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Children with recurrent UTI had significantly higher proportion of E. coli compared to control group (10.97 vs. 4.74; P = 0.014) and lower proportion of Bifidobacterium sp. (6.54 vs. 9.33; P = 0.594). In children with recurrent UTI group, E. coli proportion was found higher than Bifidobacterium sp. although not statistically significant (10.97 vs. 6.54; P = 0.819). In healthy controls, Bifidobacterium sp. proportion was significantly higher than E. coli (4.74 vs. 9.33; P = 0.021). The total amount of E. coli (996,004 vs. 1,099,271; P =