Thermal manipulation impact on microbiome in chickens
Fertile broiler eggs were incubated under either thermal manipulation (TM: 39 C and 65% relative humidity for 18 hours daily from embryonic days 10 to 18) or standard control conditions (CON: 37.8 C, 56% relative humidity). After hatching, male chicks were exposed to either chronic heat stress (CHS: 35  0.5 C for 5 days starting at day 18) or maintained at thermoneutral temperature (24  0.5 C). Cecal samples were collected on day 22 for microbiome analysis. The V3-V4 region of the 16S rRNA gene was amplified and sequenced using the Illumina MiSeq 2  300 bp paired-end protocol. Sequencing data were processed and analyzed using QIIME 2 with taxonomic assignment against the SILVA 138 database.