Salsify (Tragopogon porrifolius) and gobo (Arctium lappa) are root vegetables that contain high concentrations of naturally occurring fructooligosaccharides (FOS), nondigestible oligosaccharides that have prebiotic effects on the intestinal microflora. The objective of this study was to compare colonic microbial populations and the fermentation characteristics of gobo and salsify in breast-fed vs. formula-fed infants. Fecal inoculum from breast-fed and formula-fed infants consuming either no solid foods, cereal, or fruit and vegetable purees were fermented in vitro with sweet potato puree plus gobo, salsify puree or a control vegetable, carrot. Breast-fed and formula-fed infants had similar fecal bacteria concentrations, with the exception of Clostridium perfringens (P < 0.10). Introduction of solid foods into the diet of infants was associated with increased fecal concentrations of bifidobacteria (P < 0.10) and decreased concentrations of total aerobes (P < 0.01), C. perfringens (P < 0.001) and Escherichia coli (P < 0.10). Inoculum from feces of breast-fed infants resulted in greater acetate production, whereas inoculum from feces of formula-fed infants resulted in greater propionate and butyrate production (P < 0.05). Fermentation of FOS-containing vegetables by infant fecal inoculum did not differ significantly from fermentation of carrots as assessed by total short-chain fatty acid (SCFA) production. The addition of solids to the diet of infants was associated with increased production of acetate and total SCFA (P < 0.05). It appears that both the composition and fermentative activity of the colonic microflora of human infants is affected by breast-feeding and solid food consumption, but not by short-term exposure to low concentrations of FOS-containing substrates.