The variable microbiome of different parts of the turkey gastrointestinal tract

The aim of this study was to characterise the turkey microbiome within the small intestine, caecum, large intestine and rectal/faecal fractions of the gastrointestinal tract. The whole microbiome was studied using 16S rRNA based Ion Torrent PGM sequencing for all intestinal tract samples for eight turkeys. Campylobacter spp. 16S rRNA densities were also assessed using qPCR for all gastrointestinal tract samples for the eight turkeys in order to assess niche prevalence of this bacterium within turkeys. Sequencing revealed that the microbiome of the samples taken from the various parts of the gastrointestinal tract varied significantly from each other at phyla and genus level with the most diversity seen within the caecum. Likewise Campylobacter spp. densities was higher in the Caecum suggesting that the caecum is the natural niche for Campylobacter within turkeys. This data also suggests that rectal/faecal material is also not suitable as an inoculum to assess the effects of various interventions on the microbiome and specifically Campylobacter spp. Understanding the microbiome of the turkey gastrointestinal tract is essential for developing strategies for reducing Campylobacter load whilst also assessing the effects of dietary intervention on turkey growth and health. From each turkey, samples from four gut regions were taken: cecum (c), faeces (f), large intestine (l), and small intestine (s). Samples were analysed using Ion Torrent sequencing. These are used in sequence file names.