The lagging annotation of bacterial genomes and the inherent genetic complexity 
of many phenotypes is hindering the discovery of new drug targets and the 
development of new antimicrobials and vaccines. Here we present the method 
Tn-seq, with which it has become possible to quantitatively determine fitness 
for most genes in a microorganism and to screen for quantitative genetic 
interactions on a genome-wide scale and in a high-throughput fashion. Tn-seq can 
thus direct studies in the annotation of genes and untangle complex phenotypes. 
The method is based on the construction of a saturated Mariner transposon 
insertion library. After library selection, changes in frequency of each 
insertion mutant are determined by sequencing of the flanking regions en masse. 
These changes are used to calculate each mutant's fitness. The method has been 
developed for the Gram-positive bacterium Streptococcus pneumoniae, a causative 
agent of pneumonia and meningitis; however, due to the wide activity of the 
Mariner transposon, Tn-seq can be applied to many different microbial species.