Subnetworks illustrate in vivo niche-specific pathways. A pathway-specific subnetwork indicating the importance and specificity of each pathway for the nasopharynx and lung niches is shown. For the tryptophan/tyrosine and IMP producing pathways, we identified two neighboring genes of unknown function (SP0049 and SP1378) with similar fitness defects as their direct neighbors on the chromosome (Supplemental Table S1), and thus we expect that they are equally involved in the respective pathways.