The cecal microbiome of commercial broiler chickens varies significantly by season

Authors: OAKLEY, BB - Western University Of Health Sciences; CALLOWAY, K - Western University Of Health Sciences; RICHARDSON, E - Western University Of Health Sciences; Meinersmann, Richard - Rick; Cox Jr, Nelson; Berrang, Mark

Submitted to: Poultry Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/30/2018
Publication Date: 7/17/2018
Citation: Oakley, B., Calloway, K., Richardson, E., Meinersmann, R.J., Cox Jr, N.A., Berrang, M.E. 2018. The cecal microbiome of commercial broiler chickens varies significantly by season. Poultry Science. 97:3635-3644. https://doi.org/10.3382/ps/pey214.
DOI: https://doi.org/10.3382/ps/pey214

Interpretive Summary: The bacteria that grow in or on a higher organism are known as the microbiome of that higher organism. Recently developed DNA sequencing technology has given us a method to make a census of the bacteria that are in any microbiome. An animal’s gut microbiome can affect its health and development. Thus it may benefit the poultry industry’s effort to further optimize grow-out conditions for chickens if we know the composition of their gut microbiome. We collected intestines from chickens of 87 flocks over the course of a year and determined the species of bacteria that were present in the gut contents. There were significant changes in the gut microbiome that correlated with season, particularly distinguishing samples collected in the winter. Species that were most notably changed were members of Clostridium group IV and group XIVa which are associated with improved health and were more abundant in the winter. The presence or absence of Campylobacter in gut contents was also recorded, but there was no observed correlation of the overall microbiome composition with Campylobacter status. More studies need to be done to identify optimum microbiome composition so that strategies can be developed to enhance establishment the desired species.

Technical Abstract: Next-generation DNA sequencing is rapidly becoming a powerful tool for food animal management. One valuable use for this technology is to re-examine long-standing observations of performance differences associated with animal husbandry practices to better understand how these differences may be modulated by the GI microbiome. The influences of environmental parameters such as air temperature and relative humidity on broiler chicken performance have commonly been observed but how the GI microbiome may respond to seasonal environmental changes remains largely unknown. The purposes of this study were therefore to: 1) characterize the cecal microflora of commercial broilers (N=87) collected at harvest across all four seasons, and 2) identify any significant changes of the GI microbiome and specific taxa according to season and Campylobacter status. Whole GI tracts were removed from commercial broilers representing 87 independent flocks between April 2013-May 2014. Intact ceca were separated, cultured for Campylobacter and cecal contents were frozen. The cecal microbiome was characterized using barcoded sequencing of 16S rRNA genes on the Illumina MiSeq platform. Composition of the microbiome measured at processing was generally not affected by Campylobacter status but was most significantly affected by season of grow-out. Significantly fewer bacterial genera were found in winter than spring and summer. Bacterial genera from Clostridium clusters XIVa and IV, generally considered to be associated with positive gut health outcomes, were significantly more abundant in winter. Identifying specific attributes of GI microbiota that vary according to season can help develop novel interventions to improve husbandry practices and growth performance.