Abstract: A method for treating copper deficiency in a ruminant subject or a ruminant herd is dexcribed. In some embodiments, the method involves providing a sample from the subject or at least one subject in the herd; measuring an amount of (i) fungal infection in the sample; (ii) expression of tyrosinase (Tyr) in the sample, and/or (iii) expression of tyrosinase-related protein (Tyrp) in the sample; (c) estimating the level of copper deficiency in the subject or herd by correlating the measured amount to a reference; (d) calibrating a predicted effective copper supplementation dose based on the estimated level of coppery deficiency in the subject or herd; and (e) administering the predicted effective copper supplementation dose to the subject or at least one subject in the herd and/or inoculating the subject or at least one subject in the herd with a fungus or fungal isolate.