This Is AuburnElectronic Theses and Dissertations

Selection of Bacillus Strains for Salmonella and ammonia reduction within a poultry house environment




Stough, Joshua

Type of Degree



Biological Sciences


Salmonella species are a food safety concern associated with poultry products, causing thousands of gastrointestinal disorders every year. Currently, controlling Salmonella in poultry houses is not being performed adequately. It is assumed that chemical litter amendments used to control ammonia will also control Salmonella. It has been shown that these chemical amendments are transitively effective, while it is postulated that bacterial amendments could last indefinitely. A collection of Bacillus strains (n=244) was screened for inhibition of Salmonella enterica strains (n=10). The 30 Bacillus strains that had the highest degree of inhibition against the most Salmonella strains were selected for further evaluation. While no significant nitrification activity was observed, we did observe significant differences in the respective ability of different Bacillus strains to take up ammonia from a culture medium that contained ammonium chloride. Six strains were selected and applied in a litter trial at 107 CFU/g litter. No significant effects were observed with regards to Salmonella or ammonia levels for any treatment at any sampling time, but two Bacillus strains were re-isolated from the poultry litter demonstrating survival within the litter environment. Two of the best-performing Bacillus strains, AB01 and AP71, were selected for evaluation in feed. The genome for each of these strains was sequenced, de novo assembled and used to generate PCR primers unique to the strains for identification within poultry litter and intestinal samples. A poultry trial was conducted wherein the probiotic strains were fed to chickens at a dose of 107 CFU/g of feed, followed by inoculation by Salmonella. No Salmonella culturable counts were detected without the use of enrichments in poultry samples, with or without probiotic feed, making it impossible to conclude whether the probiotic strains had the potential to reduce Salmonella levels. Future research will evaluate the potential of the probiotic strains to reduce ammonia levels in fresh poultry litter substrate, and to reduce Salmonella levels within the chicken intestinal microbiota using next-generation sequencing of 16S rRNA genes. These probiotic strains may be useful to the poultry industry in controlling ammonia and Salmonella levels within a poultry house environment.