A nutritional deficiency may be due to a nutrient being omitted from the diet, adverse interaction between nutrients in otherwise apparently well-fortified diets, or the overriding effect of specific antinutrients. The latter two scenarios are difficult to diagnose, because diet analysis suggests a normal level of the nutrient(s) under investigation. Micronutrients such as vitamins and trace minerals are usually added to diets in the form of stand-alone micro premixes, so it is rare to see classic symptoms of deficiency of individual nutrients—rather, the effect seen is more commonly a compilation of many individual metabolic conditions. In many instances, a correct diagnosis can be made only by obtaining complete information about diet and management, clinical signs in the affected living birds, necropsies, and tissue analyses. Unfortunately, tissue, and especially liver and serum analysis, can be misleading, because relative to the time of initial occurrence of any deficiency, the bird often sequesters nutrients in the liver, and so even with deficient diets, liver assays show erroneously high values. This latter effect is most significant for minerals such as copper.
A diet that, by analysis, appears to contain just enough of one or more nutrients may actually be deficient to some degree in those nutrients. Stress (bacterial, parasitic, or viral infections; high or low temperatures; etc) may either interfere with absorption of a nutrient or increase the quantity required. Thus, a toxin or microorganism, for example, may destroy or render unavailable to the bird a particular nutrient that is present in the diet at apparently adequate levels according to conventional chemical or physical assay procedures.