In our modern world with clean water and waste disposal we keep at arms length many diseases. Even just a few hundred years ago those that considered themselves the height of civilisation threw their waste out of the window into the gutters. Disease was rife and diseases spread rapidly wiping out thousands of people.
Even animals know that they need to keep their waste separate from their living accommodation and generally have their own toilet spaces.
If the sanitation systems break down and your waste in not collected and processed for you then you need to handle your own. Urine can simply be put on the ground for the plants but solid waste needs to be handled safely, (not handled). At the very least you can dig a hole in the ground out of the way and put your waste there. It is not perfect but as long as it is buried away from foodstuffs and the water supply you should not have any issues.
However, there are ways to utilise the waste, we will have some articles on better and more efficient ways of handling waste.