THE FOOD · INVESTIGATION
The gut microbiome:
you are not
alone in
your body.
There is a whole ecosystem living inside you.
Nobody sent you a welcome pamphlet.
You've probably heard the claim: there are ten times more bacteria in your body than human cells. It's one of the most repeated facts in popular science writing.
It's also wrong — and the correction is a good first lesson in how to read a microbiome headline.
So let's start with an actual count.
THE FAMOUS STAT, CORRECTED
Closer to a tie
than a landslide.
the actual ratio of bacterial cells to human cells in your body
Not the widely repeated 10:1. A 2016 recount in PLOS Biology found roughly 38 trillion bacterial cells against 30 trillion human ones — close to even, and weighing altogether about 200 grams.Most of that bacterial population lives in your colon, and it's not one species doing all the work. A healthy gut typically hosts hundreds of different bacterial species, plus smaller numbers of archaea, fungi and viruses — and no two people's mixes look quite the same, even identical twins.
Being wrong about the ratio doesn't make the microbiome less interesting. If anything, "roughly tied with you, cell for cell" is the stranger fact.
WHAT THEY MAKE IN RETURN
Fermentation isn't just a yoghurt word.
Short-chain fatty acids — acetate, propionate and butyrate — made by fermenting fibre. Together they supply an estimated 5–15% of your daily calories.
Certain gut bacteria synthesise vitamin K and several B vitamins, contributing a modest but real top-up to what you get from food.
Hydrogen, methane and carbon dioxide — the unglamorous, entirely normal by-product of a well-fed colony.
Fibre in.
Fuel out.
Of the three short-chain fatty acids, butyrate gets the most attention for a good reason: it's the preferred fuel for the cells lining your colon, providing up to 90% of their energy needs.
Those colon cells, in turn, maintain the gut lining, produce protective mucus, and help regulate inflammation locally. A fibre-starved colony makes less butyrate — one of the more concrete, mechanistic reasons low-fibre diets are linked to poorer gut health, rather than just a correlation with no clear "why."
Different fibres feed different bacteria and produce different ratios of these acids — which is part of why "eat a variety of plants" beats "eat one fibre supplement" as advice.
It's not just
about digestion.
Except it kind of is.
Beyond fermenting fibre, the microbiome plays a genuine role in day-to-day digestion: helping regulate gut motility (how quickly things move through you), supporting the mucus layer that protects your intestinal wall, and training a large share of your immune system — a striking amount of immune tissue sits directly around the gut, effectively supervised by, and supervising, the bacteria living there.
This is also why antibiotics can leave people with digestive symptoms that outlast the infection they were treating: a course of antibiotics doesn't just remove the harmful bacteria, it disrupts the whole resident community, and rebuilding that diversity can take weeks.
WHAT WE ACTUALLY KNOW
The strongest evidence isn't subtle.
Most microbiome research is correlational — interesting, but hard to pin down as cause and effect. One area is a genuine exception.
Clostridioides difficile is a gut infection that can take hold after antibiotics wipe out someone's normal bacterial community, and it can become dangerously recurrent. Standard antibiotic treatment cures a first recurrence only around a quarter to a third of the time.
The trial was stopped early because the difference was too large to ethically keep enrolling people into the antibiotic-only group. This is about as close as microbiome science gets to a slam dunk: restore the bacterial community, and the disease the community was suppressing simply doesn't return.
It's also a useful yardstick for everything else claimed about the microbiome — most of which isn't backed by evidence this strong.
THE QUESTION I ACTUALLY CAME FOR
Okay, but should I
buy a microbiome test?
So the microbiome is real, it's genuinely influential, and in at least one case the evidence for intervening is about as strong as medical evidence gets.
Which brings us to the industry that's grown up around all of that.
The pitch sounds precise.
The science isn't there yet.
The logic behind at-home microbiome testing is appealing:
There's no agreed reference range for what a "healthy" microbiome even looks like — it varies hugely between healthy people. Commercial tests have also shown poor reproducibility: sending the same sample to different companies, or the same company twice, doesn't reliably return the same result.
That doesn't make the underlying science fake. It makes the leap from "here is your bacterial profile" to "therefore eat these specific foods" much shakier than the packaging suggests.
