It sounds like your rooster may be sick with a respiratory disease. Respiratory diseases are particularly common at this time of year, during cold and damp weather. It was a good idea isolating him from the other birds- this may help prevent the spread of the disease, though it is likely that your other birds have already been exposed.
It's possible that it is just dusty in the coop and may not be a respiratory disease. However, more birds would probably be affected if this was the case.
Viral respiratory diseases can't really be treated. Give supportive care, such as electrolytes, probiotics, and vitamins. Make sure that he is eating and drinking. This is all you can do if the disease is viral. If he gets worse, or doesn't get better, get antibiotics. Tylan50 injectable is one of the best antibiotics for respiratory diseases. You can also get a water soluable antibiotic like Terramycin or Duramycin, from a local feed store or livestock supply store. These should help if it is a bacteria-caused disease.
The unfortunate thing about respiratory diseases is that they may appear to have gone away, only to come back later, when a bird is under stress. Most respiratory diseases cause birds to become carriers, and they can pass it on to other birds. Many people choose to cull birds with respiratory diseases for this reason. But, this isn't often practical or desirable for a small backyard flock owner or an owner who cares a lot about their birds. If you decide not to cull, keep in mind that you should keep a closed flock (don't sell birds to other people), to prevent spreading the disease to other flocks.
Determining the exact respiratory disease, if it is a respiratory disease, is hard to do. He could have a mild disease, like Infectious Bronchitis, or the beginnings of a severe disease, such as Chronic Respiratory Disease.
Hopefully, it is only a mild viral disease. Or, best of all, it is caused by dusty conditions and will go away on its own. The above information is only information on what I belie to be the most probable cause (a respiratory disease).
Best wishes to you and your rooster!
