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Background Salmonella  Enteritidis (SE) is one of the major causes of human foodborne intoxication resulting from consumption of contaminated poultry products. Genetic selection of animals that are more resistant to  Salmonella  carriage and modulation of the gut microbiota are two promising ways to decrease individual  Salmonella  carriage. The aims of this study were to identify the main genetic and microbial factors that control the level of  Salmonella  carriage in chickens ( Gallus gallus ) under controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines N and 6 1  were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce recontamination of birds by  Salmonella . Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition, using a 16S rRNA gene high-throughput sequencing approach. Results Our results confirmed that the N line is more resistant to  Salmonella  carriage than the 6 1  line, and that intra-line variability is higher for the 6 1  line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Among the 617 operational taxonomic units (OTU) observed, more than 390 were differentially abundant between the two lines. Furthermore, within the 6 1  line, we found a difference in the microbiota taxonomic composition between the high and low  Salmonella  carriers, with 39 differentially abundant OTU. Using metagenome functional prediction based on 16S data, several metabolic pathways that are potentially associated to microbiota taxonomic differences (e.g. short chain fatty acids pathways) were identified between high and low carriers. Conclusions Overall, our findings demonstrate that the caecal microbiota composition differs between genetic lines of chickens. This could be one of the reasons why the investigated lines differed in  Salmonella  carriage levels under experimental infection conditions.

Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens