Why Does Stool Smell Different?

Last updated: 9 September 2026

Stool smells because bacteria in the large intestine ferment whatever food arrives undigested, and some of that fermentation produces sulphur gases. How strong the smell is on any given day depends mostly on what you ate, how long things took to pass through, and what medicines you are taking. A change that lasts a day or two and follows an obvious meal or a new tablet is ordinary. A smell that stays unusually foul for more than a week or two — particularly alongside pain, blood, unexplained weight loss, or ongoing diarrhoea — is worth a GP appointment rather than a wait-and-see.

Stool smell at a glance

• Why it smells at all: gut bacteria ferment undigested food in the colon. Sulphur-containing gases produced along the way are the main source of the odour [1].
• The biggest dietary lever: sulphur-containing amino acids. In controlled testing, cysteine raised colonic hydrogen sulphide production dramatically, while inorganic sulphate barely moved it [2].
• Fibre works the other way: readily fermentable fibres suppressed hydrogen sulphide production by around 80–90% in the same work [2].
• Transit time matters: the longer stool spends in the colon, the more the balance of fermentation shifts from carbohydrate towards protein breakdown [3].
• Medicines: antibiotics reduce the diversity of gut bacteria, and recovery varies a lot between people [4].
• When to speak to a GP: a persistent change lasting more than a few weeks, or any change arriving with bleeding, weight loss or a hard lump [5].
• What it is not: smell alone is not a self-assessment tool. It is one weak signal among several, and it means far less on its own than it does in company.

Why does stool smell at all?

Most of what you eat is absorbed in the small intestine. What is left — fibre, some starch, some protein — reaches the large intestine, where a dense population of bacteria breaks it down. That process is fermentation, and it releases gases as a by-product.

Not all of those gases smell. Hydrogen, carbon dioxide and methane are essentially odourless. The smell comes from a much smaller group of sulphur-containing compounds. When researchers measured the gases responsible for the odour of human flatus, the main sulphur component was hydrogen sulphide, followed by methanethiol and dimethyl sulphide — and the strength of the malodour tracked the hydrogen sulphide concentration closely [1].

That is the useful mental model: the volume of gas and the smell of gas are two different things. A day of noticeable wind is not necessarily a day of noticeable smell, and vice versa.

Which foods make stool smell stronger?

The foods that reliably push the smell up are the ones that deliver sulphur-containing amino acids to the colon. That means high-protein foods, particularly red meat, and the allium and brassica families — garlic, onions, broccoli, cabbage, cauliflower, Brussels sprouts.

The distinction turns out to be quite specific. In a study that profiled colonic gas directly, adding cysteine — a sulphur-containing amino acid — increased hydrogen sulphide production by more than fifteenfold, while adding inorganic sulphate produced only a marginal change [2]. So it is the sulphur bound up in protein that does the work, not sulphur in general.

Alcohol, a large jump in dairy for someone who does not tolerate lactose well, and a sudden increase in overall food volume can all shift the smell for a day or two as well. These changes have a clear trigger and a short life.

Does fibre make the smell better or worse?

Better, in most cases — which surprises people, because a big increase in fibre often produces more wind in the short term.

The same gas-profiling work found that readily fermentable fibres suppressed hydrogen sulphide sharply: resistant starch cut it by 89% and fructo-oligosaccharides by 82%. Poorly fermentable fibres such as psyllium managed less than 35% [2]. The proposed mechanism is competition — when bacteria have plenty of fermentable carbohydrate to work on, they do less protein breakdown, and it is protein breakdown that yields the sulphur gases.

So more volume of gas and less smell can happen at the same time. If you have recently increased fibre and things feel gassier but smell less pungent, that is a coherent pattern rather than a contradictory one.

How does transit time change the smell?

Transit time — how long it takes food to travel through you — varies a great deal, both between people and within the same person from week to week [6]. It also changes what the bacteria in your colon are doing.

Work measuring colonic transit alongside bacterial metabolism found that a long transit time was accompanied by a shift in colonic metabolism away from carbohydrate fermentation and towards protein breakdown [3]. Protein breakdown is the route that produces sulphur gases, so slower transit tends to mean a stronger smell.

This is part of why a constipated stretch often smells more pungent, and why a fast, loose stool smells different again rather than simply stronger or weaker. The composition has changed, not just the concentration.

Can medicines change how stool smells?

Yes, and antibiotics are the clearest example. A course of antibiotics reduces the diversity of the gut bacterial population, which changes how food is fermented while the course is running and for some time afterwards. Recovery is not uniform: one review notes it is highly individual, with some studies showing reduced microbial richness persisting for many months, and certain species not returning at all [4].

Iron supplements are another common one, and they usually change stool colour as well as smell. If a change in smell starts within a few days of a new medicine or supplement and has no other explanation, the medicine is the first place to look — and worth mentioning to whoever prescribed it if it is bothering you.

What does a change in stool smell not tell you?

