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I've seen a number of animals - dogs, cats, squirrels, ducks and geese, etc drink from puddles, some of them were muddy, others had green flora growing under water. Same goes for lakes and rivers. A human would not drink that. Do animals experience gastrointestinal discomfort or can they die from drinking water like that?

At the same time I hear about the problem of "clean water" in 3rd world countries and how diarrhea is the #1 killer of children under 5.

Are humans the only animals that require a certain purity of their drinking water? Why is it that a dog can drink from a puddle, but a human is likely to get sick from doing the same? Do baby animals get sick from drinking "dirty" water?

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Animals do sometimes experience health problems from microbiologically polluted water. But they drink it, because they probably have not so many options to choose from as humans have. Additionally, wilderness is very harsh, sick animals get eaten by predators quickly, so the short term evolutionary selection pressure in wilderness works wery strongly in favor of good immunity in animals. So yes, I would expect animals would be a little less sensitive than humans, but still susceptible to ilnesses. But i quickly google examples about dogs:

"Giardia and Cryptospori-dium ... can cause inflammation of the intestinal tract and diarrhea when in ­gested by dogs (or people) even in small numbers. Most dogs with healthy im ­mune systems are able to recover from this infection but severe diarrhea may, in some cases, lead to dehydration and significant illness. Puppies and older dogs with other un ­derlying health issues may be more severely affected. Leptospirosis is a less common ... illness transmitted by bacteria. ...(It) may lead to fever, lethargy, vomit ­ing, kidney failure, liver failure, and even death in some untreated individuals."

Another webpage talks about wildlife water-borne ilnesses. Giardiasis, leptospirosis and tularemia affect animals as well as humans.

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Also, I guess civilisation would have it's effects on the human immune system (both positive and negative).

The more exposed you are to microbiological pathogens, the better the chance of developing a more robust immune system.
In a very civilised (or rather a very clean) environment, humans would not be exposed much to external pathogens and hence would not have developed immunity to many of the diseases caused by those pathogens.

In comparison, people who live in "less clean" environments (take some of the 3rd world countries for example), would be exposed to a higher level of pathogens and would naturally develop immunity to more diseases. There's a reddit discussion on this.

The same applies to humans vs animals I guess. Animals don't usually live in artificially clean environments and hence develop a better immunity.

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I wouldn't say that a human is "likely" to get sick by drinking from a puddle, I'd say "at some risk". It isn't desperately dangerous, although don't take that as a recommendation. There are many infections you can get from water (bacterial, viral, amoebal, and I presume fungal). You don't want to risk them, but probably won't actually encounter them in that puddle in your garden you see your dog drinking from. If the water is stagnant then the list of things in it that might hurt you is longer than if it's flowing. If you can avoid the mud, and anything that's been standing long enough to grow algae, fresh rainwater is a pretty good bet as these things go.

The same is true of other species, but the risk per drink is lower, since they drink it more and develop resistance to more of the things on the list. Humans are no different. For example some areas tend to have Hepatitis A in the tap water. The local population is immune once they've been infected once, and most childhood infections cause no symptoms, so it's not a problem for the locals. But to an unvaccinated visitor, the water's not safe. Hep A normally won't kill you, but is still well worth avoiding since it will make you sick for several weeks.

So basically, humans drink clean water because we can, not because we absolutely need to.

The lifespan of humans living "in the wild" (that is, populations prior to or independent of human agriculture) is pretty well agreed to be rather less than that of typical modern lifestyles. Water-borne disease is only one of many things responsible for that. The expected lifespan of a person used to purified water and so on, dropped into "the wild", is even lower again.

The "clean-water" problem in developing countries is primarily one of high population, relative to what the same area could possibly support in the absence of agriculture and other technology. The biggest risk of water-borne disease comes from contamination by human waste (although there are other sources, for example rats can contaminate water with Weil's disease). A small group of humans living in a large area doesn't have to worry about human contamination, they just drink upstream of where they defecate. This strategy doesn't help much once the population is dense enough that someone else is doing the same thing 20 metres away from you.

And of course, human agriculture also supports a much higher rat population than would otherwise be present (they're omnivores too, so they'll eat pretty much any food humans do). I suspect most human disease can be blamed on agriculture one way or another: if not on the animals then on the close-quarters living. If the population of humans was closer to what it was in the palaeolithic (a few thousand or tens of thousands of people in Europe), and was used to drinking from natural sources, then the water would be mostly (not entirely) safe.

So it's not so much that humans need perfectly clean water, it's that humans have figured out how to live in populations so large that we tend to make all the nearby water particularly dirty. Other species aren't completely unaffected by this, but they are less affected because our waste is specifically contaminating the water with diseases that affect us.

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