Cows are given antibiotics to prevent diseases (and to promote muscle growth, although doing so is now banned in the EU and China). They shit out a large fraction of the antibiotics, and these kill soil microbes (and make the survivors antibiotic-resistant, which is absolutely great news for public health). Without soil microbes to process them, the organic matter in litter does not stay in soil and instead gets respired into the atmosphere (accelerating global warming) or washed into lakes and rivers (causing eutrophication).