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I wouldn't be so quick to make that conclusion. One of our companies is in the microbiome therapeutics space and the more we learn about respiratory and gut bacteria, the more holes in our understanding of normal function are filled in. I wouldn't be shocked if there was bacteria that feeds off collagen and that bacteria is absolutely required for proper gut lining function. We already know that there are 3 types of bacteria that are deficient (or at least very low population) in Crohn's disease patients.
I'm not saying that there is proof of this but it's not implausible.
The idea that everything is digested into simple amino acids in the gut before it's absorbed is now refuted with the nature paper from just a few years ago where they showed that plant plasmids can be incorporated into mammalian cells.
Not everything is digested into simple amino acids, but collagen is literally just amino acids. It’s taken and used by the body as it sees fit. Collagen doesn’t stay collagen. It’s like saying eating fat turns it into bodyfat.