By the past, studies have shown that diet modulate intestinal microbiota. Our objective was to compare intestinal microbiota composition of healthy subjects, according to food groups’ consumption. Our study includes 134 individuals from the Milieu Intérieur Healthy Donor Cohort, mean age 40.4y; 57.5% women. Eating habits were assessed using a food frequency questionnaire. Composition of the faecal microbiota was established by 16S rRNA gene sequencing. OTU abundance was log10 transformed and OTUs were grouped by phylum and genus. We compared taxa abundance according to eating habits of subjects (ANOVA tests –age and gender adjusted). Compared to individuals that consume more frequently the food group concerned, those who eat less often fish had more Eubacterium spp., Ruminococcus spp., Streptococcus spp. and Actinobacteria. Those who eat less often cheese had less Coprococcus spp., Faecalibacterium spp., Prevotella spp., and Bacteroidetes, and more of Actinobacteria and Verrucomicrobia. Those who eat less often deep-fried foods had less Coprobacillus spp., Turicibacter spp. and Tenericutes. This preliminary study highlights associations between eating habits and microbiota composition. Investigation of associations between gut microbiota composition and diet patterns rather than specific food compounds could be useful to identify microbiota/nutrition signatures related to health