Table 1. Training sets used for the naïve Bayesian classification of bacterial 16S rRNA gene sequences.

Abbreviation	Description	Sequence Databasea	Underlying Taxonomy
RDP TS6	RDP classifier training set v.6 (default forv. 2.3 of the RDP classifier)	8,127 bacterial and 295 archaeal sequences	Based on “The Taxonomic Outline of Bacteria and Archaea” (TOBA) 7.7 [52]
LTP	Bacterial subset of “The Living TreeProject” v. 106	8,494 bacterial sequences	“List of Prokaryotic names with Standing in Nomenclature (LPSN; http://www.bacterio.cict.fr/)
unfiltered RDP	All bacterial isolates in RDP database	31,334 non-redundant bacterial sequencesb	Based on “The Taxonomic Outline of Bacteria and Archaea” (TOBA) 7.7 [52]
filtered NCBI	All bacterial isolates in RDP database,filtered for annotation quality	21,240 non-redundant bacterial sequencesb	NCBI taxonomy [48]

^aExcept for the ‘RDP TS6’ training set, which always trains on the full sequence, numbers are only for the testing of 100 nt single-reads from the V4 region. For the three other training sets, which train only on the region to be classified, the number of sequences reflects both the number of sequences covering this region (all three training sets) and its degree of redundancy (‘unfiltered RDP’ and ‘filtered NCBI’).

^bThe numbers are for the ‘original non-redundant training set’ (see Methods section ‘Leave k out classification testing’); numbers for each leave-k-out iteration may vary slightly.