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Since I have seen many religious people drink fresh spring water, I assume that there is no concern regarding the kashrut of microorganisms in the water such as hydra and paramecia, among other similar creatures.

Similarly, certain products such as probiotics, commonly present in yogurt, contain bacteria. Some oral vaccines (It's been a while since I got the Sabin vaccine - I assume they still use it) contain viri. I assume that here, too, there is no concern regarding kashrut.

Why was there no concern considering that these are living "species"? Are they in its own non-animal category? Does the Talmud or other source discuss these? If so, where?

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    The overarching principle is that halakhah doesn't rely on instrumentation, but rather on shalta be-`eyna ("the apprehension of the [naked] eye"). In other words, if you can't see it, it's not relevant. Kol tuv. – user3342 Jul 13 '15 at 15:27
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This issue is the one behind the famous New York City non-Kosher water scandal. Basically, the issue is that there are tiny crustaceans in NYC tap water.

The Star-K gives a nice overview of the issue. In short, everybody agrees that if a micro-organism is too small to be seen without magnification, it does not cause any kashrut issue. On the other-hand, if you can see a small crustacean floating in your water, it is obviously not kosher.

The issue under debate in the New York case is over crustaceans that are large enough to be seen, but so small that they just appear to be white specks in the water. You wouldn't be able to tell what they are without magnification. In that case, there is a machloket over whether this causes a kashrut issue. As a result, at least the Star-K and the OU require tap water in New York City to be filtered.

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