Bile acids are secreted into the small intestine, conjugated with glycine or taurine. There are few conjugated products in the stool. Most transformations are accomplished by bacteria. Obligate anaerobic bacteria may deconjugate, but most aerobic bacteria do not. Subsequent conversion of deconjugated bile acids is performed by a wider range of organisms. Oxidation of conjugated bile salts without previous deconjugation can occur. Several clinical syndromes are associated with changes in the bile acid and microbial ecology, eg, ileostomies, stasis areas, and antibiotic therapy. Bile salts can also alter the growth of bacteria. Some metabolites of the bacterial metabolism of bile resemble known carcinogens.
Lewis R, Gorbach S. Modification of Bile Acids by Intestinal Bacteria. Arch Intern Med. 1972;130(4):545-549. doi:10.1001/archinte.1972.03650040071007