A deficiency was a lack of a certain biochemical compound in one's system.
In 2267, Spock speculated that Alexander likely had a biochemical deficiency relative to Platonius. Doctor Leonard McCoy later determined via a comparative test that he was unable to metabolize kironide due to a lack of pituitary hormone. (TOS: "Plato's Stepchildren")
In 2371, The Doctor speculated that a dirt-eating Kes might have a nutrient deficiency, as humanoids often craved foods with high concentrations of the vitamins or minerals they lacked. (VOY: "Elogium")