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When a species of bacteria is referred to by its strain, are they a clone of single founder or is a certain amount variation allowed?

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In theory they're clones, but depending on the age of the strain(some strains are surprisingly old: ~40 years) there's variation inside strains.

The reverse is also true. Bacteria from a single species are isolated twice and named different things by different labs and the mistake can take years to even find, much less correct.

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Bacteria effectively clone themselves so theoretically all clones are identical. However like every organism they're subject to Darwinian evolution so there's always a chance a random mutation happens. Since bacteria usually reproduce fast the rate of these mutations can happen fast resulting in the strain evolving to a (slightly) different strain.

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