Is Your Microbiome the Secret To, Well, Everything?

The garden of bacteria that rules your gut might be responsible for how your body and brain tick.

8 Minute ReadEducation by Kate Spicer


There's a great way to get a snapshot of gut health and it’s called the Blue Poo Challenge. Before I lose you, do read on. Dying our first meal of the day with royal blue dye is a bit like a home administered barium meal. It was first developed by Professor Tim Spector of the ZOE project, where they "gave blue muffins to thousands of people and discovered that gut transit time — the time it takes for food to travel from mouth to toilet through the gut — can say a lot about a person’s gut microbiome.” I did a blue poo recently, and went from being a pretty smug healthy eater to realising my transit time was slow, and my diet needed some gut-friendly tweaks.

When it comes to learning more about these? There is no better expert to turn to than Spector, the 63-year-old Professor of Genetic Epidemiology at King’s College London. Thirty years ago he founded the UK’s biggest twin study (TWINSUK). TWINSUK led to the understanding that our microbial mix is linked to our genes, as well as diet and environment. Fascinated by the impact of the microbiome on health, Spector launched his British Gut project a decade ago, before microbes became the research topic du jour.

When I spoke to him, he described a frustration that other scientists weren’t listening, “Britain came to the gut microbiome party late. It was considered an over-hyped fad that wouldn’t last by the senior scientists who influenced where science spending went. “ The US, Spector said had a small core of well-funded centres a decade before Britain.

Spector’s work proved that when it comes to diet one size does not fit all. In 2020, he launched ZOE, an app that uses microbiome profiling and levels of fats and sugars in the blood to help users understand their body’s unique responses to food. Nearly ten years ago now, via his TWINSUK studies, Spector had proved that unlike our genes, which are pretty fixed, we can make highly effective tweaks to our microbiome by just changing what and how we eat. “The aim of ZOE is not to limit food choice but to increase it. Swap your breakfast muesli for yogurt or vice versa. Or swap a banana for a pear. We also want to increase the amount of microbe friendly foods people eat.”

Tim Spector Journal image 2550x885

Those who contribute to ZOE get to learn helpful things about their body while also contributing to one of the most large-scale citizen science studies ever. As such, Spector reappropriated ZOE’s tech early in the pandemic to crowdsource Covid symptoms and the results were the first to confirm that loss of taste and smell as symptoms.

A decade ago I wrote a story about an elderly professor at UCLA who was linking the microbiome, or ‘gut flora’ as they called it then, with mental health. I spent uncalled for days researching this short article because I just couldn’t grasp how bacteria in our gastrointestinal systems could affect the mind. As someone who is constantly wondering how to optimise my health - and compensate for the things that harm it - the field really interested me. Cut to now and the microscopic worlds that live inside us all are the hottest academic topic of our times, touted as cause and cure for some of the most widespread chronic conditions that plague western society.

Covid, obesity, IBS, cancer - there is a link between microbes and almost every action in the human body, including mental health. Our bodies are the perfect climate-controlled habitat for hundreds of trillions of tiny life forms: not just bacteria, but tiny parasites, fungi, archea, and (considered non-living) viruses. In total as many as 1000 different species will outnumber human cells in the body to the power of 10.

But how do they do this? That’s a big question. I’ve heard the gut compared commonly to the Amazon rainforest (because it is such a complex ecosystem) and to space (because it is so vast and unexplored.) But we know more about space than we do our microbiomes. In fact, if we were to compare the space race to the research rush to navigate our inner universe, we haven’t even put a dog in a rocket yet.

What we do know is that having a good gut will limit inflammation, strengthen immunity and aid the digestion and absorption of nutrients. These microbes interact directly with our cells, with our DNA and with each other. In the process they breed and create waste products, including B vitamins, which can boost or bash human health.

Today, Spector’s belief that this was some of the most crucial human science of our times has been proven correct beyond any reasonable doubt. Targeted microbial medicines are the future, and not just as an alternative to antibiotics (which wipe out the good bugs as well as the bad ones.) It’s known now that these bacteria protect the intestines against toxins and mean microbes. Good health is thanks to the subtle interactions of these trillions of organisms with our own cells, so if we trash our microbiome? We are going to get ill. Here’s an example most of us can understand: in one of my early conversations with Spector, he mooted drinking yoghurt as a hangover cure, because excessive alcohol harms our precious microbe population.

