Gut microbiota impacts hen health and production. Hens in cage free systems are able to move more freely, engage with their environment and have different nutritional and management requirements. Little is known about how CF housing alters hen physiology and health.

In this study, researchers explored how cage free (CF) and conventional (CC) housing systems alters hen physiology and health by comparing and correlating eukaryotic (cells where DNA is within a distinct nucleus) microbiota in the ileal (third part of the small intestine). This study expands on previous work comparing and correlating prokaryotic (cell where there is no distinct nucleus) ileal microbiota using 16s rRNA gene amplicon sequencing. 25 hens where randomly chosen and weighted from two different houses of a CF or CC housing system at a single commercial facility. Hens were fed a standard corn-soybean diet.

Sampling found that in comparison to prokaryotic communities the eukaryotic communities had
relatively low species diversity and evenness. 83 correlations were found between prokaryotic and
eukaryotic species. Significant differences between the CC and CF ileal communities were observed at the whole community level. Disease causing organisms were present in ileal communities of both housing types, but were more abundant in CF samples, possibly due to increased exposure to fecal matter. The ileal microbiota relationships discovered may have important implications for designing probiotics.

Producer Takeaway: The ileal microbiota relationships discovered may have important implications for designing products to further enhance bird health. Cage-free hens had more disease causing organisms present than caged hens.