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

Authors: TABISH, R - Auburn University; LIN, Y - Auburn University; ROCHELL, S - Auburn University; PACHECO, W - Auburn University; BAILEY, M - Auburn University; DOZIER,III, W - Auburn University; Robinson, Kelsy; HAUCK, R - Auburn University

Submitted to: Poultry Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/19/2026
Publication Date: 6/4/2026
Citation: Tabish, R.W., Lin, Y., Rochell, S.J., Pacheco, W.J., Bailey, M.A., Dozier,III, W.A., Robinson, K., Hauck, R. 2026. Cecal metagenome and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations. Poultry Science. 105: 107151.
DOI: https://doi.org/10.1016/j.psj.2026.107151

Interpretive Summary: Clostridium perfringens is a gut infection that causes major economic losses in broiler production by slowing growth, reducing feed efficiency, and increasing sickness and death. When certain strains multiply in the small intestine, they release toxins that damage the intestinal lining and interfere with nutrient absorption. Dietary fiber can influence the gut microbiome and help protect birds during mild infections. Insoluble fiber supports a healthier gut lining and can make it harder for harmful bacteria to attach, while soluble fiber is fermented in the ceca to produce short-chain fatty acids that reduce pathogens. This study evaluated how different types of dietary fiber affected broiler gut health during a subclinical challenge. Analysis of samples collected at 21 days showed that fiber supplementation altered the gut microbiome and supported beneficial pathways involved in repairing and maintaining the intestinal lining, suggesting positive effects on overall gut health.

Technical Abstract: Growth rate depression and an increased mortality are often associated with necrotic enteritis in broiler chickens. Nutritional strategies have potential in mitigating these negative effects. Addition of insoluble fiber at small inclusion rates (2.5-3.0%) to corn-soybean meal diets extends retention time in the gizzard, increases HCl production in the proventriculus stimulating pepsin activity and other endogenous enzyme secretions, which enhances nutrient digestibility. Due to increased nutrient digestibility and changes in pH, the microbiome profile may be altered reducing the colonization of Clostridium perfringens. The type of dietary fiber may also influence the microbiome profile thereby providing protection to the broilers when exposed to sub-clinical infections through various mechanisms in the gastrointestinal tract. Dietary fiber has been studied as one of the potential solutions to influence gut physiology and the microbiome during enteric challenge. Insoluble fiber sources can stimulate gizzard development, lower gizzard pH, and modulate digesta transit, improving digestive function and creating conditions less favorable for pathogen proliferation. This study investigated the efficacy of various dietary fiber sources and combinations in mitigating subclinical enteric infection in broilers. Using a randomized complete block design, 2,160 male broilers were assigned to eight treatments: unchallenged control, challenged control, and six fiber-supplemented diets containing oat hulls (OH), soy hulls (SH), or their combinations with wheat middlings (WM) or sugar beet pulp (SBP). Birds were challenged with Eimeria spp. followed by Clostridium perfringens for shotgun metagenomic and transcriptomic analyses in cecal samples at 21 days of age. 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 TNFa, NF-'B and IFN' signaling. Overall, these findings reveal how different fiber sources affect the cecal environment through distinct but complementary mechanisms under a challenge condition. All fiber combinations had similar host responses, despite having distinct microbial compositions, notably reduced inflammatory signaling and enhanced epithelial proliferation.