A chapter from the reference 'Colonies in Space' (Heppenheimer, 1977, 2007): Up on the Farm discusses as the chapter title suggests - farming the food needs of any colony. Specifically, they discuss which type of livestock is the most viable given constraints of space and feed, specifically for meat,
The colonists will also want meat and this poses a problem. Is it feasible to raise meat in the space farm, when space in the farm is at such a premium? The ideal animal must have high productivity. For instance, if you have a herd of cattle, only 20 percent of its mass can be harvested as meat per year. But chickens and rabbits reproduce so fast and grow so rapidly that a herd of either animal can produce five times its initial weight in edible meat over a year.
And for dairy:
There is the question of which ruminant to choose. The two most common milk-producing ruminants are the cow and the goat. Cows weigh ten times as much as goats and eat ten times as much feed. But a cow will produce only four times as much milk as a goat. For a given amount of feed, a goat will produce more than twice as much milk as a cow.
So essentially, cows are out, goats chickens and rabbits are in. This is mainly due to the space required to not only house them, but the space required to grow specific food for them. This in a way, rules out domesticated pets.
However, there is a twist to the final point about space colony pets, the article Spiders Will Make Great Pets for Space Colonists (Winslow), suggests spiders may make great pets - they've been taken in space before and did fine (maybe not for everyone).
A lot of waste plant material could be decomposed by the use of fungi (which are neither plant nor algae), namely mushrooms, according to the thesis Colonization: A Permanent Habitat for the Colonization of Mars, which in itself would provide another food source.