TABLE 3.
Pyrosequencing and VITEK 2 results of the pharyngeal normal microbiota isolates
| Group and no. of strains | Pyrosequencing resulta
|
VITEK 2 result
|
||
|---|---|---|---|---|
| Species | Scoreb | Species | Confidence levelc (n) | |
| S. mitis group | ||||
| 2 | S. mitis | 100d | NDe | — (2) |
| 4 | S. mitis | 96.9 | S. intermedius | Exc (1) |
| S. mitis/S. oralis | Exc (1) or VG (2) | |||
| 1 | S. infantis | 96.9 | ND | — (1) |
| 1 | S. pneumoniae, S. pseudopneumoniae, or S. mitis | 96.9 | ND | — (1) |
| 1 | S. cristatus, S. infantis or S. peroris | 93.7 | S. mitis/S. oralis | Exc (1) |
| 1 | S. infantis | 93.7 | S. mitis/S. oralis | Exc (1) |
| 1 | S. pneumoniae, S. pseudopneumoniae or S. mitis | 93.7d | ND | — (1) |
| 1 | S. oralis | 90.5 | S. mitis/S. oralis | VG (1) |
| 1 | S. infantis | 84.2d | S. parasanguinis | VG (1) |
| 1 | S. australis | 87.4d | ND | — (1) |
| 1 | S. mitis or S. oralis (v2) | 100f | S. salivarius | Exc (1) |
| 1 | S. australis (v2) | 100d,f | S. constellatus subsp. pharyngis | Good (1) |
| 2 | S. mitis, S. oralis, or S. infantis (v2) | 93.7d,f | S. mitis/S. oralis | VG (1) or Good (1) |
| S. sanguinis group | ||||
| 1 | S. parasanguinis | 100 | S. parasanguinis | Exc (1) |
| 2 | S. gordonii | 96.9 | S. gordonii | Exc (1) |
| ND | — (1) | |||
| 1 | S. sanguinis | 96.9 | ND | — (1) |
| 1 | S. sanguinis | 90.5 | S. mitis/S. oralis | Acc (1) |
| 5 | S. parasanguinis | 93.7 | S. parasanguinis | VG (2) or Exc (3) |
| 1 | S. parasanguinis | 90.5d | Inconclusive identification | — (1) |
| 2 | S. parasanguinis (v2) | 93.7d,f | S. parasanguinis | Exc (1) or Good (1) |
| S. salivarius group | ||||
| 1 | S. salivarius or S. vestibularis | 100 | ND | — (1) |
| 1 | S. salivarius or S. vestibularis | 96.9d | S. salivarius | Acc (1) |
| Undefined group | ||||
| 1 | S. gallinaceus | 90.5 | S. mitis/S. oralis | Exc (1) |
The isolates have been listed according to the pyrosequencing result.
The score is a measure of the relatedness of the studied sequence to the type strain sequence determined by the Identifire software. Score 100 is given to sequences that are identical to each other.
Confidence level is a measure of the strength of the VITEK analysis in the descending order Exc (excellent), VG (very good), good, Acc (acceptable), and LD (low discrimination).
One of the isolates with this pyrosequencing result was sequenced by conventional sequencing. The GenBank accession numbers of the sequences are EF151144 to EF151152.
ND, not determined.
The pyrograms of the v1 region of these isolates indicated heterogeneous 16S rDNA alleles, and the isolates were tentatively identified using the v2 region.