[vox-tech] Groups and Users?

[ALLO (Alfredo Lopez)]

I have a couple of Bioinformatics applications that are accessed through a
Web server.  Some of the folders have as the User and Group: root; others
have:1000 and another set has User:543  Group:63. 
Why do I have this weird (at least to me) collection of users and groups?  I
guess that those that have root, have it because I was root when I created
them, but the others? 
Do I need to change everything to root or something else?  Does it matter?
Is there a "good practice" rule that I can follow?  I will appreciate any
insight, links to sites where I can learn more about this, book suggestions
etc.

Thanks a lot!
Alfredo