Skatole (3-methylindole) is a malodorous chemical in stored swine manure and is implicated as a component of foul-tasting pork. Definitive evidence for the skatole pathway is lacking. Deuterium-labeled substrates were employed to resolve this pathway in the acetogenic bacterium Clostridium drakei and Clostridium scatologenes and to determine if a similar pathway is used by microorganisms present in stored swine manure. Indoleacetic acid (IAA) was synthesized from tryptophan by both bacteria, and skatole was synthesized from both IAA and tryptophan. Microorganisms in swine manure produced skatole and other oxidation products from tryptophan, but IAA yielded only skatole. A catabolic mechanism for the synthesis of skatole is proposed.Storage of swine manure is associated with the generation of a number of malodorous compounds (18,22,30), and the production of odor associated with concentrated livestock facilities creates a nuisance and has resulted in considerable conflicts between producers and rural neighbors. These odors are produced as a result of anaerobic degradation of materials present in manure and include sulfides, organic acids, ammonia, phenols, amines, and other volatile compounds (30). One of the more malodorous compounds identified in swine manure odor is skatole (3-methylindole). Skatole has also been implicated as an off-flavor component of pig meat (referred to as "boar taint") (4,6,17,19) and as a contributing factor in acute bovine pulmonary edema and emphysema (15,23,27).Although the production of skatole has been attributed to the bacterial degradation of the amino acid tryptophan, the pathway by which skatole is produced from tryptophan has not been elucidated. The primary metabolite of tryptophan fermentation is indole (26,27), and skatole is produced from tryptophan and indoleacetic acid (IAA) by pig fecal slurries (13). However, very few bacterial isolates have been shown to produce skatole. A Lactobacillus species from the rumen has been reported to produce skatole from IAA but not directly from tryptophan (28,29). Clostridium scatologenes and the acetogen Clostridium drakei (originally isolated as C. scatologenes SL1) (14, 16) have also been reported to produce skatole (13, 14) and were selected for resolving the skatole catabolic pathway by using deuterium-labeled substrates and a combination of gas chromatography-mass spectrometry (GC-MS) and matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS).Bacterial strains, cultivation conditions, and swine manure. C. drakei SL1 DSM 12750 and C. scatologenes ATCC 25775 were utilized in this study. Preparation of media and inoculations were performed under anaerobic conditions using the method of Hungate as modified by Bryant (2). The basic medium for culturing C. drakei and C. scatologenes contained macrominerals, microminerals, buffers, reducing agents, and other components in routine growth medium (RGM) (9) and was supplemented with 1% (wt/vol) tryptone and either 1% (wt/vol) tryptophan or 1% (wt/vol) IAA...