Table 4.

Bacterial classification accuracy by the RDP classifier of partial sequences spanning hypervariable V3, V4, and V6 regions of 16S rRNA genes

V3V4V6
Bootstrap cutoff, %050800508005080
Human gut
 % classified10093.979.41009288.410066.245.8
 % matching89.391.699.994.596.597.774.997.699.6
Soil
 % classified10073.650.610076.456.310034.415.6
 % matching71.986.892.982.792.797.343.875.683.1
Marine
 % classified10061.448.310077.453.410052.341.7
 % matching66.094.199.981.396.998.949.388.093.7
Bovine rumen
 % classified10076.362.310079.466.799.151.443.9
 % matching76.893.499.488.696.710055.688.589.5
  • RDP classifier used training set no. 6 from March 2010. V3 and V6 regions correspond to those amplified by primers from Dethlefsen et al. (30); V3 region range, E. coli position 358–514 and length 144 ± 11 bp; V6 region range, E. coli position 986–1045 and length 60 ± 4 bp. V4 region corresponds to the amplification product of primers from this paper spanning E. coli position 578–784 and length 207 ± 1 bp. Human gut data were obtained from Dethlefsen et al. (30). Analysis was updated from Claesson et al. (31). Soil data were obtained from Elshahed et al. (32). Marine data were obtained from Walsh et al. (33). Bovine rumen data were obtained from Brulc et al. (34). % classified, fraction of sequences classified to genus level; % matching, matching of each region's classifications with full-length classification.