TABLE 4.
Comparison of bacterial populations in GAM broth determined by real-time quantitative PCR, direct counting with DAPI staining, and the culture methoda
| Primer | Species | Strain | Log10 bacteria/ml as determined by:
|
||
|---|---|---|---|---|---|
| qPCRb | DAPI | Culture | |||
| g-Ccoc | Clostridium clostridiiforme | YIT 6051T | 9.5 ± 0.1 | 9.5 ± 0.1 | 9.1 ± 0.1 |
| Clostridium coccoides | YIT 6035T | 9.3 ± 0.2 | 9.4 ± 0.3 | 8.7 ± 0.1 | |
| Clostridium nexile | YIT 6170T | 8.9 ± 0.1 | 8.7 ± 0.1 | 7.4 ± 0.3 | |
| Clostridium oroticum | YIT 6037T | 8.6 ± 0.1 | 8.5 ± 0.1 | 8.3 ± 0.1 | |
| Clostridium sphenoides | YIT 6059T | 9.1 ± 0.2 | 9.2 ± 0.2 | 9.3 ± 0.1 | |
| Eubacterium rectale | YIT 6082T | 8.9 ± 0.1 | 8.9 ± 0.1 | <7.0 | |
| Ruminococcus gnavus | YIT 6176T | 8.7 ± 0.2 | 8.7 ± 0.2 | 8.4 ± 0.1 | |
| Ruminococcus productus | YIT 6141T | 9.5 ± 0.2 | 9.3 ± 0.2 | 9.1 ± 0.1 | |
| sg-Clept | Faecalibacterium prausnitzii | YIT 6174 | 8.9 ± 0.1 | 8.9 ± 0.2 | <7.0 |
| Eubacterium siraeum | YIT 10049T | 9.1 ± 0.1 | 8.9 ± 0.2 | <7.0 | |
| Ruminococcus bromii | YIT 6078T | 9.3 ± 0.1 | 9.2 ± 0.1 | <7.0 | |
| Ruminococcus callidus | YIT 6175T | 8.5 ± 0.1 | 8.8 ± 0.2 | <7.0 | |
| Ruminococcus albus | YIT 6083T | 8.3 ± 0.1 | 9.0 ± 0.1 | <7.0 | |
| Clostridium viride | YIT 10050T | 8.0 ± 0.1 | 8.9 ± 0.1 | <7.0 | |
| Clostridium leptum | YIT 6169T | 8.1 ± 0.2 | 9.1 ± 0.1 | <7.0 | |
| g-Bfra | Bacteroides caccae | ATCC 43185T | 9.4 ± 0.1 | 9.6 ± 0.1 | 8.8 ± 0.2 |
| Bacteroides eggerthii | DSM 20697T | 9.0 ± 0.1 | 8.8 ± 0.1 | 9.4 ± 0.1 | |
| Bacteroides fragilis | YIT 6158T | 9.4 ± 0.1 | 9.4 ± 0.2 | 8.3 ± 0.3 | |
| Bacteroides ovatus | YIT 6161T | 9.1 ± 0.1 | 9.4 ± 0.2 | 8.5 ± 0.1 | |
| Bacteroides thetaiotaomicron | YIT 6163T | 8.8 ± 0.1 | 9.0 ± 0.2 | 8.8 ± 0.2 | |
| Bacteroides uniformis | YIT 6164T | 8.8 ± 0.1 | 8.8 ± 0.1 | 8.6 ± 0.1 | |
| Bacteroides vulgatus | YIT 6159T | 8.7 ± 0.1 | 8.7 ± 0.1 | 8.6 ± 0.1 | |
| c-Atopo | Atopobium parvulum | YIT 10055T | 8.8 ± 0.2 | 8.7 ± 0.1 | 9.3 ± 0.1 |
| Collinsella aerofaciens | ATCC 25986T | 9.3 ± 0.1 | 9.1 ± 0.1 | 8.9 ± 0.2 | |
| Collinsella intestinalis | YIT 10051T | 9.2 ± 0.1 | 9.3 ± 0.1 | 10.0 ± 0.1 | |
| Collinsella stercoris | YIT 10052T | 8.8 ± 0.2 | 9.0 ± 0.2 | 8.7 ± 0.2 | |
| Eggerthella lenta | YIT 6077T | 8.1 ± 0.1 | 8.7 ± 0.2 | 8.2 ± 0.1 | |
| g-Prevo | Prevotella corporis | YIT 6132T | 9.0 ± 0.1 | 8.8 ± 0.2 | 8.7 ± 0.1 |
| Prevotella denticola | YIT 6131 | 8.8 ± 0.1 | 8.9 ± 0.3 | 9.4 ± 0.1 | |
| Prevotella melaninogenica | YIT 6039T | 9.4 ± 0.1 | 9.2 ± 0.2 | 9.5 ± 0.1 | |
| Prevotella veroralis | YIT 6126T | 8.8 ± 0.1 | 8.8 ± 0.1 | 8.9 ± 0.1 | |
a
A comparison of bifidobacterial species has been reported previously (17).
b
PCR, real-time quantitative PCR.