Haskell, 183
=================
<!-- language-all: lang-hs -->

Assuming the file is in <code>file.txt</code>!

    import Data.Char
    import Data.List
    r=group.sort.(++['a'..'z'])
    u=dropWhile(==' ').concat.fmap(drop 1.maximum).transpose.fmap r.lines.fmap toLower
    main=fmap u(readFile"file.txt")>>=print

If file.txt contains, for example

    abcde
    abcdef
    aaf

The script will output

    "aabcdef"