We didn’t invent this.
We’re measuring it.

Windey K, De Preter V, Verbeke K · Molecular Nutrition & Food Research

A balanced review of how the colon ferments protein, the compounds it produces, and whether their effects on the gut — clear in the lab — actually hold up in real people.

Hughes R, Magee EA, Bingham S · Current Issues in Intestinal Microbiology

A foundational review explaining how undigested protein reaching the large intestine is broken down by bacteria into compounds like ammonia, phenols and sulfides — and why diet shapes that chemistry.

Smith EA, Macfarlane GT · Journal of Applied Bacteriology

A classic study counting the colon bacteria that turn protein building blocks into aromatic compounds like phenol and indole, and showing how pH and fiber strongly control how much they produce.

Sangu PK, Vanitha Kumar M, Meera Shiv Shekhar, et al. · Ayu (International Quarterly Journal of Research in Ayurveda)

A study revisiting the classical Ayurvedic technique of dropping oil onto urine to read health — and finding it tracks with the physical chemistry that disease changes in urine.

Wang Q, Fang Y, Tan S, Li Z, Zheng R, Ren Y, Jiang Y, Huang X · Frontiers in Oncology

A 2024 review that combined 32 studies and nearly 4,700 people to measure how accurately volatile-compound analysis and electronic-nose sensors can detect colorectal cancer.

Markar SR, Wiggins T, Antonowicz S, Chin ST, Romano A, et al. · JAMA Oncology

Researchers tested whether analyzing the volatile chemicals in a person's exhaled breath could identify cancer of the esophagus and stomach, and found it performed surprisingly well.

Batty CA, Cauchi M, Lourenco C, Hunter JO, Turner C · PLoS One

A study analyzing the gases given off by stool samples, finding that sulfur-containing compounds were notably higher in people who turned out to have colorectal cancer.

de Meij TGJ, Larbi IB, van der Schee MP, Schuurman YC, Groot PFC, Mulder CJJ, van Bodegraven AA, de Boer NKH · International Journal of Cancer

A proof-of-concept study showing that a sensor device — an 'electronic nose' — could tell apart the stool gas patterns of people with colorectal cancer, and even pre-cancerous growths, from healthy volunteers.

Altomare DF, Di Lena M, Porcelli F, Trizio L, Travaglio E, Tutino M, Rotelli M, Gentile A, De Gennaro G, Sardaro A, Colucci G, Valentini AM, Sammarco G · British Journal of Surgery

An early clinical study showing that the volatile compounds people breathe out carry a chemical pattern that distinguished those with colorectal cancer from healthy volunteers.

Multi-center study team (Gastroenterology) · Gastroenterology

Everyday wrist wearables picked up subtle heart and sleep changes that signaled inflammatory bowel disease flares about seven weeks before symptoms appeared.

Voigt RM, Forsyth CB, Green SJ, Mutlu E, Engen P, Vitaterna MH, Turek FW, Keshavarzian A · PLOS ONE

Disrupting the daily body clock — the way shift work or jet lag does — measurably scrambled the gut microbiome, especially when paired with a poor diet.

Chang Y, Hu J, Bisanz JE, Rey FE, Sung J · Nature Communications

Mayo Clinic researchers built a machine-learning index that reads a person's gut bacteria and returns a single number for how 'healthy' the microbiome looks.

Wiklund IK, Fullerton S, Hawkey CJ, Jones RH, Longstreth GF, Mayer EA, Peacock RA, Wilson IK, Naesdal J · Scandinavian Journal of Gastroenterology

A 13-question, IBS-specific symptom scale that groups gut complaints into five clusters — pain, bloating, constipation, diarrhea, and fullness — and is sensitive enough to detect small improvements from diet or probiotics.

Francis CY, Morris J, Whorwell PJ · Alimentary Pharmacology & Therapeutics

A simple five-part questionnaire that turns the severity of irritable bowel syndrome into a single 0-500 score, making it possible to track whether someone is getting better or worse.

Engen PA et al. · Sensors (MDPI)

A low-cost bathroom gas sensor picked up the chemical changes caused by eating more prebiotic fiber, tracking a real microbiome shift over just a few weeks.

