An interesting point about getting sick while training hard is the role played by glutamine.
Glutamine is indeed an amino acid essential to good health. What is very important about glutamine is that it is an amino acid in a group known as the branched chain amino acids.
The branched chain amino acids are important as they are a key pathway to centralized fatigue. Central fatigue is the long term accumulated fatigue you get from long races, extended days or weeks of hard training and other non-sporting forms of stress (work, school, social, anti-social, etc.). Central fatigue is not the tired feeling in your back and arms after a tough set of intervals where a few minutes of recovery will set you right. Central fatigue requires attention or it will compromise your season, or even career if neglected too much.
Back to glutamine, branched chain amino acids and central fatigue…
When we exercise, we burn carbohydrates, fat and protein for fuel. Each is ultimately broken down to a carbohydrate. Fats take a long time to become a carbohydrate, proteins less time. At very low intensities (i.e. walking or easy hiking) fat is consumed preferentially as there is no urgency to supply energy. As the aerobic demand increases and we need to produce energy faster (i.e. more power or speed) the balance shifts from fats to carbohydrates. Each person will differ in what percentages they use and what the end result is, but the pattern remains the same fats first, carbohydrates second. Dietary habits will affect this to some degree but not much.
There is always an underlying use of a small percentage of protein.
At high intensity race pace (from 15-20 minutes all out through to approximately 2-3 hours all out) protein contributes approximately 10% of this energy. As distances get longer than 2-3 hours the protein contribution will decrease unless it is being replaced through ingestion of a drink or solid food with biologically active protein. These are protein sources the body can digest quickly and easily (i.e. lactalbumin or egg white protein) rather than slow to digest sources (i.e. steak or plant sources).
Branched chain amino acids are used up preferentially over non branched chain amino acids as fuel sources due to their being easier to convert into carbohydrates for use in the muscles and brain. Where branch chain amino acids become important is when your blood amino acid content begins to get depleted, which is when you are working hard.
In your brain, branched chain amino acids need to be actively imported in the brain. The transport system that does this also brings in a few other molecules, and when the branch chain amino acids are lower in concentration these other molecules are brought into the brain in larger amounts. One of these is a precursor of serotonin, a central nervous system depressor. In elevated quantities this molecule will trigger a fatigue response; you will gradually loose coordination, muscular force, muscular speed and muscular power. This is a protective mechanism to protect your body from working so hard it causes itself some serious exercise induced damage.
In elite athletes with lab access, measuring the glutamine to glutamate ratio, sport scientists can advise an athlete when they are getting close to overtraining, burn out of just need a short break. It highlights the importance of hard work being balanced with recovery to produce optimal results.