Abstract The cecum plays a critical role in maintaining microbiome eubiosis and fiber fermentation. Pigs have a symbiotic relationship with their microbiome, allowing them to garner energy from short chain fatty acids (SCFAs). Understanding differences in community and function of the mucosal and digesta microbiome is critical to improving fiber utilization in swine. Our objective was to investigate how the microbiome in both the mucosa and lumen of the cecum are affected by increasing levels of dietary fiber derived from various corn coproducts. It is hypothesized that corn-based fiber sources with increased levels of insoluble dietary (IDF) will result in a more diverse cecal mucosal and luminal microbiome. To accomplish this, pigs were assigned to one of 7 dietary treatments: a fiber-deprived control CTL; 1% total dietary fiber (TDF), and 6 coproduct diets, dehulled degermed corn (DHDG; TDF=2.4%), ground corn (COR; TDF=5.6%), corn gluten meal (CGM; TDF=6.7%), dried distillers grains (DDGS; TDF=9.5%), high protein dried distillers grains (HP; TDF=14.0%), and corn bran (BRN; TDF=17.9%). After 31 days pigs were necropsied and tissue and digesta from the cecum were collected for metagenomic analysis. Features from the metagenomic analysis were normalized using the center log fold ratios (CLR) relative to the geometric mean of all features and fitted with a linear model. Correlations were calculated with Pearson’s correlation between the CLR of the metagenomic feature and SCFA concentrations. Differences were considered significant if P or Q values were 0.05 and trends if 0.05 ≥ P or Q 0.10. Results demonstrate distinct microbial communities in the mucosal and the lumen of the cecum. While the lumen microbiome had greater diversity than the mucosal associated microbiome as demonstrated with alpha diversity measurements (P 0.05), the lumen microbiome had greater similarity within and between dietary treatments compared to the mucosal microbiome as demonstrated by the principal coordinate of ordinance analysis (P 0.001). Luminal species such as Faecalibacterium prausnitzii and Cloacibacillus porcorum had positive correlations to SCFA production (P 0.05; r .70). Likewise, luminal species like Bifidobacterium thermophilum boum and Selenomonas also had positive correlations to SCFAs (P 0.05; r 0.70), they are likely connected through cross-feeding interactions. Metagenomic assembled genomes, provided insight into the functionality of the mucosal microbiome ability to ferment corn derived fibers and host mucins. Diets with increased levels of IDF had more diverse microbiomes with greater abundance of beneficial fiber fermenting bacteria (P 0.05; Q 0.05). While CTL fed pigs experienced a reduced abundance of perceived beneficial bacteria in the mucosa (Q 0.05), such as Lactobacillus and Bifidobacterium. Overall, this study provides insight into how insoluble corn-derived fibers influence the different mucosal and luminal microbiomes and their functional potential.
Miller et al. (Wed,) studied this question.