16S rRNA sequencing data for the manuscript entitled with " Microbiota signatures associated with invasive candidiasis caused by Candida albicans in the gastrointestinal tract of immunodeficient mice". The experiments included SC5314- or HLC54-infected Ragrc (Rag2-/-il2rc-/-) mice (n=7) preinfection (D0), at day 5 (D5) and 12 (D12) post-infection. (AE 161 is indicated one of two independent experiments )