Published in Nature · What happens to gut bacteria when people change the way they eat
Many people say about their digestion: this is just how I am. What researchers measure does not match that. A free five-minute check shows where your own situation stands today.
"I've been like this for years. That's just how my body works."
Today I am comparing those two sentences with what has been measured. I used a version of them myself for years.
I am Jesse van der Velde. No guru and no doctor. I study and share what published research says about your gut, and also what it has not demonstrated.
The assumption: a difficult digestion is part of who you are, you were simply born with it.
The research: in people who changed the way they ate, the make-up of their gut bacteria changed along with it quickly. Quickly. Not years later.
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Nobody talked you into this. You came to it yourself, and you had reasons for it: the complaints came back after every attempt.
I call that the "permanence story": the idea that your gut simply works this way and that nothing about it will change.
Take a look at what you assumed along the way: that what you tried matched what was really going on in your gut.
But that is not true.
If it did not fit, then the failure of those attempts says nothing about how stuck your symptoms are. It says you tried something without knowing what was going on with you.
The "permanence story" is what makes you stop trying.
In 2014 Nature published a study led by Lawrence David.¹
What was studied: how fast the bacteria in the human gut respond to a change in food.
How: for a short period participants ate entirely animal based, and separately from that entirely plant based. What was measured was which species of bacteria were living there, and also which genes those bacteria put to work.
The findings: the composition changed, and in the gene activity the difference between those two diets grew bigger than the difference between the participants themselves. On animal based food, bile tolerant bacteria increased, such as Bilophila, and the species that break down plant fibres decreased, such as Roseburia and Ruminococcus bromii.
So in the gene activity, what people ate weighed more heavily than who they were.
And the microbes that came along with the food itself, bacteria, fungi and even viruses, settled in the gut only temporarily.
Two things are not in that publication: how many people took part, and how many days each diet lasted. The researchers call it short-term and the response fast. And realise what was not measured: not a single symptom. Only which bacteria were living there and what they did.
In your gut lives a population of bacteria whose make-up changes with what you eat. Three times a day you decide what those bacteria get to eat.
The second measurement is about resilience. In Nature Microbiology, a study by Palleja and colleagues appeared in 2018.
What was studied: what happens to the gut bacteria of healthy people after a heavy course of antibiotics.
How: twelve healthy men were given three heavy antibiotics at the same time for four days, meropenem, gentamicin and vancomycin. After that the researchers followed their gut bacteria for six months with DNA sequencing.
The findings: within a month and a half the composition was almost back to the level it was at before the course. But nine species that were present in all twelve men before the course were still not to be found in most of them after 180 days.²
Here something is added that was missing in the first study. There was no control group and no placebo, and these were twelve healthy men. So this study says nothing about women, about older people, or about people who already have complaints. These were not ordinary antibiotics, but three drugs that are only used as a last resort.
The researchers name both sides: a mild but long lasting trace, and at the same time a resilient gut flora in healthy young adults. Most of it comes back. Not all of it.
And then the question that concerns you most: does eating healthily do what you expect it to?
In 2021 Cell published a randomised 17 week study by researchers from Stanford.
What was studied: whether two healthy ways of eating do the same thing to your gut bacteria and your immune defences.
How: healthy adults were divided over two groups of 18. One group ate a lot of fibre for 17 weeks, the other a lot of fermented products. Their gut bacteria and their immune response were measured throughout the whole period.
The findings: in the group with fermented foods the diversity of the gut bacteria rose steadily and the inflammatory markers came down.³ In the fibre group diversity stayed the same, while the bacteria there produced more enzymes instead to break down fibre.
And now the point that makes this study more important. The researchers had chosen one primary outcome in advance, a score for the immune response in the blood. That score did not change in this study. So the study did not meet its own main goal. There are no percentages anywhere: the publication gives directions only.
Within the fibre group there were also three different immune responses to be seen, and these matched the diversity of the gut flora a person started with.
Two more things: it was about healthy adults, so this study says nothing about complaints, and three of the researchers have interests of their own in this field.
This is the heart of it. Two healthy ways of eating did not do the same thing in the same study.
So a failed attempt was never proof that nothing works for you. It was one approach, tried once, without anyone first looking at what you were starting from.
The researchers needed DNA sequencing to see which species increased and which decreased. You were asked to guess that from the inside. And then you blamed yourself for guessing wrong.