On its own, not very much. Smell is a subjective, poorly-quantified signal, it varies enormously between individuals, and there is no colour chart equivalent for it. Two people eating the same meal can produce quite different results.

What makes it informative is company and duration. A smell change on its own, for two days, after a curry, is noise. A smell change that has persisted for a month alongside looser stools and weight you did not intend to lose is a different kind of observation, and it belongs in a GP appointment rather than a search engine.

When is a change in stool smell worth a GP appointment?

Use duration and company as the two tests. NHS guidance on bowel symptoms sets a four-week threshold for booking an appointment about an ongoing change in bowel habit, and lists a separate group of signs that warrant an urgent appointment or a call to NHS 111: losing a lot of weight for no reason, bleeding from your bottom or bloody diarrhoea, a hard lump or swelling in your tummy, or breathlessness and palpitations with paler skin than usual [5].

Those urgent signs are not about smell. But if any of them appear alongside a change in smell, the smell stops being the interesting part.

How do temporary and persistent changes in smell compare?

What is worth noting before you speak to a GP?

Duration and coincidence are the two things people forget, and the two things a GP asks for first:

• When it started, and whether it has been every time or only sometimes.
• Anything new in the fortnight before it started — medicines, supplements, a big diet change, travel, an illness.
• What else has changed: stool consistency, frequency, colour, urgency.
• Anything from the urgent list: bleeding, unintended weight loss, a lump, ongoing pain.

Frequently asked questions

Is smelly stool always a sign of a health problem?

No. Stool has an odour by default, because gut bacteria ferment undigested food into sulphur-containing gases as a normal part of digestion [1]. Diet, transit time and medicines all move the strength of that smell around from day to day. A short-lived change after a big meal or a new supplement is common. What is worth attention is a change that persists for several weeks, or one that arrives with bleeding, weight loss or ongoing pain [5].

Can antibiotics change how stool smells?

Yes. Antibiotics reduce the diversity of the gut bacterial population, which changes how food is fermented and can change the smell during a course and after it. Recovery is highly individual — one review found reduced microbial richness persisting for many months in some studies [4]. If the change comes with ongoing diarrhoea, mention it to whoever prescribed the course.

Why does stool smell worse when I am constipated?

Because time in the colon changes what the bacteria are doing. A longer colonic transit time is accompanied by a shift in metabolism from carbohydrate fermentation towards protein breakdown [3], and it is protein breakdown that produces the sulphur gases responsible for the odour [1].

Does eating more fibre make the smell worse?

Usually the opposite, even though it often produces more wind. Readily fermentable fibres suppressed hydrogen sulphide production by 82–89% in direct gas profiling, while poorly fermentable fibres achieved under 35% [2]. More gas and less smell can happen together.

Can stool smell tell me anything about my gut bacteria?

Only very loosely. Smell reflects the balance between carbohydrate and protein fermentation on a given day, which is influenced by diet and transit time as much as by which bacteria you have [2][3]. It is not a readout of your microbiome, and no home method turns a smell into a meaningful measurement of it.

Practical takeaway

Most changes in stool smell trace back to a high-protein or high-sulphur meal, a slow week, or a new medicine, and they settle within a day or two. If you want to make sense of a change, note when it started and what else changed at the same time — that pairing is far more informative than the smell itself. Book a GP appointment if a change in bowel habit has lasted four weeks or more, and do it urgently if there is bleeding, unexplained weight loss, or a lump [5].

Related reading: healthy stool colour guide, what does stool consistency tell you?, what does mucus in stool mean?, gut transit time explained, why is my poo green?, and how often should you poo?

References

1. Suarez FL, Springfield J, Levitt MD. Identification of gases responsible for the odour of human flatus and evaluation of a device purported to reduce this odour. Gut. 1998;43(1):100–104. PubMed 9771412 — small controlled study in 16 subjects; measured flatus rather than stool.
2. Yao CK, Rotbart A, Ou JZ, Kalantar-Zadeh K, Muir JG, Gibson PR. Modulation of colonic hydrogen sulfide production by diet and mesalazine utilizing a novel gas-profiling technology. Gut Microbes. 2018;9(6):510–522. PMC6287689
3. Roager HM, Hansen LBS, Bahl MI, et al. Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut. Nature Microbiology. 2016;1:16093. nature.com
4. Yang L, Bajinka O, Jarju PO, Tan Y, Taal AM, Ozdemir G. The varying effects of antibiotics on gut microbiota. AMB Express. 2021;11:116. PMC8368853
5. National Health Service. Symptoms of IBS (irritable bowel syndrome). nhs.uk — cited for its four-week GP threshold and its list of signs needing urgent advice.
6. Degen LP, Phillips SF. Variability of gastrointestinal transit in healthy women and men. Gut. 1996;39(2):299–305. PubMed 8977347

This content is for informational purposes only and does not constitute medical advice. If you have concerns about your digestive health, please speak to a healthcare professional. In the UK you can also contact NHS 111.