With my heart we have echocardiograms from before and after the antibiotics and it went from normal with good parameters to abnormal with questionable parameters. Things like E/A reversal, a large increase in deceleration time, and a significant decrease in mitral valve bloodflow velocities. These are tell-tale signs that your heart is starting to struggle that usually aren't seen until like middle aged diabetics or later on for non-diabetics. But I'm 32, and previously above average fitness.
Likewise the food sensitivity reactions are mostly diagnosis by symptoms. I've had a mild elevation in tryptase during a reaction but everything else has largely been normal.
I used to take supplements but they never really seemed to do much. When I took things I needed because of malnutrition there were improvements but that was about it. Subjectively I would say I felt more energetic while on B complex and L-Carnitine but I eventually developed a sensitivity to those medications, as I do with anything I continually intake, because my immune system's mechanism of tolerance has been disrupted by the antibiotics (and maybe something genetic who knows).