This is a protocol to generate axenic\u00a0fly cultures by sterilizing embryos. It is part of the manuscript: Gon\u00e7alves et al. Commensal bacteria and essential amino acids control food choice behavior and reproduction. Plos Biology. 2017 Apr 18.The protocol was adapted from:Wayland MT, Defaye A, Rocha J, Jayaram SA, Royet J, Miguel-Aliaga I, et al. Spotting the differences: Probing host\/microbiota interactions with a dedicated software tool for the analysis of faecal outputs in Drosophila. J Insect Physiol. 2014;69: 126\u2013135. doi:10.1016\/j.jinsphys.2014.05.023with the help of the Leulier laboratory.