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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 be-
tween 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 5 0.66, P 5 2 ! 10216). Paired an-
alyses revealed that cloacal communities were more
closely related to cecal communities from the same in-
dividual 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 in-
creases welfare for husbandry and research purposes.