The history of science fiction is replete with technology big and, over time, increasingly small. Some of the most recognised recent work has been, like Neal Stephenson's steam-punk/cyber-punk crossover The Diamond Age, fundamentally a story about nanotechnology and it's potential uses, with the "grey goo" argument replaced by lung-threatening grey dust when nanobots war with each other.
Bioengineering has not, in my admittedly limited experience, been treated nearly as well. In fact, with the exception of the odd throw-away setup like a branch of homo sapiens engineered for heavy gravity worlds (Anne McAffrey), most of the interesting biological discussions happened decades away with Frank Herbert (across most of his books, not just the Dune epic) and Isacc Asimov.
Which leads me neatly to where I was intending to go: Asimov constructed a world in which the Earth is essentially a giant metal sphere, all living done in built-up catacombs because there's no space on the surface left, and all food produced by - wait for it - yeast beds. Yeast as food found other expression in several of Asimov's books and short stories, including one in which a chef introduced actual garlic into a culinary competition instead of using the several hundred flavoured varieties of yeast available, and was ostracised when he announced it (N.B.: If this wasn't actually Asimov, please correct me).
The problem is that, despite the obvious potential for micro-organisms, which are so efficient at turning food materials into themselves when they don't have to build supporting structures and internal organs that are difficult to make productive (unless they get fed back into the process as food materials, hello prion diseases...), their potential appears to have been neglected by the science fiction community. Maybe the idea isn't sexy or shiny enough.
Actual science, however, now there's another thing entirely! Observe: 10 Ways Genetically Engineered Microbes Could Help Humanity (Discover Magazine). Ten ways is a bit of a stretch - there are four different ways of fighting disease alone - but this is seriously cool science. Constructing microbes to produce medicines is good but not particularly surprising. Engineering yeast that is much better at producing ethanol is interesting and has serious commercial potential in the current climate, and producing petroleum products instead of the corrosive and inefficient ethanol is much cooler again (we can get biodiesel straight from palms and rapeseed [that's Canola, in case you weren't aware] and hemp seeds, can we get biodiesel from random organic material via microbes? Please?)
But I think that my favourite from the entire list is the last one. Microbes have been enginered that can produce proteins that can attach to metals at stress points. I repeat, that attach to metals at stress points. This is seriously cool. A merging of organic and inorganic like this, bio-metallurgy if you will, is much more exciting than doing the same thing with nanomachines, and not much less exciting than producing nanomachines that can detect stress points on airplane wings in flight and enact running repairs in sub-zero temperatures and constantly fluctuating stresses.
Keep it up, I say, keep it up.