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

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...

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Bibliographic Details
Published in:FEMS microbiology ecology 2008-12, Vol.66 (3), p.620-629
Main Authors: Monteils, Valérie, Cauquil, Laurent, Combes, Sylvie, Godon, Jean-Jacques, Gidenne, Thierry
Format: Article
Language:English
Subjects:
Animals
Bacteria
Bacteria - classification
Bacteria - genetics
Bacteria - growth & development
Bacteria - isolation & purification
Bacteroidetes
Biodiversity
Caecum
cecum
Cecum - microbiology
Cloning
digestive ecosystem
Ecology
Firmicutes
Keystone species
Life Sciences
Microbiology
Microbiology and Parasitology
molecular library
Molecular Sequence Data
Phylogeny
rabbit
rabbits
Rabbits - microbiology
RNA, Ribosomal, 16S - genetics
rRNA 16S
Variovorax
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Summary: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).
ISSN:0168-6496
1574-6941
DOI:10.1111/j.1574-6941.2008.00611.x