What Is A Microbiome Test?
A microbiome test reveals the types and levels of bacteria and other microbes in your large intestine. Strictly speaking, you ...
Human beings have known for a long time that good health begins in the gut. But it took until the turn of the millennium until science could begin to help us explore the incredible ecosystem inside us all.
For many years, scientists studied gut bacteria by extracting them from faecal samples and growing them in lab dishes. But in the mid-2000s, DNA sequencing allowed us to discover nearly all the bacteria in our guts much more easily. Scientists are also working out ways to view the other microbes—such as yeasts, protozoa and viruses—more quickly too.
What we’re finding out about our guts and the microbes that live there is now transforming the way we see our bodies, brains and lives.
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Want to understand the importance of gut health?
Why is the microbiome so important for a healthy gut?
What is a healthy gut diet plan?
9 ways to have a healthy gut
What are the symptoms of an unhealthy gut microbiome?
Which supplements and probiotics can help to achieve a healthy gut?
What can I do to heal my gut naturally?
What are the worst foods for gut health?
If you care about your health, knowing how to look after your gut is crucial.
When you hear about gut health, you might think about conditions like IBS, constipation and diarrhoea. These are all uncomfortable gut symptoms that you want to avoid if you don’t have them, or get rid of them if you do.
But your gut affects the rest of you too.
Symptoms like fatigue, anxiety and sleep disturbances can be indications that all might not be well with your gut, as well as more serious conditions like:
It’s important to remember that research has found links between these diseases and changes in the gut, which means that we’re not yet sure what comes first, the gut issues or the disease.
We do know that there’s an intimate connection between the gut, the brain, and the microbes in our gut, that we call the microbiota-gut-brain axis. The gut and the brain ‘communicate’ with each other, so emotions can impact the gut, while the gut produces neurotransmitters such as serotonin, dopamine, and GABA that may influence mood and wellbeing.
In one mouse study, a probiotic called L. Rhamnosus caused chemical changes in the brain by reducing stress hormones (Source: PNAS). This particular piece of research showed that gut bacteria can have a direct effect on behaviour through the vagus nerve—the large nerve that runs from your large intestine to your brain.
Nearly all of the research on this so far has been carried out on animals, so we need to translate findings to humans to get concrete answers. One human study investigated the link between faecal microbiota composition and quality of life using data from more than 1,000 people. Scientists did find that certain families of bacteria were associated with higher quality of life or depression, and that microorganisms do synthesize certain neuroactive substances that appear to correlate with mental wellbeing (Source: NCBI).
Your gut bacteria shape not only your gut health, but possibly the health of your entire body and mind. Getting—or keeping—a healthy collection of gut bacteria could be the most important move you ever make for your health.
Here are some more jobs your gut bacteria do:
Alone, your body can’t break down the dietary fibre and starch in your food. Gut bacteria do it for you by fermenting fibre and starches in vegetables, legumes and grains.
Gut bacteria make most of the B vitamins (for energy, among other things) and vitamin K (for blood clotting, teeth and bones).
How well you respond to medicines like paracetamol or statins is—at least in part— down to your gut bacteria. Previously thought to be the job of your liver, scientists now believe that your gut bacteria are likely to play an equal role in metabolising (activating) many pharmaceutical drugs (Source: NCBI).
You probably already know that what we eat influences our gut bacteria. But did you know that the 1,000 families of bacteria that live in your gut could inform what food we choose to eat? In 2017, neuroscientists found that specific types of gut flora helped fruit flies detect which nutrients were missing in their food and then affected their eating choices to balance any deficits (Source: JOURNALS PLOS).
Clearly, humans and fruit flies are pretty different. However research has also found that people who crave chocolate have different microbes in their guts to people who don’t, despite eating identical diets (Source: NCBI).
Many gut bacteria can make special proteins that regulate hunger. Humans and other animals have produced antibodies against these proteins which suggests that these bacteria influence eating behaviour and interfere with appetite regulation (Source: NCBI).
