High-throughput applications such as next-generation sequencing are frequently applied in modern biological and medical research allowing for comprehensive studies at the scale unattainable by classical techniques. Recent technology advancements enable protein translation measurement on the mRNA level by massive sequencing of ribosome-captured messenger RNA footprints (i.e. ribosome profiling). This project proposal is situated on the crossroads between the state-of-the-art fields of highthroughput sequencing and proteome analysis. More specifically, translational control of small open reading frames (sORFs) of the pathogen will be studied during bacterial infection. To do this, we will employ tailored proteome- and genome-oriented technologies enabling the study of the bacterial sORF translatome and peptidome in the context of a host. Changes in sORF gene expression upon bacterial infection (e.g. Salmonella), leading to the persistence or clearance of the pathogen and a host cell response will provide an unprecedented understanding of the role of sORF encoded polypeptides and their interactions between pathogen and host, next to the identification of new pathogen virulence factors enabling a more rapid and specific detection of infectious diseases.