Answer: Testing
Longer explanation: There are different parts that make up each organism. A bacteria will have an outer surface made of specific proteins and sugars that are put together in a certain way, while fungus and viruses will have a different specific set of proteins/sugars/fats put together in a different way. Not only that, but different branches of the “tree of life” have certain compounds or markers (IE ribosomes), and within branches, the set of genes that each organism has will be generally unique. Bacteria 1 might have genes A, B, C, and D, while Bacteria 2 has genes A, D, H, and L, and Bacteria 3 has genes L, P, S, Y. By looking at the products of those genes, like enzymes, we can tell if an organism has a certain set of genes.
As a real life example for the lab I work in, when testing for Salmonella, we first use an enrichment broth based on the substance that may be contaminated. We then transfer some of that enrichment to a second type of broth that will inhibit most bacteria besides Salmonella, because there are certain compounds that Salmonella can tolerate, while other bacteria cannot. From there, we put the second broth onto agar plates that also inhibit non-Salmonella species, and since there is some variation even within Salmonella, these plates will change color based on the species of Salmonella that may be present. To confirm that yes indeed, this is Salmonella X vs Salmonella Y, we can then move on to another agar that tests for several things at once, giving us a better profile of what type of Salmonella it is (and isn’t). Then, we can do further testing with a larger number of tests – what sugars can be used, what proteins are produced, etc.
All of that will allow us to know this is Salmonella typhi, or Salmonella gaminara, or Salmonella mbandanka, etc.
So yes, we can tell the difference (in most cases), and we do so frequently.
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