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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Food Safety and Enteric Pathogens Research » Research » Publications at this Location » Publication #214330


item Scupham, Alexandra
item Patton, Toni
item Bayles, Darrell

Submitted to: Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/13/2007
Publication Date: 1/8/2008
Citation: Scupham, A.J., Patton, T.G., Bent, E., Bayles, D.O. 2008. Comparison of the cecal microbiota of domestic and wild turkeys. Microbial Ecology. 56(2):322-31. Available:

Interpretive Summary: Campylobacter is the primary cause of food-relates illness in the Unites States, and consumption of poultry has been identified as a significant risk factor for contraction of the illness. Reduction of Campylobacter in raw poultry meat is therefore of considerable interest for public health. Because of high prevalence of carriage (~90%) by poultry at slaughter, pre-harvest intervention strategies are under examination to minimize on-farm colonization by this pathogen. It is thus necessary to understand the ecology of this pathogen in vivo, and the first step in understanding the ecology of an ecosystem is to describe the species residing in that habitat. The work presented in this manuscript describes the microbial constituents of the turkey intestinal ecosystem, both in wild and commercially raised animals. The results indicate little to no differences between the microbial communities inhabiting wild turkeys harvested across a 400-mile transect through the Midwest. However, substantial differences were observed between the wild and domestic animals, and between animals obtained from different flocks at the same farm. It is likely that the failure of current intervention strategies to protect poultry flocks from colonization by pathogens is due to the variability of the intestinal microbiota. In light of the steady removal of antimicrobial from the poultry growers’ arsenal for promotion of flock health as well as the recently imposed HACCP performance standards for reduction of Campylobacter on carcasses at slaughter, development of ecology-based methods for creating homogeneous, stable poultry intestinal communities should accompany any future development of intervention strategies.

Technical Abstract: The extent to which production methods alter intestinal microbial communities of livestock is currently unknown. As the intestinal microbiota may affect animal health, nutrition and food safety, a baseline comparison of the cecal communities of domestic and wild turkeys was performed. Oligonucleotide fingerprinting of rRNA genes (OFRG) of 2990 16S rRNA clones and dot blot quantification of dominant populations were performed. Bacterial library composition was determined to include 56% Bacteroidetes (51% of which were domestic library clones, 49% wild library clones), 30% Firmicutes (58% domestic, 42% wild), 3.4% Proteobacteria (76% domestic, 24% wild), 2.6% Deferribacteres (81% domestic, 19% wild) and 7.4% unidentified (46% domestic, 54% wild), 73% of the clones belonged to uncultured genera. Within the Bacteroidetes there were clusters of clones specific to either wild or domestic birds as well as clusters shared between bird types. Genera Alistipes, Prevotella and Bacteroides were identified. Of the Clostridiales, groups IV, IX and XIV including genera Faecalibacterium, Megasphaera, Phascolarctobacterium, Papillibacter and Megamonas were predominant. Bacilli of the genera Lactobacillus, Enterococcus and Streptococcus were also identified. Beta- Delta- and Gammaproteobacteria genera included Acinetobacter, Sutterella and Escherichia; Deferribacteres clones showed high similarity to Mucispirillum schaedleri. Statistical comparison of the domestic and wild turkey clone libraries indicated similar levels of community richness and evenness. However, the two libraries shared only 30% of the clones. Together these results indicated that while high level taxonomic community structure is similar, high-density turkey production causes considerable divergence of the genera commercial bird intestinal genera from those of their wild counterparts.