Alterations in the Colonic Microbiota of Pigs Associated with Feeding Distillers Dried Grains with Solubles

Abstract

In an effort to reduce feed costs, many pork producers have increased their use of coproducts of biofuel production in commercial pig diets, including increased feeding of distiller's dried grains with solubles (DDGS). The inclusion of DDGS increases the insoluble fiber content in the ration, which has the potential to impact the colonic microbiota considerably as the large intestine contains a dynamic microenvironment with tremendous interplay between microorganisms. Any alteration to the physical or chemical properties of the colonic contents has the potential to impact the resident bacterial population and potentially favor or inhibit the establishment of pathogenic species. In the present study, colonic contents collected at necropsy from pigs fed either 30% or no DDGS were analyzed to examine the relative abundance of bacterial taxa associated with feeding this ingredient. No difference in alpha diversity (richness) was detected between diet groups. However, the beta diversity was significantly different between groups with feeding of DDGS being associated with a decreased Firmicutes:Bacteriodetes ratio (P = .004) and a significantly lower abundance of Lactobacillus spp. (P = .016). Predictive functional profiling of the microbiota revealed more predicted genes associated with carbohydrate metabolism, protein digestion, and degradation of glycans in the microbiota of pigs fed DDGS. Taken together, these findings confirm that alterations in dietary insoluble fiber significantly alter the colonic microbial profile of pigs and suggest the resultant microbiome may predispose to the development of colitis.

Fig 1. Feeding increased insoluble fiber to pigs alters beta but not alpha diversity in the colonic microbiota.

(a) Rarefaction curves comparing alpha diversity (chao1) of colonic microbiota samples from pigs fed either Diet 1 (no DDGS) or Diet 2 (30% DDGS) and revealing no significant differences in richness (P = .736; n = 10 samples per diet group). (b) PCoA plot demonstrating significant beta diversity (Bray-Curtis dissimilarity) between diet groups (P < .001).

Fig 2. Linear discriminant analysis reveals predicted biological effect sizes of differential taxa in microbiota samples from pigs fed different amounts of insoluble fiber.

(a) Cladogram revealing statistically and biologically consistent differences in detected taxa between colonic content samples from pigs fed no DDGS (Diet 1) or 30% DDGS (Diet 2) according to LEfSe. Differences are represented by the color of the diet group in which specific taxa were most abundant (Red = Diet 1, Green = Diet 2) and the diameter of each circle is proportional to the relative abundance. At the phylum level, Firmicutes were more abundant in samples from pigs fed Diet 1 whereas Bacteroidetes were more abundant in samples from pigs fed Diet 2. (b) Histogram of linear discriminant analysis (LDA) scores computed by LEfSe revealing differentially abundant taxa in the microbiota of the two diet groups including overabundance of Prevotella spp. and depletion of Lactobacillus spp. in pigs fed 30% DDGS (Diet 2).

Fig 3. Feeding increased insoluble fiber was associated with shifts in the relative abundance of major phyla in microbiota samples.

Stacked bar charts representing proportional abundance of major phyla in the colonic microbiota of twenty 9-week-old pigs fed either no DDGS or 30% DDGS for 5 weeks. Firmicutes:Bacteroidetes ratios were significantly lower in pigs fed 30% DDGS (P = .004).