TABLE 2.

Overview of some publicly and commercially available reference databases for bacterial identification using 16S rRNA gene sequence interpretation^a

Database	DNA target(s)	No. of sequences	Curation	Alignment of clustered sequences	Link	Comment
NCBI nt (Genbank NCBI)	All	≈21,000,000	Limited	No	https://blast.ncbi.nlm.nih.gov/Blast.cgi (select appropriate dataset in the menu in order to restrict and accelerate the search); for downloads, ftp://ftp.ncbi.nlm.nih.gov/blast/db/	Hosts all published sequences; excellent coverage; frequent updates; many redundant entries; frequent erroneous entries; use for unusual or new species
Greengenes (consortium comprised of Second Genome Inc., University of Colorado, and University of Queensland)	16S rRNA genes	≈1,200,000	Yes; manual sequences >12,000 bp; taxonomy curation	Yes: sequence clusters at various similarity percentages	Searches, http://greengenes.lbl.gov/Download/Tutorial/Tutorial_19Dec05.pdf; downloads, https://greengenes.secondgenome.com/	Includes several tools from chromatogram analysis to alignments; latest version from 2013; unclear updates, some taxonomy information may be outdated
RDP (Michigan State University)	16S rRNA	≈3,200,000	Yes; manual sequences >12,000 bp; taxonomy curation	Yes; Aligned	Searches, https://rdp.cme.msu.edu/seqmatch/seqmatch_intro.jsp and https://rdp.cme.msu.edu/index.jsp	Manually and not regularly updated; last update was May 2015; various tools available to analyze user data further
SILVA (Max Plank Institute for Marine Microbiology)		≈5,000,000, includes small ribosomal subunit for eukaryotes	Yes; manual sequence quality; taxonomy curation	Yes; multiple cluster sets available	Search, http://www.arb-silva.de/aligner/; downloads, http://www.arb-silva.de/download/arb-files/	Continually updated; tools available to analyze user data; genes other than 16S rRNA
Molzym SepsiTest		≈7,043	Manual	No		CE-IVD database works with kit but also with sequences generated otherwise
SmartGene IDNS Bacteria Module 3.9.x	16S rRNA and rpoB	≈800,000 16S, 358,000 centroid annotated	Yes; quality filters for sequence quality, centroid annotation for annotation qualification	Centroid annotation for most representative sequence per species		CE-IVD; proprietary centroid annotation; quality filtered, continually updated; tools available to analyze user data; genes other than 16S rRNA
MicroSEQ 3.1	16S rRNA	2,300	Sequences of collection and type strains	No		Compatible with the MicroSEQ sequencing kit of ThermoFisher; mainly for 500-bp sequencing

^aEntries with gray shading represent publicly available databases, and those without gray shading represent commercially available databases. See reference 5.