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. 2008 Dec;66(3):620-9.
doi: 10.1111/j.1574-6941.2008.00611.x.

Potential core species and satellite species in the bacterial community within the rabbit caecum

Valérie Monteils  1 , Laurent Cauquil, Sylvie Combes, Jean-Jacques Godon, Thierry Gidenne
Affiliations

Potential core species and satellite species in the bacterial community within the rabbit caecum

Valérie Monteils et al. FEMS Microbiol Ecol. 2008 Dec.

Abstract

A bacteria library was constructed from the caecum of a rabbit maintained under standard conditions. The complete gene 16S rRNA gene was sequenced. The 228 clones obtained were distributed in 70 operational taxonomic units (OTUs). The large majority of the OTUs were composed of one or two clones and seven OTUs contained half of the sequences. Fourteen sequences had high similarity to the sequence already registered in databases (threshold of 97%). Only one of these sequences has been identified as Variovorax sp. (99% identity). Units were distributed mainly (94%) in the Firmicutes phylum. Three sequences were related to Bacteroidetes. Nine clusters were defined in the phylogenic tree. A great diversity of caecal bacteria of the rabbit was shown. Half of the sequences generated in this library were distributed in the phylogenetic tree near the sequences characterized previously in rabbit caecum (potential core species), and the other half of the sequences were well separated (satellite species).

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Figures

Fig. 1
Fig. 1
Rarefaction curve generated for the 16S rRNA gene in the bacterial library (228 clones) from adult rabbit caecum with analytic rarefaction 1.3 software. The different clones were grouped into OTUs at a level of sequence identity ≥97%. Error bars indicated 95% confidence intervals.
Fig. 2
Fig. 2
Phylogeny placement of total 16S rRNA gene sequence data recovered from the caecum of an adult rabbit for bacteria. The tree was constructed using the SILVA project and the ARB sequence environment using a maximum parsimony method. Bootstrap values derived from 1000 iterations; only the values <90% are marked with an asterisk. Scale bar represents the number of substitutions per nucleotide position.
Fig. 2
Fig. 2
Phylogeny placement of total 16S rRNA gene sequence data recovered from the caecum of an adult rabbit for bacteria. The tree was constructed using the SILVA project and the ARB sequence environment using a maximum parsimony method. Bootstrap values derived from 1000 iterations; only the values <90% are marked with an asterisk. Scale bar represents the number of substitutions per nucleotide position.
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