Journal of Crohn's and Colitis (systematic review and meta-analysis) · Journal of Crohn's and Colitis

Pooling more than 1,300 people across many studies, this review found that volatile compounds in breath, stool, and urine can reliably tell people with inflammatory bowel disease apart from healthy people.

Sensors (MDPI) · Sensors (MDPI)

A single gas sensor, by varying its temperature and watching how its response unfolds over time, was able to estimate the makeup of a two-gas mixture — not just detect that a gas was present.

Song et al. · Advanced Science

A newly described measurement — the pause after the last stool passes — captures a dimension of bowel health that stool shape alone completely misses.

Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Barzilai MJ, Bhatt AS, Gendelman HE, Knight R, Mazmanian SK · Cell

A landmark study showed that gut bacteria are required for the motor problems and brain inflammation seen in a mouse model of Parkinson's disease.

Roager HM, Licht TR · Nature Communications

This review explains how gut bacteria convert the dietary amino acid tryptophan into a family of compounds — including indole and skatole — that influence the immune system, the gut barrier, appetite, and even the brain.

Walton C, Fowler DP, Turner C, Jia W, Whitehead RN, Griffiths L, Dawson C, Waring RH, Ramsden DB, Cole JA, Cauchi M, Bessant C, Hunter JO · Inflammatory Bowel Diseases

The volatile chemistry of stool differs measurably in inflammatory bowel disease, and — importantly — those differences shrink back toward normal after treatment.

Aghdassi E, Allard JP · Free Radical Biology and Medicine

Two simple gases in exhaled breath — ethane and pentane — rise when the body is under oxidative stress, including in conditions like inflammatory bowel disease.

Pelli MA, Trovarelli G, Capodicasa E, De Medio GE, Bassotti G · Diseases of the Colon & Rectum

Using a refined lab method, this study confirmed that people with active inflammatory bowel disease genuinely exhale more pentane and ethane — and that this signal was not a measurement artifact.

Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Bhatt DL, Sonnenburg JL, Peer I, Nielsen J, Bork P, Zeller G, Sunagawa S · Nature Medicine

By pooling stool studies from around the world, researchers identified a consistent set of gut bacteria linked to colorectal cancer that holds up across different countries and laboratories.

Kostic AD, Chun E, Robertson L, Glickman JN, Gallini CA, Michaud M, Clancy TE, Chung DC, Lochhead P, Hold GL, El-Omar EM, Brenner D, Fuchs CS, Meyerson M, Garrett WS · Cell Host & Microbe

This study moved beyond simply finding Fusobacterium nucleatum in colon tumors and showed, in mice, that the bacterium can actively encourage tumors to form and reshape the immune environment around them.

Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA · Genome Research

Researchers discovered that a bacterium normally found in the mouth, Fusobacterium nucleatum, is dramatically over-represented in colorectal cancer tissue compared with healthy tissue from the same person.

Ríos-Covián D, Ruas-Madiedo P, Margolles A, Gueimonde M, de los Reyes-Gavilán CG, Salazar N · Frontiers in Microbiology

An updated review of how diet shapes the short-chain fatty acids your gut bacteria produce, which microbes make each one, and how they influence health from the immune system to metabolism.

Canani RB, Di Costanzo M, Leone L, Pedata M, Meli R, Calignano A · World Journal of Gastroenterology

A wide-ranging review of how butyrate — made when gut bacteria ferment fiber — protects the gut and benefits health throughout the body.

Wong JMW, de Souza R, Kendall CWC, Emam A, Jenkins DJA · Journal of Clinical Gastroenterology

A foundational review of how gut bacteria ferment fiber into short-chain fatty acids, and how these compounds support the colon and overall health.

Macfarlane S, Macfarlane GT · Proceedings of the Nutrition Society

A review explaining what determines the type and amount of short-chain fatty acids your gut bacteria produce, and why fiber and protein fermentation lead to very different by-products.

Pimentel M, Saad RJ, Long MD, Rao SSC · American Journal of Gastroenterology

A leading group of gastroenterologists published the first formal guideline for diagnosing and treating small intestinal bacterial overgrowth, including the gases used to test for it.

