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.

Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum

“…The majority of OTUs detected in ileal or caecal contents that were not detected in non-invasive samples were of low abundance. This is similar to [ 61 ], which demonstrated that ~99% of the OTUs found in caecal samples were present in excreta and ~87% of the OTUs found in ileal samples were present in excreta, but higher than [ 62 ], reporting that ~60% of the OTUs found in caecal swabs were present in the cloacal swabs. Differences among studies could be attributed due to differences in sample size, sampling techniques, age of the birds, DNA extraction methods, feed, breed or other factors.…”

Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range

“…To ensure the cloacal swabs contained enough fecal material, the cloacal swabs were inserted deeply into the cloacal opening to enter the last part of the colon and the swabs were visually assessed prior to DNA extraction. Although research has shown that cloacal and fecal microbiota of chickens might not be an accurate representative of the cecal composition and are more variable ( Williams and Athrey, 2020 ), it has also been shown that fecal samples are qualitatively similar to the cecal microbiota ( Stanley et al, 2015 ) and non-shared taxa between cloacal and cecal samples accounted for a very low percentage of the diversity: 0.49% in one case ( Andreani et al, 2020 ) and 0.75% in another ( Stanley et al, 2015 ). Furthermore, it has been reported that cloacal swabs are similar to fecal samples ( Videvall et al, 2018 ), and shifts in microbiota composition have been detected successfully using fecal samples ( Oakley and Kogut, 2016 ; Jurburg et al, 2019 ).…”

Choice of Commercial DNA Extraction Method Does Not Affect 16S Sequencing Outcomes in Cloacal Swabs

“…One phyla, Proteobacteria, was found to be significantly less relatively abundant in Method 4 than the three other extraction methods; however, there were no differences in genera. Firmicutes, Proteobacteria, and Actinobacteria have been found to be the most abundant phyla in cloacal samples in broiler and laying hens [ 7 , 22 , 23 , 24 , 25 ]. The most abundant genus across all samples was Lactobacillus, which has been previously described in young broiler chicks [ 25 ], but other groups have found that Pseudomonas and Romboutsia are the most abundant genera in laying hen cloacal swabs [ 7 , 23 ].…”

“…Therefore, it is important to highlight that although it has shortcomings, cloacal swabs are the most appropriate choice of sampling for these study designs in birds where euthanasia is not feasible. Nevertheless, other studies have concluded that the cloacal microbiome is reasonably similar to the cecal microbiome in broiler chickens to allow for inferences [ 22 ]. It should also be noted that gastrointestinal anatomy can differ by bird species and sampling wild birds is subject to different challenges and complications than sampling broiler or laying chickens in agricultural settings; as this study analyzed cloacal samples from laying hens, we refrain from making further generalizations to different bird species.…”