The importance of the bacterial make-up of our guts has also now been shown in obesity, anorexia, and forms of severe acute malnutrition (Source: NCBI).
We now know that bacteria play a role in encouraging immune tissue to grow in a baby’s gut, setting up their immune system for the rest of their lives (Source: NCBI). In adults, they also help to prevent infections like food poisoning or influenza by stopping pathogenic bacteria from getting a foothold in your gut (Source: NCBI).
Though research in this area is just beginning, it appears that bacteria in your gut can impact your brain and influence mental health. There are definite links between specific families of bacteria and mood disorders like anxiety (Source: NCBI) and panic disorder (Source: NCBI).
As you read this, scientists are working on mapping all of the bacterial genes that live in our intestines. If and when this happens, we’ll be able to provide truly personalised medicine with an individual diagnosis and treatment for every person, for a range of conditions.
A healthy gut diet plan is different for everyone. The advice you’ll find on how to get a healthy gut in the UK will be different to the information you’d find in China, for instance. However, there are common features across most cultures. A good way to think about the right diet for your gut and general health is to look at what we’ve been eating for the 200,000 years we’ve been human, instead of the last 200, or—even worse—the last 20.
Here’s where to start:
This doesn’t mean we need to eat grubs from the garden, but we do need to stick to eating whole foods. Traditional societies that don’t have access to supermarkets and takeaways— such as the Hadza of Tanzania—have a diet of fruit, vegetables, game and birds they’ve hunted. According to scientists, the Hadza have the most diverse gut bacteria of anyone anywhere in the world.
Microbial diversity is key to gut health. The Hadza noticeably lack many common western ailments including diabetes, obesity and asthma. And, according to the scientists that worked with them, they don’t suffer from IBS either, having two or three comfortable bowel movements a day.
If you want to have a healthy microbiome, and to get a healthy gut naturally, it’s all about whole, high-fibre foods. Our bacteria love fibre. Unlike cows or sheep, we don’t use fibre because we can’t digest it. The fact that bacteria do, and perform many processes essential to our health while they’re doing it, is evidence of how important fibre is.
Without fibre, the mucus layer on the inside of our guts begins to degrade, and along with it many of the bacteria we’ve evolved with over hundreds of centuries (Source: NCBI). Adults should be getting around 30 grams of fibre a day to avoid the diseases associated with not getting enough (Source: NCBI).
Some gut health superstars are relative newcomers to our plates. Humans didn’t start fermenting foods until about 10,000 years ago, but when they did, they discovered an incredibly powerful way not only to preserve food for winter or periods of famine, but to unlock nutrients and boost their gut health with friendly bacteria too. Studies have revealed that fermented foods like sauerkraut (cabbage) and kefir (soured milk) can improve the function of your intestinal barrier (Source: NCBI).
How can you start developing healthy gut bacteria?
Whether you want to heal your leaky gut, get a healthy gut, heal your gut lining or all three (and they’re all inextricably linked) you need to pay attention to your gut bacteria.
We all start developing our gut bacteria before birth. Until recently, experts thought we received our first bacteria in the birth canal, but new research has shown that our mother’s placenta contains bacteria that likely seeds our guts when we’re still in the womb (Source: NCBI).
In other words, you already have plenty of gut bacteria. It’s hard to know exactly how healthy it is, but the new breed of gut tests that use DNA sequencing can give you valuable insight into the ecosystem inside your large intestine.
If you’d like to follow a plan on how to build healthy gut flora, or how to help your gut recover if you’ve recently taken a course of antibiotics, check out our Gut Program. You’ll get 12 weekly video lessons, delivered by our expert practitioners, plus recipes, meal plans and motivational guides to keep you on track.
While a good diet is the foundation of building a healthy microbiome, there are other factors that are fundamental too. Here are nine of the most powerful ways to get a healthy gut.
Most processed foods a) lack fibre and nutrients b) are high-calorie and c) taste good. This is a lethal combination because the taste drives us to eat more and more of something that doesn’t nourish us and won’t make us feel full.
