1 After the Lord Jesus had prayed for His disciples whom He had with Him at the time, and had conjoined with them others who were also His own, by saying, “Neither pray I for these alone, but for them also who shall believe in me through their word,” as if we were inquiring what or wherefore He prayed for them, He straightway subjoined, “That they all may be one; as Thou, Father, [art] in me, and I in You, that they also may be one in us.” And a little above, while still praying for the disciples alone who were then with Him, He said, “Holy Father, keep in Your own name those whom You have given me, that they may be one, as we are”.
It is the same thing, therefore, that He now also prayed for in our behalf, as He did at that time in theirs, namely, that all— to wit, both we and they— may be one. And here we must take particular notice that the Lord did not say that we all may be one, but, “that they all may be one; as Thou Father, in me, and I in You” (where is to be understood are one, as is more clearly expressed afterwards); because He had also said before of the disciples who were with Him, “That they may be one, as we are.”
The Father, therefore, is in the Son, and the Son in the Father, in such a way as to be one, because they are of one substance; but while we may indeed be in them, we cannot be one with them; for they and we are not of one substance, in as far as the Son is God along with the Father. But in as far as He is man, He is of the same substance as we are. But at present He wished rather to call attention to that other statement which He made use of in another place, “I and the Father are one,” where He intimated that His own nature was the same with that of the Father.
And accordingly, though the Father and Son, or even the Holy Spirit, are in us, we must not suppose that they are of one nature with ourselves. And hence they are in us, or we are in them, in this sense, that they are one in their own nature, and we are one in ours. For they are in us, as God in His temple; but we are in them, as the creature in its Creator.
Source: Tractates on the Gospel of John (New Advent)