Fastq files used for the microbiome profiling of the terminal ileal and caecum content. Sequencing of the terminal ileal content was performed at the Institute Hospitalo-Universitaire Méditerannée Infection, Marseille, France. Sequencing of the caecum content was performed at Genoscreen, Lille, France The sequencing methodology is described on the methods part of the paper "A physiological mouse model of severe acute malnutrition reveals prolonged dysbiosis and altered immunity under nutritional intervention, Hidalgo-Villeda et al.". The metadata.xlsx table present the description and correspondance of each fastq files.