Patients with Alpha-1 Antitrypsin Deficiency (A1AD) have abnormally low levels of the protein Alpha-1 Antitrypsin (AAT) in their blood, because of a double mutation that makes the protein misfold and instead collect in the liver (sometimes even causing cirrhosis). The currently accepted single dosage (SD) of AAT supplements does not produce AAT blood concentrations anywhere near normal levels; they typically only reach the effect of having a single mutation. Some have therefore advocated for a double dosage (DD) of these treatments, which generally would be enough to approach these normal concentrations. Levels of cytokines, produced by the immune system in response to an attack, have already been observed to drop dramatically when A1AD patients consuming single dosage started taking double dosage, and then either remain the same or increase again upon return to a single dosage regimen. In this study we administer the same dosage sequence to A1AD patients (SD, DD, SD) for one month each and view the effects on their lung microbiome and metabolome. We analyze both at the end of each stage, comparing and contrasting and discovering potential biomarkers for each stage, and concluding with a discussion of potential implications.