Another way to replenish you gut flora is by utilizing raw, cultured veggies. Mmmmmm saurkraut.
Consider getting as much organic produce as possible because it supplies more nutrition (especially when utilized raw).
Also, when using nuts it is very important to soak them for 24 hours first to get rid of the tannins (enzyme inhibiors) so that you can digest them properly and get all of the nutrition that you have coming to you.