Fiber deprivation and insoluble corn-based fibrous co-products modulate gastrointestinal mucosa-associated microbiota, extracellular matrix remodeling, and intestinal morphology in growing pigs

This study examined how insoluble corn-based fibrous coproducts (ICBF) affect gastrointestinal (GI) mucosal microbiota, gene expression, and intestinal morphology in growing pigs compared to fiber deprivation. Fifty-six gilts (26.7 ± 2.5 kg BW) were randomly assigned to one of seven semi-synthetic diets. Treatments included a fiber-deprived control (CTL;<1% insoluble dietary fiber [IDF]), and six diets where an ICBF replaced 30% of corn starch: dehulled degermed corn (DHDG; IDF = 1.7%), ground corn (COR; IDF = 4.7%), corn gluten meal (CGM; IDF = 5.2%), dried distillers grains (DDGS; IDF = 8.6%), high protein dried distillers grains (HP; IDF = 13.5%), and corn bran (BRN; IDF = 17.5%). Pigs were individually housed and limit-fed 2.4 times maintenance. On day 31, duodenum, jejunum, ileum, and colon tissues were collected. Microbial 16S rRNA sequencing of mucosal material, tissue transcriptomics, and histological analyses were conducted in various intestinal regions. Data were analyzed using mixed models with diet as a fixed effect and linear and quadratic contrasts to assess response IDF. A negative binomial model with FDR correction were used for operational taxonomic unit (OTU) analysis, and transcriptomics were evaluated with DESeq2 comparing ICBF sources to CTL (Q ≤ 0.05, |log2FC| ≥ 2). In the ileal mucosa, Shannon and Simpson diversity indices linearly increased with IDF%, while in the colon mucosa Chao1 and Shannon diversity responded quadratically (P < 0.05). Among the top 100 most abundant OTUs, 60 and 86 differed in ileal and colonic mucosa, respectively (Q < 0.05). In the ileum and colon, pigs fed low-ICBF diets (CTL, DHDG) had increased abundance of OTUs containing opportunistic or potentially pathogenic species (e.g., Enterobacteriaceae, Campylobacter, and Streptococcus). However, moderate-to-high ICBF diets, CGM, DDGS, and BRN, enriched mucosal-associated Lactobacillus, Bifidobacterium, and Akkermansia. In the duodenum and ileum, villous height had a positive quadratic relationship to increasing IDF, while the jejunum villous height linearly decreased (P < 0.05). Gene expression profiles revealed that moderate-to-high ICBF (DDGS, HP, and BRN) upregulated genes associated with cell structure and extracellular matrix (ECM) remodeling (TPPP3, MUC5AC, SERPINA1). Fiber-deprivation upregulated genes associated with ECM degradation (MMP9, MMP12) and collagen formation (COL26A1). Thus, both fiber deprivation and excessive ICBF can disrupt mucosal microbial and host homeostasis.