Comparison of the Cecal Microbiota of Domestic and Wild Turkeys

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. beta- delta- and gamma-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.

Gut Bacterial Diversity of the House Sparrow (Passer domesticus) Inferred by 16S rRNA Sequence Analysis

“…Our study described the presence of a higher number of bacteria in the gut of a wild bird than those reported by previous studies for the gut of birds, some mammals, and even humans [16,22,32,34,62]. Because the analysis we used not only eliminated sequences that include chimera, homopolymer sequences, and sequences created by errors of pyrosequencing [56], but also it removed some real bacterial sequences by its stringent criteria, we expect the total number of OTUs present in the House Sparrow's gut to be higher.…”

Evidence for a core gut microbiota in the zebrafish

“…Our results complement a limited number of previous 16S rRNA gene sequence-based comparisons of gut microbiotas in wild and domesticated animals. Analysis of wild and domesticated mice (Wilson et al, 2006), turkeys (Scupham et al, 2008), parrots (Xenoulis et al, 2010), fruitflies (Cox and Gilmore, 2007) and hydra (Fraune and Bosch, 2007) indicate that members of the same species tend to possess gut bacterial communities of similar taxonomic composition at the phylum or class level regardless of domestication status, with some differences between wild and domestic individuals emerging at shallower phylogenetic resolution. These previous studies have revealed varying effects of domestication on gut bacterial diversity, with increased diversity in wild mice (Wilson et al, 2006) and fruitflies (Cox and Gilmore, 2007) compared with domesticated controls, and decreased diversity in wild versus domesticated parrots (Xenoulis et al, 2010).…”

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

“…We included sequences from the Zebra, Horse, Wild Ass, Banteng, Indian and Black Rhinoceros, Capybara, Gazelle, Giraffe, Okapi, Kangaroo, Springbok, Takin and Sheep all from . We also included sequences from other studies that satisfied the inclusion criteria of sequence length 4500 bp, and data sets containing 450 sequences from each particular host species, these included: sequences from the dairy cow rumen (Chin EC, Lim WJ, Kim H and Yun HD unpublished data available in the GenBank database); sequences from cow manure (Nakai Y and Yamamoto N, unpublished data available in the GenBank database), sequences from the chicken cecum (Massias B, Urdaci MC unpublished data available in the GenBank database), sequences from Turkey cecum (Scupham et al, 2008) and Hoatzin clone sequences (Godoy-Vitorino et al, 2008). The hoatzin and cow G2Chip OTUs, correspond to the representative sequences of the OTUs detected by the PhyloChip through hybridization with foregut and hindgut DNA from the wild Venezuelan Hoatzins and pasturing cows (this study).…”