Dynamics of bacterial community analyzed in poultry litter treated with LitterGuardRTM using DGGE and pyrosequencing

Poultry bird's performance is largely affected by intestinal and litter bacterial communities in poultry houses. Poultry litter, mixture of sawdust and manure, provides baseline to analyze the bacterial communities found in poultry houses. The effect of LitterGuard®, especially designed with Bacillus subtilis spores to reduce pathogens in poultry litter and help performance of birds as probiotics, was studied based on 16S rRNA gene using DGGE (Denaturing Gradient Gel Electrophoresis) and pyrosequencing. DNA was extracted from samples collected at eight different time points from four broiler houses during two flock rotations. Total of 128 samples were processed with DGGE and 40 samples with pyrosequencing. Multivariate analysis was performed to analyze the overall data. Results of DGGE showed average richness of 300 bacterial taxa in all the houses. However, no significant difference in richness and composition of bacterial communities was reported between the houses. Taxanomical assignment of the sequences from pyrosequencing was done using RDP Classifier and phylogenetic analysis. Total of 239 taxa were identified using RDP Classifier and 111 taxa including six Bacillus spp. were identified using phylogenetic analysis. Taxa such as Cornybacterium spp., Stapylococcus spp., Lactobacillus spp., Salinicoccus spp., Nocardiopsaceae spp. and Yania spp. were found to be highly abundant. Multivariate analysis of the data showed a significant difference in the relative percent abundance of taxa between the samples collected in an interval of 108 days. However, no significant difference was identified in relative percent abundance of taxa including Bacillus spp. between treated and untreated houses. No significant effect of LitterGuard® was identified.