Rezaie A, Buresi M, Lembo A, Lin H, McCallum R, Rao S, Schmulson M, Valdovinos M, Zakko S, Pimentel M · American Journal of Gastroenterology

A panel of experts agreed on how breath tests for hydrogen and methane should be prepared, performed, and interpreted across common digestive conditions.

Asnicar F, Leeming ER, Dimidi E, Mazidi M, Franks PW, Al Khatib H, Valdes AM, Davies R, Bakker E, Francis L, Chan A, Gibson R, Hadjigeorgiou G, Wolf J, Spector TD, Berry SE, Segata N · Gut

A simple blue food-dye test reveals how fast food moves through your gut — and that number turns out to be the strongest predictor of your gut microbiome.

Drossman DA et al. (Rome Foundation) · Gastroenterology

The internationally agreed criteria that define IBS, functional constipation and related conditions — and set the benchmark for what 'normal' bowel habits actually look like.

Garner CE, Smith S, de Lacy Costello B, White P, Spencer R, Probert CSJ, Ratcliffe NM · FASEB Journal

The landmark catalogue of the gas chemistry of human stool — 297 distinct volatile organic compounds, 13 of them present in every healthy sample.

Lewis SJ, Heaton KW · Scandinavian Journal of Gastroenterology

The 7-point picture chart that turned stool shape into a reliable, at-a-glance measure of how fast your gut is moving.

Carbonero F, Benefiel AC, Alizadeh-Ghamsari AH, Gaskins HR · Frontiers in Physiology

A comprehensive review mapping the three different ways gut bacteria produce hydrogen sulfide gas, and how this links to digestive health and disease.

Levitt MD, Furne J, Springfield J, Suarez F, DeMaster E · Journal of Clinical Investigation

This study revealed how the colon neutralizes the toxic gas hydrogen sulfide, converting it almost entirely into a harmless compound at remarkable speed.

Pitcher MC, Cummings JH · Gut

An influential paper proposing that hydrogen sulfide made by gut bacteria may act as a toxin that damages the colon in ulcerative colitis.

Roediger WEW · The Lancet

A landmark paper proposing that ulcerative colitis is driven by an energy shortage in the cells lining the colon, which cannot properly burn their main fuel.

Various / historical · Clinical literature review

Long before lab tests, physicians across the world diagnosed disease by the smell of urine — and modern chemistry has confirmed exactly which molecules they were detecting.

Brial F, Chilloux J, Nielsen T, Vieira-Silva S, Falony G, Andrikopoulos P, Hoyles L, Gunter MJ, Raes J, Dumas ME, Pedersen O, Ehrlich SD, Clément K, Blaser MJ, et al. · Gut

A urine molecule called hippurate turns out to be the single best chemical readout of gut microbiome diversity and metabolic health.

Wen Q, Boshier P, Myridakis A, Belluomo I, Hanna GB · Metabolites

A review of 13 studies and over 1,200 people identified 48 urinary volatile compounds with diagnostic signal for cancer — many of them gut-derived.

Khalid T, Shrive M, Ewen R, White P, Persad R, Bain L, de Lacy Costello B, Probert CSJ, Ratcliffe NM · PLOS ONE

Volatile compounds in urine added a small amount of diagnostic value on top of the standard PSA test for prostate cancer.

Amann A, de Lacy Costello B, Miekisch W, Schubert J, Buszewski B, Pleil J, Ratcliffe N, Risby T · Journal of Breath Research

The definitive reference catalogue of every volatile compound documented from the healthy human body — 1,765 in total, including 279 found in urine.

Khalid T, White P, de Lacy Costello B, Persad R, Ewen R, Johnson H, Probert CSJ, Ratcliffe NM · PLOS ONE

A pilot study showed that a gas sensor analysing the vapour above urine could distinguish bladder cancer patients from controls with high accuracy.

Mochalski P, King J, Klieber M, Unterkofler K, Hinterhuber H, Baumann M, Amann A · Analyst

In end-stage kidney disease, gut-microbe-derived volatile compounds accumulate dramatically — illustrating the gut-kidney axis at its extreme.