When handling pigeon poop, always wear a dust mask. There are things in pigeon poop than can really mess up the human body, especially if inhaled as a dust. I own pigeons and won't get into the scientific medical terms, but their droppings can be a health hazard.
My Dr. knows I own pigeons so if I ever get something strange, he has a heads up about the pigeons.
I would recommend wearing a dust mask when handling any animal waste that will be used for fertilizer. A paper mask, 99 cents. A doctor visit, $100+.