Impact of dietary fibre: starch ratio in shaping caecal archaea revealed in rabbits

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The digestive tracts of rabbits have adapted by enlargement of the caecum, representing up to 40% of their gastrointestinal tract, allowing them to digest fibrous feed. In rabbits, the caecum is the main site of microbial fermentation in the gut, and it accounts for 30–40% of the maintenance energy requirement in adult rabbits, which is provided by the production and absorption of short‐chain fatty acids (Parker, 1976; Marty and Vernay, 1984). Adult rabbit guts harbour bacteria and methanogenic archaea at concentrations of up to 1011 cells/g of gut content (Kovács et al., 2006). Previous studies that have analysed methane in the breath and faecal samples of rabbits and the methanogenic potential in vitro fermentation tests have revealed that methanogenic archaea only occur when a mature symbiotic microbiota has been established (Hackstein and van Alen, 1996; Piattoni et al., 1996; Marounek et al., 1999). Archaea and symbiotic bacteria in caecum provide 30–40% of the maintenance energy by microbial fermentation in adult rabbits (Marty and Vernay, 1984).
Several studies have used molecular approaches instead of traditional culture experiments to study the structure of the microbiota inhabiting the rabbit caecum (Bennegadi et al., 2003; Abecia et al., 2005; Monteils et al., 2008). Bennegadi et al. (2003) studied the microbiota in rabbits as a percentage of the relative rRNA index and reported that Archaea represented 22% and 12% of the total microbial community in weaning and 70‐day‐old rabbits respectively. These results indicate a significant archaeal population inhabiting rabbit caecum that should not be overlooked, particularly because the reported abundance was at a much higher level compared with the gut microbial populations in other mammals studied (Morvan et al., 1994). Methanogens in the digestive tract belong exclusively to the domain of Archaea (Jones et al., 1987). They play an important role in the decay of organic matter by gut micro‐organisms at the final stage. Methanogens use the hydrogen released in the gut by micro‐organisms utilizing organic matter to reduce the carbon dioxide and formate to methane. In addition, hydrogenotrophic acetogenic bacteria use hydrogen for acetate production and compete with methanogens.
Some studies have found that changes in the diet components of rabbits by modifying the dietary fibre and starch can result in evolution of the microbial ecosystem (Gidenne et al., 2004). However, it remains to be fully understood how different proportions of dietary fibre and starch influence the gut ecosystem in the gut of weaned rabbits. In this study, we aimed to compare the archaeal communities in the digestive tract of rabbits exposed to different diets. Archaeal communities were studied using 454 16S rDNA pyrosequencing of the V3 region of the archaeal 16S rRNA gene fragment. Libraries of 16S rDNA gene enable the discovery of novel sequence information without prior knowledge of the ecosystem being studied or the need for culture of micro‐organisms. Here, we first validated the representativeness of the caecal contents to describe the archaeal community in the caecum of rabbits subjected to different diets.
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