Abstract
BackgroundIn 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.ResultsHens 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.ConclusionsHens 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.
Highlights
In the EU conventional cages for laying hens are forbidden beginning in January 2012, concerns about a higher transmission rate of Salmonella in alternative cages systems have been raised
Using molecular methods as Terminal Restriction Fragment Length Polymorphism (T-RFLP) and generation sequencing, the aim of this study was to describe the effect of the housing system on the distribution of the dominating bacterial species in the intestinal microbiota in laying hens housed in different cage systems before and after inoculation with Salmonella Enteritidis
T-RFLP analysis of the impact of cage type on intestinal microbiota The microbiota in ileal and caecal samples from the first experiment were characterised by creating individual TRFLP fingerprint profiles for each sample
Summary
In the EU conventional cages for laying hens are forbidden beginning in January 2012, concerns about a higher transmission rate of Salmonella in alternative cages systems have been raised. An increased risk of transmission of Salmonella to humans due to a general higher level of microbial contamination of the shell of eggs derived from hens housed in alternative housing systems [3] It is not known whether the combination of larger group sizes and social stress may increase the susceptibility to colonization by Salmonella. Stressing laying hens by feed withdrawal is a traditional method to induce molting, and in several studies this have resulted in an increase in the susceptibility towards colonization by Salmonella [4,5] The mechanism behind this is not well understood, but the starvation may affect the balance between different microbial populations in the intestinal microbiota [5,6,7], as a reduction in diversity is observed which may lower the natural competitive barrier [5]. The generated sequences do not cover the whole gene, Huse et al [17] were able to achieve a 99% correlation of identification, when compared with full length sequencing of a library from the human microbiota
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