Scientific research demonstrates that two indigenous gut bacteria, Lactobacillus and Bifidobacterium can contribute to human health. Although these bacteria can be consumed as probiotics, they can also be produced in the gut by bacteria, and are then called prebiotics. The primary objective of this in vitro study was to quantitatively analyze at the genus level how two dietary fibers, wheat dextrin (WD) and partially hydrolyzed guar gum (PHGG) changed the levels of these two gut bacteria at 12 and 24 h, via real time qualitative polymerase chain reaction (qPCR). Secondary objectives were changes in fecal pH, short chain fatty acids (SCFAs) and total gas volume produced. At 12 h WD was more bifidogenic (9.50 CFU log10/mL) than PHGG (9.30 CFU log10/mL) (p = 0.052), and also at 24 h WD (9.41 CFU log10/mL) compared with PHGG (9.27 CFU log10/mL) (p = 0.043). WD produced less total SCFAs at both 12 and 24 h than PHGG, and produced significantly lower amounts of gas at 12 and 24 h (p < 0.001). Both PHGG and WD also promoted growth of Lactobacilli when measured at 12 and 24 h compared with the 0 h analysis, indicating that both fibers are lactogenic. These results demonstrate the prebiotic effect of WD and PHGG. Based on fermentation kinetics, PHGG is more rapidly fermented than WD, and both fibers show prebiotic effects as early as 12 h.