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

Monteils V, Cauquil L, Combes S, Godon JJ, Gidenne T - FEMS Microbiol. Ecol. (2008)

Bottom Line: Units were distributed mainly (94%) in the Firmicutes phylum.Three sequences were related to Bacteroidetes.Nine clusters were defined in the phylogenic tree.

View Article: PubMed Central - PubMed

Affiliation: INRA, Université de Toulouse, UMR 1289, Tissus Animaux, Nutrition, Digestion, Ecosystème et Métabolisme, Chemin de Borde-Rouge, Auzeville,Castanet-Tolosan, France. valerie.monteils@ensat.fr

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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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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fig02: 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.

Mentions: The nearest sequence in the database and their environment origin were mentioned. A cross-reference to the phylogenetic tree presented in Fig. 2 was made with the cluster number.


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

Monteils V, Cauquil L, Combes S, Godon JJ, Gidenne T - FEMS Microbiol. Ecol. (2008)

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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2667309&req=5

fig02: 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.
Mentions: The nearest sequence in the database and their environment origin were mentioned. A cross-reference to the phylogenetic tree presented in Fig. 2 was made with the cluster number.

Bottom Line: Units were distributed mainly (94%) in the Firmicutes phylum.Three sequences were related to Bacteroidetes.Nine clusters were defined in the phylogenic tree.

View Article: PubMed Central - PubMed

Affiliation: INRA, Université de Toulouse, UMR 1289, Tissus Animaux, Nutrition, Digestion, Ecosystème et Métabolisme, Chemin de Borde-Rouge, Auzeville,Castanet-Tolosan, France. valerie.monteils@ensat.fr

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).

Show MeSH