Amount of bacteria is one thing. Type of bacteria is quite a different thing. Some bacteria will cause a problem when ingested by humans, while others won't. It would be useful to see a breakdown of amounts by type.
You make the basic point. There are bacteria all over everything all the time. The air is full of them. Ponds are full of them. But most are harmless.
Human waste is another matter. It tends to be filled with harmful bacteria. That's why it's OK to fertilize the fields with cow or horse manure, which team with bacteria, but you want to be careful about using human waste.
In places like India and China they do traditionally use human waste to fertilize the fields. But you have to adapt to it, and foreigners are likely to get sick if they eat raw fruit or vegetables for that reason.
So, the question is, what KIND of bacteria? Numbers are less important.