Over millions of generations, natural selection has favored those microbes that could make the fruit objectionable or unusable to larger organisms. Methods used by the microbes include toxins, antibiotics, and substrate degradation. Once a fruit becomes ripe, many chemical defenses against microbes break down. Ripe fruit is heavier and therefore it falls to the ground more often. Abrasion often occurs when the fruit has contact with the ground.
Animals are also much more interested in ripe fruit and small nibbles can penetrate the skin.
Whatever the source, microbes soon enter the fruit and begin their work to render the fruit inedible. One method used by microbes to ward off larger organisms, is nutrient alteration. Microbes rapidly convert the nutrients present in the fruit and form inedible, unwanted, or toxic compounds. Humans will not eat a rotten apple because the nutrients have been altered. The second method, most often used by bacteria and fungi, produces toxicants.