Phylogenetic depth

Comparative 16S rDNA sequence analysis of pure cultures has shown that it is not possible to delineate ranks at any level purely on the basis of similarity or dissimilarity values. For example, the phylogenetic depth of the taxon "species" (higher than about 70% DNA reassociation) may range from 97% 16S rDNA similarity to absolute sequence identity [3]. 

The use of clone libraries is recommended when an in-depth knowledge of the structure of bacterial communities is desired. It is also useful in revealing the composition of bacterial consortia. The decision to use this method depends on the number of samples since the construction of a clone hbrary requires a lot of time and effort. A major advantage of clone libraries is the generation of long sequences, which enables phylogenetic analysis and the design of probes and primers needed for further specific detection. 

Tap J, Mondot S, Levenez F, et al. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol. 2009 11 2574-2584. Salonen A, Salojarvi J, Lahti L, de Vos WM. The adult intestinal core microbiota is determined by analysis depth and health status. Clin... 

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