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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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Whereas a clone (or clonal population) is the current population of individuals descended from a single particular ancestral individual, a strain can be understood as the whole line of individuals down and up to that single particular individual.

But as noted in the other answers, even though the isogenic character is often taken as a more or less tacit approximation, none of those two concepts forbid genetic variation or assume that all the individuals of the said clone or strain are isogenic.

The concept of species for microbial organisms is more intricate.

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