The lungs are not sterile or free from bacteria; rather, they harbor a distinct microbiome
whose composition is driven by different ecological rules than for the gastrointestinal tract.
During disease, there is often a shift in community composition towards
Gammaproteobacteria, the bacterial class that contains many common lung-associated
gram-negative “pathogens.” Numerous byproducts of host inflammation are growth factors
for these bacteria. The extracellular nutrient supply for bacteria in the lungs, which is …