



I've cracked the mystery of the barrels!
I think I've cracked the mystery of what's in the barrels from The Last Guardian! The short answer is the blue stuff in the barrels, crucibles, and giant pots is... Trico bile; specifically the run-off covering the humans brought to the Master of the Valley.
Some suggest the mine carts and machines in the Game could have used to harvest the blue substance, but I think mining the materials to create wood barrels and iron crucibles (as well as carts and tracks for transport) makes more sense, and why there are mine carts all over. The armor use the machines around the Nest, not unlike when they transported and lowered Trico into his prison, to help harvest the run-off.
The fact 2 humans (1 child and adult, from the looks) sends out one barrel (preloaded), this means only one Trico is feed, nurturing hostility among the other Trico to get more humans for a possible treat. The companion guide even says the humans don't become the substance in the barrels "right away", which could be a mistranslation of "automatically": "The humans aren't turned into the barrels right away. They are used to power the Master of the Valley and everything he controls, and the "blue goo" might be a byproduct given to the Tricos to reward them."
Also, consider the tattoos the humans gain from being in the Trico, which the Yoroi are able to use to disable any escapees. If the bile has enough magic properties for that, it could still be considered a byproduct from when the humans are given to the Master, and returned to the Trico as barrels.
Given we see the Boy and other humans in "blue goo" when eaten and regurgitated by the Trico, I think the Master just found a way to recycle all the vomit without it pilling up in the Nest. Humans go through one tube to the Master and become part of his hive mind, and other pipes seperate the bile to be contained. The smell of his own bile could be what attracts Trico to said barrels and crucibles full of it, as it's both familiar and remembers it as the "treat" from the Master and the Boy. Mammals eating their bile is quite common, and Trico is no exception.