A Bird Box of Microbial Communities: Looking at Shifts in the Cloacal Microbiome

C Escallón, L K Belden, I T Moore; The Cloacal Microbiome Changes with the Breeding Season in a Wild Bird, Integrative Organismal Biology, Volume 1, Issue 1, 1 January 2019

The New Year has been trending with “Bird Box” memes, which consists of individuals performing some risky tasks without visibility, which I do not suggest doing.  Whereas, Escallón et al. has provided insight on some unique relationships operating in the region of a bird that is usually not visible, the cloaca. In the paper I have chosen to highlight for Integrative Organismal Biology, Escallón et al. have set out to determine whether there is a shift in the cloacal microbiome of free-living rufous-collared sparrows (Zonotrichia capensis) throughout sequential breeding and non-breeding seasons.  This was a unique opportunity for Escallón et al. to monitor a dynamic microbiome of the bird cloaca at multiple time points to observe whether there is a shift in bacterial diversity throughout three consecutive years.  This also provided an opportunity to determine whether new bacterial members are introduced to the cloacal microbiome through copulation. In this paper, Escallón et al. were set to test two hypotheses, the bacterial clearance hypothesis and the bacterial accumulation hypothesis.  The former is where bacterial diversity would be higher during the onset of mating seasons than during the non-breeding seasons.  The latter describes that the bacterial diversity in the cloaca would continually increase throughout sequential breeding seasons.  In addition, the group investigated blood plasma testosterone concentrations and cloacal bacterial communities within males during the breeding and non-breeding seasons to determine whether there is a relationship with the hormone environment and the cloacal bacterial community.  To test their hypotheses, their study was conducted with wild breeding populations of Z. capensis in a rural region of the Colombian Andes.  Males, females, and juveniles were caught, and a cloacal swab sample was taken for every individual for sequencing and determine the cloacal community composition.  Juveniles were included in this study and were expected to have low cloacal bacterial diversity because they have not copulated yet. So, what was the outcome of this study?  Their results showed support for the bacterial clearance hypothesis, where males had bacterial communities that were more diverse from the transition from non-breeding to breeding seasons, and a decrease in bacterial diversity as they transitioned from breeding to non-breeding seasons.  While females showed no changes in bacterial diversity during any of the transitions. As for the bacterial accumulation hypothesis, there was significant variation across the sequential breeding seasons, but there was not an accumulation of bacterial taxa from one breeding season to the next.  Lastly, they showed support and confirmed that hormone environment influences the cloacal microbial community, where an increase in testosterone in males had more phylogenetic diversity of bacteria.  This confirmed some of the work previously accomplished by Escallón et al. 2017. In this study, Escallón et al. had anticipated that both males and females would have similar microbial community shifts because copulation occurs in stable social pair bonds, and females could possibly have more microbial diversity due to receiving a higher proportion of bacteria during copulation.  However, this was not the case and prompts future work to understand why males have diverse cloacal bacterial communities than females during the onset of reproduction. Future studies described by Escallón et al. would be to analyze the costs and benefits of having a diverse cloacal microbial community. This study gives us a chance to peak from the blindfold and gain a better glimpse at how microbial communities may drive an organism’s life history strategies, behavior and physiology.


Dr. Joe Heras is an adjunct faculty member at California State University, Los Angeles.  His interests include comparative genomics and transcriptomics, bioinformatics, and evolutionary adaptations within marine systems.  For more information see my website.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s