Studies have found that stress triggers a fight-or-flight response that releases hormones in various parts of your body, which in turn affects your microbiome (Source: NCBI). To compound the situation, that altered gut microbial population then affects the regulation of neurotransmitters, intensifying stress further (Source: NCBI).
Our bacteria love fibre. Foods that pack the biggest fibre punches include:
Just like humans, animals that live good lives on their natural diet are healthier, and produce healthier milk, eggs and meat as a result (Source: NCBI). Avoid processed meats and choose eggs and meat from free-range animals, never industrial farms.
Our fruits and vegetables take the nutrients from the soil they’re grown in. Soil on farms today contains far lower levels of nutrients compared to the soil of the 1970s (Source: NCBI). Buy your fruit and vegetables in season (Source: NCBI) and locally grown (Source: NCBI) to maximise the polyphenols and other compounds that friendly bacteria love (Source: NCBI).
Alcohol is a recent invention in our history, and while there’s plenty of evidence that a small amount of some kinds of red wine can be beneficial for our health (Source: NCBI) we know that excess alcohol damages our microbiome and contributes to intestinal permeability (leaky gut) (Source: NCBI).
Researchers at Stanford University screened more than 900,000 genetic samples from the stool of healthy men and women who took the antibiotic ciprofloxacin. They found that most of the gut microbiome returned to normal after four weeks, but that the numbers of some bacteria were still reduced six months later (Source: NCBI). In a subsequent study, they concluded that the full consequences of that course of antibiotics remain unknown. (Source: NCBI).
Smoking can reduce diversity in your microbiome and alter it to resemble one typical of someone with inflammatory bowel disease or obesity (Source: NCBI).
Mice who were forced to stay awake at night and sleep during the day suffered a drop in microbiome diversity and increased intestinal permeability that was made even worse by a low-quality diet (Source: JOURNALS PLOS).
The symptoms of an unhealthy gut microbiome don’t just play out in your gut itself: they can turn up almost anywhere else in your body too.
Frequent, loose stools are a sign that your gut isn’t happy. You should let your doctor know if you have diarrhoea for longer than a day (Source: NCBI). Chronic diarrhoea can also wash out gut bacteria, which could affect microbial diversity and compound the problem.
There are many different reasons why you might be constipated, but research shows that your microbiome is likely to be involved (Source: NCBI).
The link between our microbiomes and our brains (Source: NCBI) is one of the hottest topics in neuroscience right now.
Other signs include
While some experts believe that we could all achieve a healthy gut with the right diet, our modern diets and lifestyles mean that most of us could benefit from a bit of a helping hand. Few people today live in traditional communities and the closest we get to hunting or gathering is choosing the best-looking apples in the supermarket.
Here are some examples of the supplements that come with evidence to back up their effectiveness:
This leaky gut superhero that could play a big role in bolstering our gut barrier (Source: NCBI).
Also known by its full name fructooligosaccharide, FOS is available as a prebiotic supplement and found naturally in onion, chicory, garlic, asparagus, banana, artichoke, among many other fruits and vegetables (Source: NCBI). It’s been found to ease constipation and increase numbers of friendly bacteria.
Galactooligosaccharide, or GOS, increases the production of short-chain fatty acids (SCFAs). These lower colonic pH and stimulate the growth of the friendly bacteria lactobacilli and bifidobacteria, suppressing the growth of their more undesirable relatives (Source: NCBI).
These two ‘friendly’ bacteria are the probiotic genera (a fancy way to say ‘categories’) with the biggest weight of evidence behind them for helping conditions like IBS (Source: NCBI), fibromyalgia (Source: NCBI) and depression (Source: NCBI). However, that doesn’t mean they’re good for everyone: responses to probiotics are as individual as the person taking them.
When it comes to healing your gut, you’ll have your own path to follow. Our microbiomes are as unique as our fingerprints, and they sit in a body made up of complex, interdependent systems we are only beginning to understand.
For you, tweaking your diet might be enough to get on top of your gut health. But someone else suffering the same symptoms may spend months or years exploring different approaches to solving their problem.
