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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Egg and Poultry Production Safety Research Unit » Research » Publications at this Location » Publication #365569
Research Project: Reduction of Invasive Salmonella enterica in Poultry through Genomics, Phenomics and Field Investigations of Small Multi-Species Farm Environments

Location: Egg and Poultry Production Safety Research Unit

Title: Assessment of a potential role of Dickeya dadantii DSM 18020 as a pectinase producer for utilization in poultry diets based on in silico analyses.

Author
item DITTOE, D - University Of Arkansas
item BARABITE, RAVI - University Of Arkansas
item Rothrock, Michael
item RICKE, STEVEN - University Of Arkansas

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/30/2020
Publication Date: 4/23/2020
Citation: Dittoe, D.K., Barabite, R.D., Rothrock Jr, M.J., Ricke, S.C. 2020. Assessment of a potential role of Dickeya dadantii DSM 18020 as a pectinase producer for utilization in poultry diets based on in silico analyses. Frontiers in Microbiology. 11:751.

Interpretive Summary: Currently, the poultry industry has been faced with consumer pressure to utilize only vegetable feedstuffs in poultry diets, eliminate antibiotics from poultry production, and rear poultry in free range systems. To maintain current production standards, the industry must determine ways to enhance nutrient uptake and utilization further. One possible solution is the supplementation of pectinase, an enzyme that degrades pectin within the cell walls of plants, in poultry diets. Therefore, the objective of the current study was to determine the potential role of a pectinase producer, Dickeya dadantii DSM 18020, as a commercially utilized pectinase producer in poultry diets against other known pectinase produces, in silico. In the current study, whole genomes of Dickeya dadantii DSM 18020 (NZ_CP023467.1), D. dadantii 3937 (NC_014500.1), D. solani IPO 2222 (NZ_CP015137.1), Bacillus halodurans C-125 (NC_002570.2), and B. subtilis subsp. subtilis str. 168 (NC_000964.3) were compared using bioinformatic approaches to compare the chromosomal genome size, GC content, protein coding genes (CDS), total genes, average protein length (a.a.) and determine the predicted metabolic pathways, predicted pectin degrading enzymes, and pectin-degradation pathways across pectinase producers. Due to insufficient information surrounding the genome of D. dadantii DSM 18020, D. dadantii 3937, a 99% identical genome to D. dadantii DSM 18020, was utilized to compare pectinase-associated enzymes and pathways. The results from the current study demonstrated that D. dadantii 3937 possessed the most significant proportion of pathways presented and the highest number of pathways related to degradation, assimilation, and utilization of pectin. Also, D. dadantii DSM 18020 also exhibited a high number of pectinase-related enzymes. Both D. dadantii 3937 and D. solani IPO 2222 shared the pectin degradation I pathway via the EC 3.1.1.11, EC 3.2.1.82, and EC 4.2.2.- enzymes, but did not share this pathway with either Bacillus species. In conclusion, the results of the current study demonstrated the extensive capability of D. dadantii DSM 18020 to become a commercially viable enzyme producer for the poultry industry.

Technical Abstract: Currently, the poultry industry has been faced with consumer pressure to utilize only vegetable feedstuffs in poultry diets, eliminate antibiotics from poultry production, and rear poultry in free range systems. To maintain current production standards, the industry must determine ways to enhance nutrient uptake and utilization further. One possible solution is the supplementation of pectinase, an enzyme that degrades pectin within the cell walls of plants, in poultry diets. Therefore, the objective of the current study was to determine the potential role of a pectinase producer, Dickeya dadantii DSM 18020, as a commercially utilized pectinase producer in poultry diets against other known pectinase produces, in silico. In the current study, whole genomes of Dickeya dadantii DSM 18020 (NZ_CP023467.1), D. dadantii 3937 (NC_014500.1), D. solani IPO 2222 (NZ_CP015137.1), Bacillus halodurans C-125 (NC_002570.2), and B. subtilis subsp. subtilis str. 168 (NC_000964.3) were compared using bioinformatic approaches to compare the chromosomal genome size, GC content, protein coding genes (CDS), total genes, average protein length (a.a.) and determine the predicted metabolic pathways, predicted pectin degrading enzymes, and pectin-degradation pathways across pectinase producers. Due to insufficient information surrounding the genome of D. dadantii DSM 18020, D. dadantii 3937, a 99% identical genome to D. dadantii DSM 18020, was utilized to compare pectinase-associated enzymes and pathways. The results from the current study demonstrated that D. dadantii 3937 possessed the most significant proportion of pathways presented and the highest number of pathways related to degradation, assimilation, and utilization of pectin. Also, D. dadantii DSM 18020 also exhibited a high number of pectinase-related enzymes. Both D. dadantii 3937 and D. solani IPO 2222 shared the pectin degradation I pathway via the EC 3.1.1.11, EC 3.2.1.82, and EC 4.2.2.- enzymes, but did not share this pathway with either Bacillus species. In conclusion, the results of the current study demonstrated the extensive capability of D. dadantii DSM 18020 to become a commercially viable enzyme producer for the poultry industry.