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

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.

Lifestyle and geographic insights into the distinct gut microbiota in elderly women from two different geographic locations

“…In addition, the most interesting finding was that the island and inland groups had distinct gut microbiota profiles. The butyric acid-producing genus Butyricimonas of the phylum Bacteroidetes was highly abundant in inland subjects [25, 26]. Butyric acid is a short-chain fatty acid and a product of the fermentation of dietary fiber by the gut microbiota [27].…”

Chicken faecal microbiota and disturbances induced by single or repeated therapy with tetracycline and streptomycin

“…The gut microbiology of Gallus gallus has received considerable prior attention, however, the majority of experiments have been performed with broilers, and the gut microbiota composition in egg laying hens has been characterised much less frequently [1-4]. The reason why the majority of experiments have been performed in broilers is quite clear, as the gut microbiota, especially its altered development, significantly reduces the profitability of broiler producers [5].…”

Horizontal transmission of Salmonella Enteritidis in experimentally infected laying hens housed in conventional or enriched cages

“…Conversely, other investigators have attributed a greater risk of Salmonella infection to cage-based housing, especially when rodent population densities are high (Huneau-Salaün et al, 2009;Snow et al, 2010;Van Hoorebeke et al, 2010b). Moreover, some studies have concluded that no significant differences in the prevalence of either environmental contamination or fecal shedding of Salmonella in laying flocks were evident between cage and cage-free systems (Siemon et al, 2007;Jones et al, 2012) or between conventional and enriched cage systems (De Vylder et al, 2009;Nordentoft et al, 2011;Van Hoorebeke et al, 2011). The current study sought to expand the implications of these earlier results by monitoring horizontal transmission of Salmonella Enteritidis infection among hens in conventional and enriched colony cage systems.…”