Something to think about you could do this in the way of Star Trek Voyager. Where they had enough food stored at first but then had to add too for a long journey. How about this starting with a small diverse flock say 15 total. You will have ship stores food so will not need much from what is brought on for colony. Then if colony is many light years away you will breed said animals replacing some used stores and biulding flock slowly till you reach destination of the colony which by that time you could have a flock of 50 to 100.