Table 3. Detailed results for group-specific direct 16S sequencing from clinical samples.
Species in parenthesis (n = 5) indicates cross-reactivity between primer groups.
| ID | Sample type | Primer pair A | Primer pair B | Primer pair C |
| 1 | Abscess brain | Gemella haemolysans/morbillorum | – | Fusobacterium nucleatum |
| Parvimonas sp. | ||||
| Streptococcus intermedius* | ||||
| 2 | Abscess brain | S. intermedius | – | F. nucleatum |
| 3 | Abscess brain | Parvimonas micra | Aggregatibacter aphrophilus† | F. nucleatum |
| S. intermedius | Eikenella corrodens | F. nucleatum subsp. polymorphum | ||
| Neisseria elongata | ||||
| 4 | Abscess brain | Actinomyces meyeri | Campylobacter gracilis | F. nucleatum |
| S. intermedius | Prevotella pleuritidis | |||
| 5 | Abscess brain | A. meyeri | C. gracilis | Fusobacterium sp. |
| Peptostreptococcus sp. | Eikenella sp. | |||
| 6 | Abscess liver | Enterococcus faecium/durans | Escherichia coli/Shigella spp.† | Lactobacillus rhamnosus |
| Staphylococcus haemolyticus | ||||
| 7 | Abscess liver | G. haemolysans | – | Prevotella melaninogenica |
| Streptococcus mitis group | (S. parasanguinis) | |||
| Streptococcus parasanguinis | ||||
| 8 | Abscess liver | – | E. coli/Shigella spp. | Clostridium perfringens |
| 9 | Abscess muscle | P. micra | E. corrodens | F. nucleatum |
| S. constellatus/intermedius | Porphyromonas circumdentaria | |||
| 10 | Abscess ovarian | Parvimonas sp. | – | F. nucleatum |
| 11 | Abscess pancreas | Enterococcus faecium (Bacteroides fragilis) | – | Bacteroides fragilis |
| 12 | Abscess pancreas | A. meyeri (P. melaninogenica) | Campylobacter concisus | P. melaninogenica/histicola |
| Staphylococcus epidermidis | ||||
| 13 | Abscess para-aortic | Corynebacterium tuberculostearicum | – | S. haemolyticus/epidermidis |
| Corynebacterium appendicis | ||||
| 14 | Abscess psoas | E. faecium | Enterobacter hormaechei | – |
| 15 | Abscess spleen | Enterococcus casseliflavus/gallinarum | E. coli/Shigella spp. | F. nucleatum |
| Enterococcus faecalis | S. epidermidis | |||
| Streptococcus anginosus | ||||
| 16 | Abscess subcutaneous | E. faecium | – | (E. faecium) |
| Finegoldia magna | (F. magna) | |||
| 17 | Abscess retroperitoneal | E. faecium/durans | Klebsiella pneumoniae | – |
| 18 | Bile | – | E. coli/Shigella spp. | F. nucleatum |
| 19 | Bile | Enterococcus caccae | – | S. epidermidis |
| E. casseliflavus/gallinarum | ||||
| E. faecalis | ||||
| 20 | Empyema | P. micra | – | Prevotella nigrescens |
| S. anginosus | Peptostreptococcus stomatis | |||
| 21 | Empyema | S. intermedius | C. gracilis | Fusobacterium sp. |
| 22 | Empyema | P. micra | C. gracilis | F. nucleatum |
| S. intermedius | ||||
| 23 | Empyema | P. micra | C. gracilis | F. nucleatum |
| S. constellatus | Haemophilus parainfluenzae | P. melaninogenica | ||
| 24 | Empyema | P. micra | C. gracilis | Prevotella pleuritidis |
| S. intermedius | E. corrodens | |||
| 25 | Empyema | Dialister invisus | – | P. nigrescens † |
| Dialister micraerophilus | Prevotella veroralis | |||
| P. micra |
*
Differentiation between S. constellatus and S. intermedius based on type strains only.
†
Chromatogram too complex to allow for complete analysis. Only dominant peaks included.