Metagenomics Analysis of Broiler and Layer Chicks Cecal Content from High Fiber Diets

An experiment was conducted to evaluate the effects of feeding different concentrations of dietary fiber on cecal microbiota of broiler and layer chicks. The lower fiber diet was based on corn-soybean meal (SBM), and the higher fiber diet was formulated using SBM adding 60.0g/kg of dried distillers grains with solubles and wheat bran for days 1-12 that increased to 80.0g/kg for days 13-21. Treatment groups were randomly assigned to battery cages in a completely randomized design with 11 replicates of 8 chicks for each of the 4 treatments. Three ceca were collected from each replicate, one cecum underwent short chain fatty acids (SCFA) concentration analysis and the other two ceca underwent bacterial DNA isolation for terminal restriction fragment length polymorphism (TRFLP) and whole genome shotgun sequencing for metagenomics analyses. TRFLP analysis showed microbial differences due to diet (P=0.02) and bird line (P=0.03). Metagenomics analysis identified increases in relative abundance for species involved with polysaccharide degradation, Helicobacter pullorum and Megamonas hypermegale, for broilers fed the high fiber diet and layers fed the low fiber diet. These two treatments also had higher acetic acid and total SCFA based on the SCFA concentration analysis, and higher Firmicutes/Bacteroidetes ratios, which is a signal for decreased gut health. Finally, the metagenomics analysis also identified increases in species associated with inflammatory response, Campylobacter jejuni (broilers) and Escherichia coli (both lines), for chicks fed the higher fiber diet. In conclusion, our experiment suggests that increasing dietary fiber diet decreases chick’s gut health.