That was the first question that came to mind after reading this article:
Scientists at The University of Nottingham are leading an ambitious research project to develop an in vivo biological cell-equivalent of a computer operating system. The success of the project to create a 're-programmable cell' could revolutionise synthetic biology and would pave the way for scientists to create completely new and useful forms of life using a relatively hassle-free approach.
I mean, why build nanites if you can program a cell to perform any nano-scale tasks you need to do? Mother Nature has already mastered problems that nanotech grapples with (self-replication, energy source, mobility), so why reinvent the wheel? Stunning visualizations of the inner workings of our own bodies show that we've already got trillions of molecular factories inside of us, and there would be no need for specialized and artificial "nano-hives" if we could harness the machinery we already have.
Of course, this is all wildly speculative, but I'm interested to hear what other folks think about this.