Previously obtained 16S rRNA reference sequences for lesser-known taxa in human and canine oral microbiomes (1 (link), 2 (link)) were used for BLASTN searches of Greengenes and NCBI databases to identify similar sequences. These sequences plus those included in key papers relevant for each taxon were downloaded and manually aligned in our curated secondary structure-based rRNA database (1 (link)). The primary design goal was to obtain primer pairs that would specifically amplify 16S rDNA for lineages including known oral taxa. The secondary design goal was to design primer pairs with broad coverage to amplify the entire phylum or candidate division. Because we wanted taxa-selective primer pairs that amplified nearly the entire 16S rDNA gene, primers were designed close to each end of the 16S rDNA molecule: 5′ within base positions 9–46 (Escherichia coli numbering) and 3′ within base positions 1464–1509. Target regions were selected by inspection of the alignments and candidate primers analyzed for melting temperature, hairpin formation and primer dimer formation using OligoAnalyzer (Integrated DNA Technologies).