If we know that every organism's external appearance and capabilities are governed by it's genetic material, then if we change the genetic material, we basicaly mutate the organism.
Bacteria and especially viruses have a very simple genetic make-up for example most bacteria have DNA only thousands of nucleotides in lenght, compared to the millions of nucleotides that make up a sinle human gene. So my first point is: Bacteria and viruses need a very small change in genetic material to mutate them considerably.
Now, to see how these changes are brought about let's take viruses first.
Viruses are acelular, they are basically a packet of DNA or RNA wrapped up in a protein coat. They have no organelles of their own so to multiply they must invade a cell and hijack its biochemistry to make multiple copies of their DNA or RNA to make lots of themselves. Now, suppose two different strains of the similar virus attack the same cell! e.g. H5N1 (bird flu) and human flu. As copies of both the viruses' DNA are floating about they become mixed-up the terrible result is a virus, incurable like H5N1 but can spread like human flu and given the thousands of virus patricles in an infected humans' body and the millions of cells that make that body up, the above mix-up is most likely (don't panic this hasn't happened yet but if it does that's how it'll happen!)
As for bacteria, well as I said they are pretty simple organisms so they don't have mating rituals or exchange phone numbers, they go straight for the exchamge of genetic material, which they do with great ease through straw-like projections called pilli. Once new DNA is inside the bacterium, it will be expressed.
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