Minimal number of species for ecosystem...

Charles Stross posted interesting question on his blog a while back - what is the minimal ecosystem with humans in it?
He's kind of biased though to show that other science fiction writers get it wrong disregarding the issue, and he considers 'genetically engineered algae that makes everything you need' to be a magic wand (It is very easy to argue that something never done cannot be done or is very hard to do). He probably intends to write some fiction where he 'gets it right' in portraying the immense difficulties of building such ecosystem.

In reality though, while we're still very long way off from building a starship, we can genetically engineer rice, corn, some bacteria, etc to produce a variety of vitamins.
In my opinion, the spaceship ecosystem, if it will ever be done, would consist of:
1: Waste incinerator and chemical plant (for processing ash).
2: Many tanks of genetically engineered algae and possibly yeasts (feeding on algae), the tanks capable of being fully sterilized.
3: Food processing plant.
4: Humans and internal symbiotic bacteria etc.
5: Frozen, radiation shielded specimens of all algae, yeasts, and human symbiotic bacteria, for reseeding through the mission.
6: Genetics lab just in case.
The problem with more complex ecosystems is that them tie up a lot of carbon, oxygen, hydrogen, etc etc. as non-human mass - wastes being processed, worms feeding on wastes, etc etc. Very small payload to weight ratio.

On topic of keeping humans on generation ship (a ship which is going on for hundreds years) civilized enough to maintain their plumbing, consider a normal small town, if you wish, on isolated island. In that town people are watching hollywood movies(they cant make movies themselves), kids are studying in school with books written elsewhere, they're believing in religion which came from elsewhere, they have social structure which 'feels right' because it matches what they see in movies, they do plumbing based on instructions from elsewhere, and so on and so forth. Right here on earth, not only such towns do not develop some widely divergent civilizations but the cultural diversity of such towns is diminishing, and been diminishing even before the Internet. Science fiction writers came up with a lot of strange social organization types for a generation ship (my personal scifi favourite is Heinlein's Orphans of the Sky), but it seems nobody explored the boring possibility that the people on generation ship mostly sit on the couch watching TV. (I don't think anyone would ever make a generation starship, but anyway)