organic acid which gives vinegar its sour taste and pungent smell. Produced by acetic acid bacteria including Clostridium acetobutylicum and Acetobacter, found universally in food, water and soil, produced in food spoilage and in the human body - for example, in vaginal lubrication.  This  second simplest carboxylic acid (after formic acid) is an important chemical reagent and industrial chemical, mainly used in the production of cellulose acetate for photographic film and polyvinyl acetate for wood glue, as well as synthetic fibers and fabrics. the acid that gives vinegar its characteristic taste. 
One of short chain fatty acids (SCFAs, also called volatile fatty acids) containing fewer than 6 carbons: Formic acid (C1), acetic acid (C2), propionic acid (C3), butyric acid (C4), and valeric acid (C5). The gut microbial metabolites SCFAs profoundly regulate T cell differentiation in the body, boosting immune system.

if raised, suggests bacterial fermentation due to excess carbohydrate reaching the colon; levels are not significantly altered in patients with malignancy or diabetes mellitus, but severe liver disease and severe acidosis were both associated with increased acetate concentrations. Elevated blood acetate is also an indicator of fast ethanol elimination in chronic alcoholics.

simplest aromatic ketone, in small amounts can be found in apple, apricots, cheese, chicory, banana, beef, and cauliflower. It is a precursor to useful resins and fragrances, is used in chewing gum and is an  ingredient in fragrances that resemble smell of almond, cherry, honeysuckle, jasmine, and strawberry. 
In humans, acetophenone is metabolized to benzoic acid, carbonic acid, and acetone, but it can be also excreted in its original form in feces and saliva.
Deuterated acetophenone smells fruitier than ordinary acetophenone. It also smells slightly of bitter almonds, just like many compounds containing the cyanide or nitrile group (C≡N) - as both C–D and C≡N bonds vibrate at the same frequency (about 2200 cm-1).   See also 2-aminoacetophenone

Nitrogen trihydride NH3,  colorless gas with a characteristic pungent smell (like vinegar or a very long-stayed urine). Household ammonia is a 5-10% solution of ammonia in water. It is also called Ammonium hydroxide and used as a general purpose cleaner for glass, porcelain and steel surfaces or to dissolve grease. NH3 is extensively used to manufacture fertilizers and a wide variety of nitrogen-containing organic and inorganic chemicals.

Inhalation of ammonia may cause olfactory fatique, eye injury, nasopharyngeal and tracheal burns, bronchiolar and alveolar edema, and airway destruction resulting in respiratory distress or failure.

Ammonia is a nitrogen waste compound that is normally excreted in the urine. It can be also detected in breath and skin emissions of healthy people. Main factors affecting the concentration of mouth-exhaled ammonia are: oral fluid pH, urea concentration, and urease activity. 
Ammonia is a major metabolite of glycine. In brain it is synthesized by glutamine synthaze to form glutamine which may serve to protect the brain from hyperamonemia in liver failure. 
Levels of ammonia might correlate with neurological symptoms.
Elevated blood ammonia can happen for a variety of reasons. It is fairly common in infants with certain genetic conditions such as argininosuccinic acid synthase and argininosuccinic acid lyase deficiencies (1 per 35,000 live births per year in USA). Carbamoyl phosphate synthetase I deficiency is an autosomal recessive inborn error of metabolism of the urea cycle which also causes hyperammonemia. In children, it may be related to Reye’s syndrome, while in adults, it may indicate kidney or liver damage or an underlying metabolic disease. In some cases, an elevated blood ammonia level will resolve on its own without treatment.

Short-chain fatty acid, produced by gut bacteria, occurring in the form of esters in animal fats and used in disinfectants, emulsifying agents, and pharmaceuticals. Colorless, syrupy liquid organic acid with the extremely unpleasant smell of rancid butter or putrefying cheese.  
Chemical Formula:  C4H8O2    CAS Number:  107-92-6
Synonyms: n-Butanoic acid; n-Butyric acid; Ethylacetic acid; Propylformic acid; 1-Butyric acid; 1-Propanecarboxylic acid; n-C3H7COOH; Propanecarboxylic acid; Butanic acid; Buttersaeure; IMET 3393; Kyselina maselna; UN 2820; 1-butanoic acid

Butyrate and other short-chain fatty acids produced by gut bacteria can decrease intestinal permeability and boost immune system, protect the brain, and may help reduce scarring in arteries after vascular surgery. Gut microbiota (Clostridium - especially Faecalibacterium prausnitzii and Eubacterium rectale/Roseburia spp., Eubacterium, Butyrivibrio and others) produce butyrate by fermenting carbohydrates in a high fiber diet. Some studies have shown that patients suffering from inflammatory bowel disease lack butyrate-producing bacteria and have lower levels of butyrate in their gut. 

