TABLE 3.

Characteristics of 16S rRNA gene data sets and phylogenies for different taxonomic levelsa

Taxonomic groupTaxonomic levelNo. of taxa16S rRNA (complete gene)Resolutionb16S rRNA (DGGE fragment)Resolutionb
No. of nucleotide positionsGINo. of nucleotide positionsGI
BacteriaDomain501,2410.690.3320/475110.690.3311/47
ActinobacteriaPhylum111,4280.670.496/85630.670.495/8
ChlamydiaceaeFamily71,512ND0.762/4588ND0.762/4
FirmicutesPhylum331,3620.680.4317/305370.680.4313/30
    BacillalesOrder111,4980.540.564/85850.540.565/8
    LactobacillalesOrder121,4770.530.534/95820.530.535/9
    StreptococcusGenus91,510ND0.844/6588ND0.844/6
    MycoplasmataceaeFamily61,4530.640.323/35750.640.322/3
ProteobacteriaPhylum461,3290.720.4828/435330.720.4820/43
    AlphaproteobacteriaClass91,4200.870.592/65590.870.591/6
    GammaproteobacteriaClass291,4620.820.5520/265770.820.5510/26
    EnterobacterialesOrder141,4940.600.527/115880.600.526/11
E. coli/S. flexneriSpecies51,505NDND0/2588NDND0/2
  • a ND, value cannot be defined (data set is too small and/or lacks informative positions).

  • b Number of nodes resolved (>80% bootstrap support value) out of total nodes, with bold type indicating the gene (rpoB or 16S rRNA) displaying the most resolved node.