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Open Access Highly Accessed Research article

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

Steen Nordentoft1*, Lars Mølbak2, Lotte Bjerrum3, Jantina De Vylder4, Filip Van Immerseel4 and Karl Pedersen5

Author Affiliations

1 National Veterinary Institute, Technical University of Denmark, Section for Poultry, Fish and Fur Animals, Hangovej 2, DK-8200 Aarhus N, Denmark

2 National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, DK-1790 V, Denmark

3 Danish Technological Institute, Kongsvang Allé 29, DK-8000 Aarhus C, Denmark

4 Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent, University, Salisburylaan 133, B-9820 Merelbeke, Belgium

5 National Food Institute, Technical University of Denmark, Bülowsvej 27, DK-1790 V, Denmark

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BMC Microbiology 2011, 11:187  doi:10.1186/1471-2180-11-187

Published: 22 August 2011



In the EU conventional cages for laying hens are forbidden beginning in January 2012, however concerns about a higher transmission rate of Salmonella in alternative cages systems have been raised. The extent to which cage systems may affect the intestinal microbiota of laying hens is not known, and different microbiota may demonstrate different resistance towards colonization with Salmonella. To investigate this, 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.


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 could be observed between Salmonella positive and negative samples from 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.


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, we did not observe differences in colonization and excretion pattern of Salmonella from these groups. We suggest, that differences in group size and exposure to a more faecally contaminated environment in the alternative systems may explain the observed differences in diversity of the caecal microbiota.