Rotting-flesh sickly-sweet smelling compound produced from amino acid lysine by microbes such as E. coli, Shewanella putrefaciens, Vibrio spp., and Morganella morganii.  Also known as  1,5-pentanediamine and pentamethylenediamine. 
Cadaverine is one of the best-characterized chemicals responsible for the "smell of death" (from decomposing, putrefying body) repelling most animals. Cadaverine levels are also associated with oral malodor, independently of the level of Volatile Sulfur Compounds.

Colorless odorless highly flammable gas, the lightest and most abundant element in the Universe. 
Hydrogen is used in the production of synthetic ammonia and methanol, in petroleum refining. It is added to fats and oils, such as peanut oil, through a process called hydrogenation.

Hydrogen is the most abundant element and is present in Earth’s atmosphere at about 0.5 ppm (parts per million). It is produced naturally by gut bacterial degradation of oligosaccharides and is present in human breath. Humans produce hydrogen at about 50 mg/day. Hydrogen is found in aircraft and space-shuttle air at about 100 ppm. 

Since its introduction as a diagnostic test in 1969 by Levitt and Calloway, the breath hydrogen test has gained in popularity for the diagnosis of intestinal disaccharidase deficiency (intolerance to lactose, fructose, or sucrose), being more sensitive than blood glucose based tests In selected conditions like celiac disease, it may be preferable to enzyme analysis of biopsy because it measures the response of the entire intestinal tract not just a small area which may not demonstrate enzyme deficiency in these cases. It is especially useful in blind loop syndrome (BLS), commonly referred to in the literature as small intestinal bacterial overgrowth (SIBO) or bacterial overgrowth syndrome (BOS). Diagnosis can be made if there is rise of more than 10 or 20 ppm after ingesting a certain substance.
Hydrogen could constitute from 0.000005 to 50% of human gas. 
The paper, published in 1969, found that: 'Flatus gases varied widely within dietary groups but much more gas was generated with diet S (Gemini-type: shrimp cocktail, chicken and vegetables, butterscotch pudding, apple sauce, etc) than with F (a bland formula). 
'In the first 12-hour collection, subjects fed S passed 3 to 209 ml of rectal H2 and 24 to 156 ml from the lungs.

​Indican is a colorless glycoside, soluble in water, naturally occurring in Indigofera plants. In the body it is produced by bacteria  - by sulfonation of indole (absorbed by the colon and transported to the liver), a compound with intense fecal odor, degradation product of tryptophan which is derived from protein foods. 
IUPAC Name: 1H-indol-3-yl hydrogen sulfate | CAS Registry Number: 487-94-5
Synonyms: Indoxyl sulfate, 3-Indoxyl sulfate, Indoxylsulfuric acid, INDICAN, 3-Indoxylsulfuric acid, Indican (metabolic indican), 3-SULFOOXY-1H-INDOLE, CID10258, Indican (metabolic indolyl sulfate), 2642-37-7 (mono-potassium salt), 1H-Indol-3-ol, hydrogen sulfate (ester), IOS, 1336-79-4, 487-94-5

A high excretion of indican in the urine, mostly combined with a low urinary tryptophan, is a symptom of tryptophan (protein) malabsorption in the small intestine. It also indicates an overgrowth of opportunistic or pathogenic bacteria or yeast in the bowel and more serious conditions like Hartnup's disease, blue diaper syndrome, intestinal toxemia, or peritonitis.

Low indican excretion could indicate the presence of steatorrhoea (reduced absorption of fat) especially if it rises to above normal on pancreatic enzyme therapy.
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The urine indican's (or Obermeyer) test quantifies indican in the urine based on its decomposition and subsequent oxidation to indigo blue. Check MeBO-Biolab studies (NCT02692495) for more. 

organic compound,  a bacterial degradation product of amino acid tryptophan that occurs naturally in human feces and coal tar. In its pure form, indole smells like moth balls, possessing the same heavy, sweet, tar-like pungency. At very low concentrations, however, it has a pleasant, flowery smell. Natural jasmine oil, used in the perfume industry, contains around 2.5% of indole.  Orange blossom and Neroli contain even more indoles than jasmine. Fragrances like Chanel Cristalle, By Kilian Love & Tears and L’Artisan Parfumeur La Chasse Aux Papillons rely on a delicate touch of indoles to give radiance and bloom to their floral accords.In trace amounts, Indoles are also used to create chocolate, coffee and various fruity accords in flavors, including food.
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Indole is an important biomarker in biological and clinical specimens. It can be detected in human breath, feces, saliva and urine. The normal smell of human feces is largely due to this compound. 
Indole is an example of a microbe-generated signal substance that has positive effects on our health and the health of the microbiome. Normal-smelling feces may be an underestimated health indicator.

In the liver indole is sulfonated to indican (3-indolesulfonic acid) and its levels  could be also indirectly measured by indicans test. See MeBO-Biolab studies (NCT02692495) for more.