll take great care of you.

The microbiome is a world-class entrepreneur that can take low-grade sources of food and turn them into valuable and useable energy. The great news is that it’s within us right now, working wonders to make sure we have energy to meet all of our physiological needs.

Given the daily emerging research about the microbiome and its importance on quality of life, prioritising the health of the microbiome is essential - a healthy microbiome literally means we’re more likely to have a healthy life.

As always, wishing you the best health,


* To get your microbiome tested, contact AtlasBioMed or Viome UK