There are a few ways to do this, but I think the first thing that should be asked is if you care that it's a shell script or if using something else would be fine. (I.E python).
If this is for a class assignment or something where you have to use a shell script, you can use grep to find lines that begin with Organism and/or use sed to do something like s/Organism:([\S]+)^/\1/ as a regular expression to capture the directory name, and a similar regular expression can be used to snag whatever you want from the header.
There are probably like 50 ways to go about this though.