If your answers aren’t coming easily, look into testing, or try an elimination diet to identify which foods could be causing you problems. Our practitioners are on hand to guide you with either of these.
If you’ve tried tidying up your diet and your gut health still isn’t where you’d like it to be, there are a number of laboratory tests that could help you get to the root cause of your symptoms. For instance, if you’ve got IBS or bloating, it’s possible you have SIBO: a condition where too many bacteria live in the small intestine, an area which should harbour minimal amounts of microbes. Research has shown that up to eighty percent of people with IBS have SIBO (Source: NCBI).
Food intolerances and sensitivities often crop up when our guts are compromised. Take onions as an example. If onions make you bloated, as well as avoiding onions, take your symptoms as a sign that you need to dig deeper into your gut health. A lack of diversity in the bacteria in your large intestine could be the reason you’re finding it hard to tolerate certain foods (Source: NCBI).
If you’d like to know more about the microbes that have set up shop in your gut, a stool test can shine a light on the types and levels of bacteria, yeasts and other microbes you share your body with.
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The worst foods for gut health all have something in common: they are not found in nature. That doesn’t mean that everything natural is good for your gut, but it does mean that in general, your food should come from the earth, not a factory.
One study found that the environment created in the gut by ultra-processed foods (sweets, crisps, biscuits and takeaways, for example) ‘is an evolutionarily unique selection ground for microbes that can promote diverse forms of inflammatory disease’ (Source: NCBI). In other words, never before have human beings existed on a diet so likely to make us chronically ill.
Gram for gram, sugar gives you the most calories with the least nutritional reward of any food out there. Countless studies have shown its detrimental effects on our health, including that of our gut. As the most concentrated form of carbohydrate you can eat, it’s rocket fuel for certain families of bacteria that multiply like mad and disturb the delicate, complex ecosystem of your gut, causing dysbiosis (Source: NCBI).
Refined, processed oils like the ones found in convenience and takeaway foods are harmful to health (Source: OPENHEART BMJ), (Source: JOURNALS PLOS) and have been found to encourage the development of a less-desirable microbiome in mice (Source: NCBI). Although we must be careful not to assume the same effect in humans, this doesn’t bode well if you’re on first-name terms with your local chip shop owner.
Balancing two types of fats in your diet—omega-6 and omega-3—is key to so many aspects of your health, including your microbiome (Source: NCBI). The tasty, ‘treat’ foods we all know and love like cake, crisps and chips heavily tip the scales in favour of omega-6. Key sources of omega-3 oils include fish, flaxseeds, hemp seeds and walnuts.
Drinking alcohol can influence what kind and how many bacteria live in your gut. Even a single episode of drinking can damage the gut wall (Source: SCIENCE DIRECT). From one study, we know that people who regularly drink alcohol have microbiomes that look very different to those of people who drink little to no alcohol (Source: NCBI).
The human microbiome is a staggeringly complex world that we’re only just beginning to discover. With over 100 trillion organisms living inside a body with its own genetic code, your precise recipe for a healthy gut is different to anyone else’s.
Having said that, research has revealed some gut health rules that we should all live by in the quest for a happy gut:
Alexandra Falconer MA (Dist) DipCNM mBANT is a Registered Nutritional Therapist specialising in IBS and related conditions. A graduate of Brighton’s College of Naturopathic Medicine, she is committed to fighting the root causes of chronic illness and bringing functional medicine to everyone who needs it.
Before her natural health career, Alex was a journalist and copywriter. She continues to write for magazines and media agencies, and now combines her two great passions—writing and health—by creating content that empowers people to claim their right to a healthy body and mind.
A microbiome test reveals the types and levels of bacteria and other microbes in your large intestine. Strictly speaking, you ...
Constipation and diarrhoea can be warning signs of IBS. But if you’ve had a bout of constipation or diarrhoea, ...
Small intestinal bacterial overgrowth—better known as ‘SIBO’—has got a lot of press in recent years. Your small intestine ...
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