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Comparison of the Cecal Microbiota of Domestic and Wild Turkeys

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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 ribosomal RNA (rRNA) genes (OFRG) of 2,990 16S rRNA clones and dot blot quantification of dominant populations were used to identify the dominant bacterial taxa. Seventy-three percent of all the clones belonged to as yet uncultured genera. However, at a higher phylogenetic level, the OFRG library was composed of 54% Bacteroidetes clones (52% of the domestic library clones, 56% of the wild library clones), 30% Firmicutes clones (33% of the domestic library clones, 32% of the wild library clones), 3% Proteobacteria clones (5% domestic, 2% wild), and 3% Deferribacteres clones (4% domestic, 1% wild). Seven percent of the clones were unidentifiable (6% domestic, 9% wild). Bacteroidetes clones included the genera Alistipes, Prevotella, Megamonas, and Bacteroides. Of the Clostridiales clones, groups IV, IX, and XIV including genera Faecalibacterium, Megasphaera, Phascolarctobacterium, and Papillibacter were predominant. Lactobacillus, Enterococcus, and Streptococcus bacilli were also identified. β- δ- and γ-proteobacterial 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 despite the fact that the two libraries shared only 30% of the total clone operational taxonomic units. Together these results indicate that although high level taxonomic community structure is similar, high-density turkey production causes considerable divergence of the genera found in the ceca of commercial birds from those of their wild counterparts.

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Acknowledgments

The authors gratefully acknowledge the technical assistance of Jennifer A. Jones for all stages of data generation. We also thank David P. Alt and Karen Hollum for sequencing services.

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Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.

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Authors and Affiliations

  1. Pre-Harvest Food Safety and Enteric Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, US Department of Agriculture, Ames, IA, 50010, USA

    Alexandra J Scupham & Toni G. Patton

  2. Department of Plant Pathology, University of California, Riverside, CA, 92521, USA

    Elizabeth Bent

  3. Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, US Department of Agriculture, Ames, IA, 50010, USA

    Darrell O. Bayles

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  1. Alexandra J Scupham
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Correspondence to Alexandra J Scupham.

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Dendrogram of the 2407 domestic and wild turkey clones and 39 control clones. The dendrogram was created using greedy clique partitioning of the oligonucleotide fingerprinting of rRNA genes (OFRG) fingerprints for each clone. Taxonomy for the labeled clones was determined by sequence analysis of the clone and RDP II classification of the sequence. Clone taxa appended with an asterisk (*) indicate taxonomy was determined by comparison of the fingerprint to theoretical fingerprints generated from GenBank sequence data (DOC 19 kb)

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J Scupham, A., Patton, T.G., Bent, E. et al. Comparison of the Cecal Microbiota of Domestic and Wild Turkeys. Microb Ecol 56, 322–331 (2008). https://doi.org/10.1007/s00248-007-9349-4

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