Does this sound familiar? Take the free check now.
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Rapidly. That is the word the researchers themselves used for the speed at which the composition and the gene activity of the gut bacteria followed a change in diet, in the study in Nature.¹
180 days. Twelve men were given meropenem, gentamicin and vancomycin at the same time for four days. Nine species were still not back in most of them after 180 days.² Most of it came back. Those nine did not.
17 weeks. That is how long the study ran in which fermented foods brought diversity up and inflammatory markers down.³ Seventeen weeks is just over four months.
There was a week like that.
One last attempt, the third jar of probiotics or that strict month, ended like all the others. After that you let the subject rest with the thought "this is just me now".
About that week, the measurements above say something very precise. Your conclusion was logical. Your evidence was not sound.
Every attempt you kept as proof was a standard approach, let loose on a gut nobody had looked at. The study in Cell shows that most clearly: two healthy ways of eating, two different outcomes, in the same piece of research.³
The problem was never that you tried too little. The problem was that you did not know what was going on in your gut.
Think about that for a moment.
You did not fail. The "permanence story" failed, and it is not your fault. It can be different.
1. The next jar of probiotics. Capsule after capsule, brand after brand. Whether you take them is of course entirely up to you.
But be aware of what was measured. In Cell in 2018, researchers looked directly into the gut wall with an endoscope, instead of into the stool, and that way they checked whether a probiotic with eleven strains settled there.
That is why this study matters more than most: the stool could not tell you whether it had worked. In one person the strains attached to the gut wall, in another they did not, and that difference was linked to the profile that person started with.⁴ The strains did survive the journey through the gastrointestinal tract. So that was not where the problem lay.
What this study does not say: not a single symptom was measured, part of the evidence comes from mice, and it involved one product. The effect was temporary and different from person to person.
Then the largest overview of this research that exists. A meta-analysis from 2018 searched three medical databases up to July 2017, found 4,017 publications, and kept 53 of them, with 5,545 people between them.
The researchers' conclusion: certain strains and combinations seemed to help with the symptoms and the abdominal pain, but exactly which ones, no firm conclusion could be drawn about that.⁵
Note what kind of research this is. In a meta-analysis no new measurements are taken. Existing studies are added together, and the outcome can never be stronger than what goes into it.
The only hard number, moreover, belongs to a prescription antibiotic, and the authors themselves call that effect modest. On prebiotics and synbiotics there was too little research. And it was always about people whose gut complaints had already been diagnosed.
Translated to your cupboard of jars: trying brand after brand was not stupid. It is just that not a single jar said which strains would settle in you.
2. A month of discipline. Thirty days of doing everything right, without knowing what was going on in your own body. The fibre group from the study in Cell shows how that works out: nobody has anything against that way of eating, and still diversity stood still across those 17 weeks.³
3. Sitting it out. Waiting for it to pass on its own. The study in Nature shows that gut bacteria do not stand still in the meantime. They shift along with what is eaten, including in the years when you decided nothing about it.¹
Three attempts, one shared problem: not one of them ever looked at what is going on in your own gut. That has nothing to do with your discipline.
Every approach you have chosen so far went at that population of bacteria in your gut blind.
The new option is simple: look first.
Your complaints, when they come, and what you eat and do at those moments. That pattern can be read.
One condition. You look first, and only then do you try something new. You have paid enough for blind attempts.
And it costs you nothing. Add up what all those tubs have cost you, and put that next to five free minutes.
BioProfile has built that analysis. A scientifically validated questionnaire, five minutes, free and without an account.
It maps out your complaints and their pattern and shows which signals in your profile speak loudest. So that the next thing you try is aimed at something.
Not a medical examination. An analysis of your own answers. You use the outcome yourself, or you put it on the table with your doctor or your coach.
And that is exactly the difference with the "permanence story". This one does give you a next step.
In those studies the outcome differed per approach and per person. That is why the analysis comes first.
The composition you call permanent shifted in the measurements as soon as people started eating differently.¹
And the story that nothing works for you anyway has never been tested against an analysis of your own situation.
Take the free check. Five minutes, no account, and there is nothing to buy.
Let go of the "permanence story". Not of trying. In all those years that story has given you not one result.
Our scientifically validated questionnaire gives you answers
The scan is not a medical examination. It is an analysis of your own answers. If complaints persist, consult your doctor.