After the Blue Poo result, I started thinking about this crucial inner quantum farm far more. I wanted to tend to it; it was an almost maternal feeling. I started fermenting my own ginger beer (non-alcoholic), I drank ayran (lightly salted drinking yoghurt) instead of fruit juice, I got over my fear of cheese being fattening and instead viewed it as a health food. It’s a long list, and while one person’s experience does not a clinical trial make, my weight remained steady while inflammation hot spots in my body (like an old dodgy ankle that was often a bit puffy) noticeably calmed down.

The whole concept still feels trippy to me. But actively nurturing my microbial guests paid off for me. Here are more tips via Spector’s prolific advice. Happy farming.

Get into tweaking your microbiome

In academic parlance, an out of whack microbiome has “gut microbial imbalance” or “dysbiosis”. This is caused by your genes, antibiotic use, a crap diet and/or a lifestyle that causes inflammation. By eating wide and smart we can do so much to improve health. One example is happiness: the production of ‘happy hormones’ like serotonin, dopamine, oxytocin and endorphins are influenced by the tens to hundreds of trillions of bacteria that live in our guts.

Your microbes are fun lovers

While your average health influencer wants you existing on green juices and herb teas, our microbes are up for a way more exciting menu. Spector starts every day with good coffee; in his first book about food, The Diet Myth, he turbocharged his microbiome with a daily diet of stinky, delicious, French cheeses. In his recent book, Spoon Fed, he gives a science-led thumbs up for wine, butter, olive oil, decent chocolate, good bread, steak, and the list goes on. All play a role in gut health if bundled along with a rainbow cornucopia of plant foods - 30 different types in a week he recommends. Basically, what your gut really, really wants is decent food that hasn’t been messed about with, and in as many different colours and varieties as possible.

Obesity is determined by our microbes

A study by Spector of nearly 500 identical twins, published in 2014, found a bacteria species called Christensenellaceae that is more common in slender people. Transplanted into mice, it caused them to lose weight. It’s the supermodel microbe and one day, rather than bariatric surgery or other painful traumatic procedures, a probiotic containing this may be the answer to weight loss.

Microbes need exercise and fibre

Exercise helps produce a microbe byproduct called butyrate, a very simple 'short chain’ fatty acid. It’s also produced when certain microbes break down fibre. Butyrate is an incredible substance that regulates everything from colon health to mental health. Exercise and fibre are the least we can do to thank it for all its incredible health preserving work.

Let your gut have some down time too

Research has found that fasting periods - ranging from  several hours to a day - support the health of the gut microbiome. It doesn’t have to be too Biblical in scale: a simple overnight fast, and a general reduction in snacking between meals, will give the microbes that clean your gut lining a chance to do their work.

Fermented foods are the new probiotics

Big one, this. Especially of interest to the gen Z. There is research that links a reduction in our ingestion of fermented foods, which are stuffed unusually full of good microbes, to a decline in human health. In the days before artificial preservatives, fermentation was an essential means of keeping foods edible and healthy long term. Nowadays our processed foods and drinks, and especially ultra-processed foods, kill those friendly bugs with their armoury of chemicals that can keep them ‘fresh’ on the shelves for years.

Living a fermented life is actually pretty fun. Wine, after all, is fermented (though obviously to be consumed responsibly). Cheese, kimchi and sourdough - all fermented - are the three ingredients required for an absolutely banging toastie. One study found consumption of fermented foods “is associated with lower severity and prevalence of depression.” Which I think means a grilled cheese is the new Prozac.

Probiotics are not all they’re cracked up to be

Spector’s take on over-the-counter probiotics is that they aren’t helpful, and could even cause disruption to gut health. His advice is to get it all from food, wine and ale.

Get acquainted with your microbial visitors

One of the biggest advances in the understanding of this innerverse came when it became possible to read the DNA of your microbes via a small poo sample. This is called ‘taxonomic functional shotgun metagenomic sequencing’ and it’s expensive. Subscribers to ZOE can have this done, or for the rest of us, there’s the blue poo route.

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