Cecal metagenome and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber...

This study evaluated the effects of dietary fiber supplementation on broiler gut health during a subclinical enteric challenge. Birds were assigned to either an unchallenged control or a challenged control, followed by six dietary treatments applied to challenged birds. These treatments included 3% oat hulls (OH), 3% soy hulls (SH), and four combinations of 1.5% OH or SH with 1.5% wheat middlings (WM) or sugar beet pulp (SBP). A randomized complete block design was used with 2,160 day-old YP × Ross 708 male broiler chicks allocated to eight treatments, each with nine replicate floor pens and 30 birds per pen. Birds were inoculated with Eimeria followed by Clostridium perfringens, and cecal samples were collected at 21 days of age for shotgun metagenomic and transcriptomic analyses. The enteric challenge significantly reduced microbial diversity, depleted butyrate-producing bacteria, and enriched pathways associated with bacterial growth and virulence while triggering inflammatory signaling and suppressing proliferative pathways in the host. Supplementation with dietary fiber modulated these responses through distinct yet complementary mechanisms. The group receiving OH with WM enriched butyrate-producing bacteria, including Faecalibacterium prausnitzii, reduced C. perfringens abundance, and downregulated inflammatory pathways. Birds fed OH with SBP showed increased populations of lactic acid producing bacteria and Bifidobacterium animalis while suppressing TNFα, NF-κB and IFNγ signaling. Diets containing SH combinations enhanced metabolic pathways related to pyruvate fermentation and stachyose degradation, primarily driven by Lactobacillus species. Despite having distinct microbial compositions, all fiber treatments restored epithelial proliferation pathways in the host transcriptome, indicating convergent potentially beneficial effects on intestinal health. Integration of bacteriome and transcriptome data revealed coordinated relationships between specific bacterial species, including Stutzerimonas stutzeri, Bacteroides caecae, and Eubacteriaceae bacterium ES3, and host genes involved in immune function and energy metabolism. These findings provide a mechanistic framework for developing targeted nutritional strategies using specific fiber combinations to enhance gut resilience in antibiotic-free broiler production systems.