I am not sure if there has been one microbe that has lived the longest. But there are a group of microbes called spore formers that can survive for really long times.
Spore formers are microbes that can package themselves into a spore, or tough shell. While in the shell they can hibernate and survive without nutrients or water. They can even survive really hot, or really cold conditions. When they sense conditions that they like-plenty of moisture, warmth (but not too hot), and lots of nutrients, they can burst from their shell and start growing again. They can survive cleaning in dairy processing facilities and survive in dairy powders for a very long time.
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Marcello commented on :
On a test that I did on a sample of milk for cheese I have found a population of lactobacillus able to survive even after a year and a half.