Illumina MiSeq paired end sequencing
Amplicon-based metagenomic sequencing (16S V3V4 region) of the chicken gut microbiota, from 1 to 21days of age with a Salmonella experimental infection performed at 7 days and inoculation of a candidate E.faecium probiotic strain from 1 to 6 days of age
Thirteen chicks were bred in isolator during 21 days and orally inoculated with the S. Enteritidis LA5 strain at day 7. Faecal samples were collected at 5, 7, 11, 14 days of age; caecal and mucus samples at 21 days of age. After total DNA extraction, performed using a QIAamp DNA Stool mini-kit, the gut microbiota composition was determined by 16S rRNA gene high-troughput sequencing.