Some of the Gut Bacteria Compounds on Supplement Labels Are Made by Your Own Body
Postbiotic labels have started naming specific molecules, which I actually welcome, because a named molecule is a checkable claim. Indole 3 lactate now turns up on packaging and in podcast reads, always resting on the same premise: your gut bacteria make it, so feed or seed your gut bacteria and you will have more of it. A team at Ludwig Princeton went and tested the premise. It turns out to be substantially wrong.
- The postbiotic category rests on the idea that beneficial indole and phenol metabolites, compounds like indole 3 lactate and indole 3 acetate, are made exclusively by gut bacteria.
- Using stable isotope tracing across cell culture, mice, rats and human patient samples, researchers found mammalian metabolism produces many of these compounds on its own, with no microbial input required.
- The cleanest proof was antibiotics. After the microbiome was wiped out, host producible metabolites stayed in circulation, while genuinely microbe exclusive ones such as indole 3 propionate and para cresol sulfate dropped. The same pattern showed up in human patients on antibiotics.
- This is not a finding that probiotics do not work, and it is not an attack on fiber, which comes out of this fine. It is a sharper line between what your microbiome actually does and what gets credited to it.
The claim underneath the category
The category this lands on. Postbiotic labels have started naming specific molecules, which is what makes the claim checkable.
Corn cheeseCC BY 4.0
Illustrative. Not a product named in this research.
For most of the past decade the gut health aisle sold you bacteria. Lately it has started selling you what the bacteria supposedly make. That shift is why molecule names have begun appearing on labels and in ad copy, and the argument runs in a straight line: this metabolite does useful things for immune and metabolic health, your gut bacteria produce it, so a product that supports your gut bacteria gives you more of it. Every step in that chain has to hold for the pitch to work.
How you find out who made a molecule
Stable isotope tracing is the tool for this. You feed in a precursor built with heavier atoms, then follow where those atoms end up, which lets you watch a molecule being assembled and see whose machinery assembled it. Run that in mammalian cells with no microbes anywhere in the system, and if the compound still appears, the body made it. That is what happened. Mammalian metabolism produced aryl pyruvates, aryl lactates, aryl acetates and aryl carboxylic acids on its own, including indole 3 lactate and indole 3 acetate, two of the most studied compounds in this whole conversation.
The antibiotic test
Take the bacteria away and see what goes missing. What stays was never theirs to begin with.
This is the part I will remember, because it is the kind of experiment you can explain to anyone. Wipe out the microbiome with antibiotics, then look at what is still circulating. The metabolites the body can make itself held steady. The genuinely microbial ones fell. And the same split showed up in human patients who were on antibiotics, which is what lifts this above a mouse result. It gives you a real dividing line between microbiome derived and merely microbiome adjacent.
Your body can make these
Indole 3 lactate and indole 3 acetate held steady in circulation after the microbiome was wiped out. These are the ones turning up in postbiotic marketing.
Genuinely microbe exclusive
Indole 3 propionate and para cresol sulfate fell away when the bacteria did. For these, the microbiome really is the source.
Most of the tracing is in cell culture, mice and rats. The human component is sampling of patients already taking antibiotics, which is observational rather than a controlled test.
Honest caveat
This does not say the microbiome is unimportant, and it does not say probiotics do not work. I want to be careful here, because the version of this story that travels furthest on social media will be a much dumber one. What the paper says is narrower and more useful: the attribution of certain circulating metabolites to gut bacteria was overstated, and the paper itself confirms that other metabolites remain genuinely microbe exclusive. The bulk of the tracing work sits in mice, rats and cell culture. The human component is observational sampling of patients on antibiotics rather than a controlled human trial, and antibiotics disturb host physiology as well as microbes, which muddies clean attribution. This is one lab, not yet independently replicated, though the work existed as a preprint in October 2025 and has since cleared peer review, which counts in its favour.
What this means for you
Do not throw anything out. If a probiotic has been helping you, this paper has not touched that, and if you have been eating more fiber and plants, this research quietly supports you, because the metabolites that really do depend on your bacteria still depend on feeding them. What changes is what you should accept as an explanation, which is the same thing that changed for me with the protein research and the sweetener research. The mechanism on the label is a claim, and claims can be checked.
So the practical version is short. When a gut product names a molecule, that is a good sign, because vagueness is harder to hold accountable. Then ask whether that molecule is one your body makes anyway. Indole 3 lactate and indole 3 acetate now sit on the host producible side of the line. Indole 3 propionate and para cresol sulfate sit on the microbial side. That is one more honest filter to run a product through, and honestly, filters are most of what protects your money in this category.
Primary sources
- AbuSalim, J.E. et al., "Host metabolism can produce many indoles and phenols independently of the microbiome," Nature Metabolism, 2026;8(7):1528. DOI 10.1038/s42255-026-01550-8. nature.com
- Ludwig Institute for Cancer Research announcement, via ScienceDaily, August 15, 2026. sciencedaily.com
- "Many circulating indole and phenol metabolites are host derived," bioRxiv preprint, October 2025, the earlier version of the same work. biorxiv.org
Common questions
Does this mean probiotics do not work?
No, and the paper does not claim that. It is a narrower point: some circulating metabolites that were credited to gut bacteria are produced by your own cells too, which weakens that particular marketing mechanism. Other metabolites in the same family, including indole 3 propionate and para cresol sulfate, really are microbe exclusive, and the study confirms it. Whether any given probiotic helps you is a separate question that depends on the strain, the dose and the trial behind it.
What is indole 3 lactate and why is it on labels?
It is a compound made from tryptophan, the amino acid you get from protein, and it has been studied for effects on immune signalling and metabolic health. It reached supplement labels because it was understood as something gut bacteria produce, which made it a neat way to explain why a postbiotic or probiotic product should matter. This research shows mammalian metabolism also produces it, so its presence in your blood is not proof that your microbiome, or a product aimed at your microbiome, put it there.
Should I stop taking a postbiotic supplement?
That is your call and worth making with your doctor if you are managing a real gut condition. My own read is that this is a reason to ask a better question rather than to bin anything. If the product's whole case rests on raising a metabolite your body already produces, the case is thinner than the packaging suggests. If it has human trial data behind it, that evidence stands on its own regardless of which cells make the molecule.
Stay Curious.
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