Jejunal histopathology, 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; HOERR, F - Auburn University; Robinson, Kelsy; HAUCK, R - Auburn University

Submitted to: Poultry Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/1/2026
Publication Date: 6/17/2026
Citation: Tabish, R.W., Lin, Y., Rochell, S.J., Pacheco, W.J., Bailey, M.A., Dozier, III, W.A., Hoerr, F.J., Robinson, K., Hauck, R. 2026. Jejunal histopathology, metagenome, and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations. Poultry Science. 105: 107215. https://doi.org/10.1016/j.psj.2026.107215.
DOI: https://doi.org/10.1016/j.psj.2026.107215

Interpretive Summary: Clostridium perfringens is an intestinal parasitic infection that possesses significant economic significance to broiler production by decreasing body weight gain, increased feed conversion, and increased incidence of morbidity and mortality. Clostridium perfringens strains producing certain toxins and multiply to high numbers in the jejunum, their toxins cause extensive necrosis of the mucosa. This results in intestinal damage and nutrient malabsorption. 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. Insoluble fiber may be beneficial in altering mucin composition which may be advantageous in beneficial bacteria colonizing to the mucosa as mucins serve to protect the mucosa from pathogens. Due to its structural composition, insoluble fiber, may provide friction with the mucosal layer preventing pathogenic bacteria from colonizing. Conversely, soluble fiber sources are fermented in the ceca producing short chain fatty acids that can reduce the number of pathogenic bacteria in lower gastrointestinal tract. This study evaluated evaluating eight dietary treatments consisting of insoluble and soluble sources of fiber and the addition of an unchallenged control fed a diet without a supplemental fiber source and a challenged control without a supplemental fiber source included in the diet to analyze jejunal histopathology, microbiome, and host mucosal transcriptome.. Combinations of insoluble and soluble fibers such as OH-WM, OH-SBP and SH-WM provided the most significant protection against challenge-induced intestinal pathology. The observed effects were fiber-specific, with OH generally exhibiting stronger anti-inflammatory properties while SH more robustly enhanced oxidative phosphorylation and metabolic pathways.

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, and a multi-omics approach was employed to analyze jejunal histopathology, microbiome, and host mucosal transcriptome. Each fiber source altered the microbiome distinctively: OH increased Romboutsia sp., OH-SBP enriched beneficial Limosilactobacillus spp., and SH combinations enhanced butyrate-producing Dysosmobacter welbionis Transcriptome analysis revealed that fiber supplementation suppressed inflammatory pathways while upregulating cell cycle progression and DNA repair pathways. Integration of bacteriome with host gene expression data revealed coordinated associations, including a link between Glutamicibacter protophormiae, Spirosoma, Eggerthella, and Blautia through host genes, indicating a correlation of fiber-degrading bacteria with host lipid metabolism and extracellular matrix remodeling. Overall, these findings suggest that combining insoluble and soluble fibers may create a more resilient gut environment against enteric challenges through complementary mechanisms, with OH based combinations notably exhibiting reduced pathology, stronger anti-inflammatory response and suppression of opportunistic species.