There are generally two reasons for discoloration and thickening of the nail plate on the toes, infection or chronic trauma.
An infection in the toenail could be caused by fungus, yeast, mold or less commonly, bacteria.
A nail biopsy and culture is the only way to correctly diagnose disorders of the toenail.
In the absence of an infecting organism, benign thickening due to low grade chronic trauma is the culprit.
Treatment of either of these problems is more successful in the early stages, once the entire nail plate is affected results of treatment are not as predictable.