Table 1.
Level of rpoB partial sequence similarity among six species of oral Veillonella.
Fig 1.
The location and sequence of species-specific primers for the rpoB gene of oral Veillonella.
Underlined red font indicates the nucleotide sequences of each reverse primer for different Veillonella species. Numbers indicate the nucleotide positions in the rpoB gene of Veillonella species. Black font indicates sequences of the rpoB gene of other species of Veillonella corresponding to the same nucleotide positions of the reverse primers indicated.
Fig 2.
The products of the polymerase chain reaction obtained by using a mixture of primers.
Molecular weight marker is in lane 1. Primers were a mixture of VF, ATYR, DENR, DISR, PARR, ROGR, and TOBR. Template DNA was from V. atypica, lane 2; V. denticariosi, lane 3; V. dispar, lane 4; V. parvula, lane 5; V. rogosae, lane 6; V. tobetsuensis, lane 7; the mixture of all PCR products of Veillonella species, lane 8.
Fig 3.
Sensitivity of the PCR for decreasing concentrations of genomic DNA purified from Veillonella species using species-specific primer sets.
A molecular weight marker is shown in lanes 1, 9, 17, 25, 33, and 41. Lane 2 to lane 8: V. atypica, lane 10 to 16: V. denticariosi, lane 18 to 24: V. dispar, lane 26 to 32: V. parvula, lane 34 to 40: V. rogosae, lane 42 to 48: V. tobetsuensis. Amount of the target genomic DNA in the reaction mixture is as follows. Lane 2, 10, 18, 26, 34, and 42: 10 ng; lane 3, 11, 19, 27, 35, and 43: 1 ng; lane 4, 12, 20, 28, 36, and 44: 0.1 ng, lane 5, 13, 21, 29, 38, and 45: 0.01 ng; lane 6, 14, 22, 30, 38, and 46: 1 pg; lane 7, 15, 23, 31, 39, and 47: 0.1 pg; lane 8, 16, 24, 32, 40, and 48: 0.01 pg.
Table 2.
The first group (Good oral hygiene).
Table 3.
The second group (Moderate oral hygiene).
Table 4.
The third group (Poor oral hygiene).
Fig 4.
Neighbour-joining tree based on rpoB gene sequences (559nt), showing the relationship between the representative 11 unknown strains T11011-4, T44370-5, T34266-2, T44370-18, T14073-2, T44370-2, T23132-1, T14073-3, T34266-20, T34266-13 and T12034-6 and the strains of the recognized members of the genus Veillonella.
The strain of each species and GenBank/EMBL/DDBJ accession numbers for rpoB gene sequences are shown as follows; V. atypica ATCC 17744T (EF185159), V. caviae ATCC 33540T (EF185163), V. criceti ATCC 17747T, V. denticariosi ATCC JCM 15641T (EF185162), V. dispar ATCC 17748T (EF185161), V. magna lac18T (GU479075), V. montpellierensis ADV 281.99T (EF411194), V. parvula ATCC 10790T (EF185158), V. ratti ATCC 17746T (EF185165), V. rodentium ATCC 17743T (EF185166), V. rogosae JCM 15642T (EF211831), V. seminalis strain 08/01/13-B-2228 (KJ580479), V. tobetsuensis ATCC BAA-2400T (AB698646), T; Type strain. Bootstrap values are indicated at corresponding nodes. Bar, 0.05 substitutions per site.