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Orally administered enzymes can have profound effects on the composition of the gut microbiota and may serve as an appealing alternative modulating agent. Basically, enzymes can influence the gut microbiota through three different ways. However, the modified gut microbioal flora on improved health is not easily distinguished from those incurred by other functions of the enzymes. We discovered that five xylanases with different modes of action and varying ability to stimulate bacterial growth behaved differently in the in vitro and in vivo nutrient digestion rates. However, the changes were not always consistent with the improved growth performance. Further analysis of the gut flora indicated that there was difference among the xylanase-treated groups, which was verified by stimulation growth of selected gut bacteria by xylanases. The results suggest that, orally administered xylanase incurred change of gut microbiota, whose effect on growth promotion cannot be overlooked. Furthermore, the change of the gut microbiome by specific xylanases led to resistance to Clostridium perfringens infection.