The protocol would not be much different. Instead of the enzymatic digestion, just use the mechanical lysis of cells. Rest of the procedure would be the same since it is a column based extraction method. However, you might need to do few additional steps to remove any inhibitory chemicals which might be present in the faecal samples. But I don't think there will be any problem of inhibition if you don't have any additional wash step. You will get good quantity and quality with DNeasy kit.