Influence of Housing System on Salmonella Colonisation of the Gut of Laying Hens

Researchers in Denmark observed a more diverse gut microflora in hens housed in furnished cages or aviaries than conventional battery cages but there were no differences in Salmonella colonisation or excretion patterns between the groups.
calendar icon 2 October 2011
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In the EU, conventional cages for laying hens are forbidden from 1 January 2012, according to Steen Nordentoft of the Technical University of Denmark and co-authors there and at the Danish Technological Institute and the University of Ghent in Belgium. In their paper published in the journal, BMC Microbiology, they say that concerns about a higher transmission rate of Salmonella have been raised for alternative cages systems.

The extent to which cage systems affect the intestinal microbiota of laying hens is not known, and different microbiota may demonstrate different resistance towards colonisation with Salmonella.

To investigate this, the researchers studied ileal and caecal samples from two experimental studies where laying hens were inoculated with Salmonella Enteritidis and housed in different systems – conventional cage, furnished cage or aviary – were compared using Terminal Restriction Fragment Length Polymorphism (T-RFLP). The distribution of genera in the microbiota in caecum was furthermore described by next generation sequencing of 16S rDNA libraries.

They found that hens in the same cage type developed similar T-RFLP fingerprints of the ileal and caecal microbiota, and these could be separated from layers in the other cages types. No significant difference in the fingerprint profiles were observed between Salmonella-positive and Salmonella-negative samples from the same cage.

By deep sequencing of 16S rDNA libraries from caecum, 197 different Operational Taxonomic Units (OTU) were identified, and 195 and 196 OTU respectively, were found in hens in aviary and furnished cages, but only 178 OTU of these were recovered from conventional cages. The ratio between the dominating phyla or families and genera in the microbiota remained fairly constant throughout the study. Faecalibacterium and Butyricimonas were the most prevalent genera found in the caecal microbiota of layers, irrespective of the cage type.

Nordentoft and co-authors concluded that hens confined in the same cage group tend to develop similar microbiota in their ileum and caecum possibly due to isolation, while differences in the microbiota between cages may be caused by environmental or individual bird factors.

Although the cages type had influence on composition of the microbiota in the layers by promoting higher diversity in furnished and aviary systems, the researchers did not observe differences in colonisation and excretion pattern of Salmonella from these groups.

The authors suggest that differences in group size and exposure to an environment more contaminated with faeces with the alternative systems may explain the observed differences in diversity of the caecal microbiota.

Although they found no evidence that the cage systems itself was able to change the intestinal microbiota in a way which made it more likely to encourage colonisation by Salmonella in the birds, Nordentoft and co-authors stressed that hygiene in alternative systems is a particularly critical factor in preventing the spread of Salmonella within a flock.


Nordentoft S., L. Molbak, L. Bjerrum, J. De Vylder, F. Van Immerseel and K. Pedersen. 2011. The influence of the cage system and colonisation of Salmonella Enteritidis on the microbial gut flora of laying hens studied by T-RFLP and 454 pyrosequencing. BMC Microbiology, 11:187 doi:10.1186/1471-2180-11-187

Further Reading

- You can view the full report (as a PDF file) by clicking here.

October 2011
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