Characterisation of the turkey microbiome along the gastrointestinal tract of growing turkeys reveals that Campylobacter spp. are most prevalent in 10 week old birds

The turkey microbiome is largely understudied, despite the prevalence of human pathogens, such as Campylobacter spp. within their gastrointestinal tract. In this study we investigated the whole microbiome within the small intestine (SI), caecum (C), large intestine (LI) and rectum (R) of turkeys at 6, 10 and 16 weeks of age. Eight turkeys were dissected within each age category and the contents of the SI, C, LI and R were harvested. Total bacterial QPCR revealed that the caecum, particularly within mature 16 week old birds, contained the most 16S rDNA concentration indicative of a higher bacterial load. Campylobacter spp. QPCR revealed that the caecum, particularly within mature 10 week old birds, contained the most 16S rDNA concentration indicative of a higher Campylobacter load. Ion torrent based sequencing of the 16S rDNA gene for all sample locations for 3 birds within each age category showed, on a genus level, an abundance of Lactobacillus, Streptococcus and Clostridium XI (approx. 38.2, 28.1 and 13.0% respectively) in all birds irrespective of GI tract locations and age. Most identified bacterial genera were found in all locations of the GI tract, with the most differences in abundance seen in the caecum of birds from all stages of maturity. Interestingly, ion torrent based sequencing showed that Campylobacter spp., were only apparent within the caeca of 10 week old birds which is slightly different to the QPCR results but nonetheless confirms prevalence within the caeca of birds of this age. Understanding the microbial ecology of the turkey gastrointestinal tract is essential in order to develop novel strategies, which effectively target Campylobacter spp.