The host environment reshapes microbial genetic accessibility to transposon mutagenesis in the chicken gut microbiome
Himar1 transposon libraries were generated from chicken gut microbial communities under two conditions differing only in the site of conjugation: ex vivo mating of the MAGIC donor strain with cecal communities on aerobic agar (M1, M2, and M3), and in vivo delivery by oral gavage into live broiler chickens (M4, M5, and M6). Both arms were processed through an identical genome-resolved pipeline mapping insertion sites to 12,339 metagenome-assembled genomes (MAGs).