Thomas Aquinas Commentary Lamentations 3:4-6

"My flesh and my skin hath he made old; he hath broken my bones. He hath builded against me, and compassed me with gall and travail. He hath made me to dwell in dark places, as those that have been long dead." — Lamentations 3:4-6 (ASV)

Here the author presents the effect of the divine scourging, just as a bruise is the effect of a rod. Concerning this, he explains three things.

1. The wasting away of the entire nation. The skin signifies the people as a whole, the flesh signifies the delicate and frail, and the bones signify the strong men and warriors. All of these, representing the whole nation, waste away as if from old age. How does it happen, O Israel, that you are in your enemies’ land? You have grown old in a strange country .
2. The siege of an already weakened people. He has built round about me refers to a besieging army, and gall refers to an army that has brought hardship and bitterness. Am I a sea, or a whale, that you have enclosed me in a prison? (Job 7:12).
3. The captivity of those already imprisoned. He has set me in dark places means to be imprisoned, and as those that are dead refers to those who have been sentenced to death. He has made me to dwell in darkness as those that have been dead of old (Psalms 142:3).

These things can also be understood to refer to Jeremiah himself, whose body was wasting away from many hardships and who was locked up in prison.