CONTEXT MATTERS
So when does the microbiome deserve real attention?
Recurrent C. difficile infection, where FMT is an established, evidence-backed treatment
Diagnosed IBS or IBD, under a gastroenterologist's guidance
Digestive symptoms following a course of antibiotics
A diet genuinely low in fibre variety, regardless of any test result
The less useful question is:
"What does my microbiome report say I should eat?"The more useful one is:
"Am I actually feeding this ecosystem a variety of fibre, regardless of what any test claims to show?"THREE MYTHS, RETIRED
What wellness culture stretched past the evidence.
THE MYTH
"Leaky gut syndrome is poisoning your whole body."
THE EVIDENCE
Increased intestinal permeability is real and measurable, and it shows up in certain diseases like coeliac and Crohn's. But "leaky gut syndrome" as a standalone diagnosis, causing everything from brain fog to skin problems, is not a recognised medical condition — and there's no validated test that diagnoses it.
THE MYTH
"A probiotic supplement will fix my gut health."
THE EVIDENCE
Some specific strains, for specific situations — like preventing antibiotic-associated diarrhoea — have real evidence behind them. "Probiotics" as a general wellness purchase for an otherwise healthy person has a much thinner evidence base than the supplement aisle implies.
THE MYTH
"You need to detox or reset your gut."
THE EVIDENCE
Your liver and kidneys already do this, continuously, without a juice cleanse. What actually shifts microbiome composition in studies is sustained dietary change — more fibre variety, day after day — not a short, dramatic "reset."
SO, WHAT DID I ACTUALLY LEARN?
Your gutmates probably don't need
those fancy supplements.
I started this expecting either a wellness pitch or a debunking. What I found was somewhere more interesting than either: a genuinely vast, genuinely influential ecosystem, one spectacular piece of causal proof that it matters, and an entire industry that's sprinted several steps ahead of what the rest of the evidence can actually support.
Feed it fibre, and feed it a variety of fibre — that's the one piece of advice with real mechanism behind it.
Treat "microbiome" claims on a spectrum, from FMT-level solid to detox-tea-level fiction.
A test result isn't a diagnosis, and a supplement isn't a substitute for the diet that actually shapes this ecosystem daily.
Not a marketing gimmick.
Not a mystical organ with opinions about your lifestyle.
Just an ecosystem, roughly your own size, doing genuinely load-bearing work.
AND MAYBE THAT'S THE PART I WAS LOOKING FOR
Understanding gives us
better questions to ask.
I don't think the lesson of the microbiome is that we need to map our own bacteria before deciding what's for dinner.
I think it's that the most reliable advice was the least exotic one — variety and fibre — hiding in plain sight under a lot of genuinely impressive-sounding science.
"What does my gut bacteria need me to buy?"
becomes"Am I eating a genuinely varied range of plants this week?"
"Is this claim closer to the FMT trial, or closer to a detox tea?"
"Do I actually have a diagnosed reason to intervene, or just a curiosity?"
And if the honest answer is "mostly curiosity"?
Because nutrition is supposed to exist within our lives.
Not become a second job managing an ecosystem you can't see, on the advice of a company that mailed you a tube.
I came into this half-expecting to walk away either scared of my own gut or sold on a supplement. Instead I walked away with a longer grocery list of plants and a healthy amount of scepticism for anything promising to "reset" what was never actually broken.
And the several trillion tiny roommates you're doing it with.
READ THE EVIDENCE
Sources
- Sender, R., Fuchs, S., & Milo, R. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLOS Biology.
- Koh, A., De Vadder, F., Kovatcheva-Datchary, P., & Bäckhed, F. (2016). From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites. Cell.
- van Nood, E., et al. (2013). Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile. New England Journal of Medicine.
- Camilleri, M. (2019). Leaky Gut: Mechanisms, Measurement and Clinical Implications in Humans. Gut.
- National Center for Complementary and Integrative Health (NIH). Probiotics: What You Need To Know.
- Walter, J., & Ley, R. (2011). The Human Gut Microbiome: Ecology and Recent Evolutionary Changes. Annual Review of Microbiology.