Having the exact salt in the same database as the user data defeats the purpose of the salt.

Normally you have a global salt, somewhere in your source-code, which you combine with the per-user generated salt. It also doesn't have to be something obvious in the database (like a column named user_salt :)), you could just use something like HMAC_MD5(global_salt, email + username + joined_date) for each user.

Of course, this may seem like security by obscurity, but even in the case of SSH you keep your private key safe and as a business if you have both your database and your source-code compromised, you're fucked anyway.