A reasonable correlation between cloacal and caecal microbiomes in broiler chickens

Gut microbiota play an important role in animal health. For livestock, an understanding of the effect of husbandry interventions on gut microbiota helps develop methods that increase sustainable productivity, animal welfare and food safety. Poultry microbiota of the mid- and hind-gut can only be investigated post-mortem; however, samples from the terminal cloaca may be collected from live animals. This study tests whether cloacal microbiota reflect caecal microbiota in European broiler poultry by evaluating total and paired caecal and cloacal microbiomes from 47 animals. 16S amplicon libraries were constructed and sequenced with a MiSeq 250bp PE read metric. The composition of cloaca and caecal microbiomes were significantly affected by the age and location of animals, but the effect was very small. Bacilli were relatively more abundant in caeca, and Clostridia in cloaca. There was an overlap of 99.5% for the abundances and 59% for the types of taxa between cloacal and caecal communities, but the small fraction of rare non-shared taxa were sufficient to produce a signal for differentiation between caecal and cloacal communities. There was a significant positive correlation between specific taxa abundances in cloacal and caecal communities (Rho = 0.66, P = 2x10-16). Paired analyses revealed that cloacal communities were more closely related to caecal communities from the same individual than expected by chance. This study is in line with the only other study to evaluate the relationship between caecal and cloacal microbiomes in broiler poultry, but it extends previous findings by analysing paired caecal-cloacal samples from the same birds and reveals that abundant bacterial taxa in caeca may be reasonably inferred by sampling cloaca. Together, the findings from Europe and Australasia demonstrate that sampling cloaca shows promise as a method to estimate caecal microbiota, and especially abundant taxa, from live broiler poultry in a manner which reduces cost and increases welfare for husbandry and research purposes.