A reasonable correlation between cloacal and cecal microbiomes in broiler chickens

Abstract

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-gut and hind-gut can only be investigated postmortem; however, samples from the terminal cloaca may be collected from live animals. This study tests whether cloacal microbiota reflect cecal microbiota in European broiler poultry by evaluating total and paired cecal and cloacal microbiomes from 47 animals. 16S amplicon libraries were constructed and sequenced with a MiSeq 250 bp PE read metric. The composition of cloacal and cecal microbiomes were significantly affected by the age and location of animals, but the effect was very small. Bacilli were relatively more abundant in ceca and Clostridia in cloaca. There was an overlap of 99.5% for the abundances and 59% for the types of taxa between cloacal and cecal communities, but the small fraction of rare nonshared taxa were sufficient to produce a signal for differentiation between cecal and cloacal communities. There was a significant positive correlation between specific taxa abundances in cloacal and cecal communities (Rho = 0.66, P = 2 × 10^-16). Paired analyses revealed that cloacal communities were more closely related to cecal communities from the same individual than expected by chance. This study is in line with the only other study to evaluate the relationship between cecal and cloacal microbiomes in broiler poultry, but it extends previous findings by analyzing paired cecal-cloacal samples from the same birds and reveals that abundant bacterial taxa in ceca 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 cecal microbiota, and especially abundant taxa, from live broiler poultry in a manner which reduces cost and increases welfare for husbandry and research purposes.

Keywords: 16S rRNA amplicon sequencing; 3Rs; cecal communities; cloacal communities; poultry microbiome.

Figure 1

Total number of taxa in cloacal and cecal samples. Venn diagram showing the total and overlap of species in cloaca and ceca.

Figure 2

Main bacterial classes recorded in cloacal and cecal samples. Pie chart showing the similarity in number of species in cloaca (internal circle) and ceca (external circle) differentiated at class level. Classes representing less than 0.5% of the total number of species are collapsed to the “other” category.

Figure 3

Correlation between cumulative abundances of taxa in cloacal and cecal samples. The plot represents the correlations between cumulative abundances of cecal and cloacal samples. Indicator species of cloacal samples are not included in the present picture. Pearson's cor = 0.76, P ≤ 2 × 10⁻¹⁶, Spearman's Rho = 0.72, P ≤ 2 × 10⁻¹⁶.

Figure 4

Cloacal indicator taxa. Mean (±SD) log abundance of the indicator species (at adjusted P < 0.005) of cloacal samples (light gray) to abundances in cecal samples (dark gray).