"I did not know him" - How can John the Baptist say he didn't know the Lord? Clearly he knew him! Jesus was his relative, and he had recognized the Lord from the womb. Further, as soon as John saw Jesus, he readily stated that "I ought to be baptized by you!" Further, he knew Jesus would institute a new baptism, in the Holy Spirit. Additionally, he even knew that Jesus was God - "He existed before me."
What John came to understand is that Jesus is always the primary minister of baptism - whosoever baptizes, it is always Christ who baptizes. Jesus gives the sacraments their power, and he is the source of unity in the Church.
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