Decoding early-life gut microbiota: discrete and reproducible maturation stages in broiler chickens

Abstract Background: The intestinal microbiota of broilers undergoes substantial changes during the first two weeks post-hatch, however the temporal organisation of this early-life microbial maturation remains poorly characterised. Therefore, we performed daily sampling of ileal and caecal contents between days 2 – 11 post-hatch, with additional samples taken on days 22 and 29, to resolve distinct microbial maturation stages using Dirichlet multinomial mixtures (DMM) clustering with high temporal resolution. Picrust2 was additionally used to investigate predicted functional changes across maturation stages. Results: Two ileal gut microbiota (GM) maturation stages were identified, characterised by a shift in predominance of Enterococcaceae to Lactobacillaceae around 11 days post-hatch. In contrast, the caeca revealed four distinct GM maturation stages. Enterobacteriaceae dominated caecal GM maturation stage I (day 2 – 6) and linearly decreased across all subsequent stages. Concurrently, butyrate-producing Lachnospiraceae and Ruminococcaceae steadily increased with age. The high temporal resolution uncovered two distinct transitional stages in caecal microbial development between days 6 – 22, before reaching the most advanced maturation stage IV (day 22 – 29), which could largely be distinguished by the high abundance of obligate anaerobic, short chain fatty acid (SCFA)-producing Faecalibacterium . The four caecal microbiota maturation stages repeatedly appeared across three cohorts and two broiler genotypes, demonstrating that broiler microbiota maturation follows a conserved and reproducible developmental trajectory. Conclusions: Distinct and reproducible maturation stages occur in the ileal and caecal microbiota of broilers during the first two weeks post-hatch. The frequent sampling schedule applied in the current study provides a high temporal resolution insight into the taxonomic and functional fluctuations of the maturing gut microbiota, which can support further research on early post-hatch microbial modulation strategies.