Table 1.
Mean levels of species/taxa in caries-free (CF), coronal caries (CC) and dentin caries (DC).
| Family | Species/Taxon | CF (n = 4) | CF SEM | CC (n = 5) | CC SEM | DC (n = 6) | DC SEM |
|---|---|---|---|---|---|---|---|
| Actinobacteria | Actinobaculum sp. HOT 183 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.10E-02 | 2.10E-02 |
| Actinobaculum genus | 2.50E-04 | 2.50E-04 | 8.00E-04 | 3.74E-04 | 4.00E-03 | 3.27E-03 | |
| Actinomyces georgiae | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | 8.00E-04 | 8.00E-04 | |
| Actinomyces johnsonii | 5.00E-04 | 5.00E-04 | 0.00E+ 00 | 0.00E+ 00 | 6.60E-03 | 4.28E-03 | |
| Actinomyces massiliensis | 7.50E-04 | 4.79E-04 | 8.80E-03 | 6.58E-03 | 7.60E-03 | 6.62E-03 | |
| Actinomyces naeslundii | 2.25E-03 | 1.65E-03 | 1.06E-02 | 8.85E-03 | 4.88E-02 | 2.66E-02 | |
| Actinomyces odontolyticus | 1.00E-03 | 1.00E-03 | 2.00E-04 | 2.00E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Actinomyces oris | 7.50E-04 | 7.50E-04 | 9.20E-03 | 5.12E-03 | 1.96E-02 | 8.86E-03 | |
| Actinomyces sp. HOT 448 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 3.60E-02 | 2.33E-02 | |
| Actinomyces viscosus | 7.50E-04 | 4.79E-04 | 8.80E-03 | 6.20E-03 | 5.00E-03 | 3.56E-03 | |
| Brevibacterium genus | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Corynebacterium durum | 1.00E-03 | 1.00E-03 | 1.00E-03 | 6.32E-04 | 4.40E-03 | 2.32E-03 | |
| Corynebacterium matruchotii | 3.25E-03 | 2.93E-03 | 1.28E-02 | 7.28E-03 | 4.40E-03 | 1.91E-03 | |
| Rothia aeria | 3.00E-03 | 2.04E-03 | 4.00E-03 | 1.10E-03 | 1.46E-02 | 1.03E-02 | |
| Rothia dentocariosaa | 5.00E-04 | 2.89E-04 | 6.80E-03 | 4.09E-03 | 1.10E-02 | 7.22E-03 | |
| Rothia mucilaginosa | 5.00E-04 | 5.00E-04 | 4.00E-04 | 2.45E-04 | 3.60E-03 | 2.20E-03 | |
| Rothia genusa | 1.55E-02 | 5.75E-03 | 6.78E-02 | 1.51E-02 | 7.54E-02 | 6.64E-02 | |
| Propionibacterium acnes | 2.50E-04 | 2.50E-04 | 6.00E-04 | 4.00E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Propionibacterium propionicum | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 1.00E-03 | 6.32E-04 | |
| Bifidobacterium dentium | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 1.60E-03 | 1.60E-03 | |
| Scardovia genus | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 1.42E-02 | 1.42E-02 | |
| Scardovia wiggsiaed | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 9.04E-02 | 6.71E-02 | |
| Atopobium parvulumd | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 6.40E-03 | 3.08E-03 | |
| Atopobium rimaed | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 1.70E-02 | 1.35E-02 | |
| Cryptobacterium curtum | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.40E-03 | 1.47E-03 | |
| Olsenella genus | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | |
| Bacteroidetes | Porphyromonas catoniae | 1.23E-02 | 1.23E-02 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 |
| Alloprevotella tannerae | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 4.00E-04 | 4.00E-04 | |
| Alloprevotella genus | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 6.00E-04 | 6.00E-04 | |
| Prevotella denticola | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 3.68E-02 | 2.85E-02 | |
| Prevotella melaninogenica | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 6.00E-04 | 4.00E-04 | |
| Prevotella nigrescensd | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.80E-03 | 1.53E-03 | |
| Prevotella orisd | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.64E-02 | 1.99E-02 | |
| Prevotella oulorumd | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 4.20E-03 | 2.06E-03 | |
| Prevotella pallens | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | |
| Prevotella salivae | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | |
| Prevotella veroralis | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 3.80E-03 | 3.80E-03 | |
| Capnocytophaga gingivalis | 2.50E-04 | 2.50E-04 | 0.00E+ 00 | 0.00E+ 00 | 6.00E-04 | 4.00E-04 | |
| Capnocytophaga genus | 7.50E-04 | 4.79E-04 | 3.40E-03 | 1.94E-03 | 1.12E-02 | 7.06E-03 | |
| Riemerella genus | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | |
| TM7 | TM7 TM7b | 0.00E+ 00 | 0.00E+ 00 | 4.00E-03 | 3.10E-03 | 4.00E-04 | 4.00E-04 |
| TM7 TM7c | 0.00E+ 00 | 0.00E+ 00 | 3.80E-03 | 2.46E-03 | 2.00E-04 | 2.00E-04 | |
| Firmicutes | Gemella haemolysans | 1.75E-03 | 1.75E-03 | 3.20E-03 | 1.66E-03 | 2.00E-04 | 2.00E-04 |
| Gemella morbillorum | 2.50E-04 | 2.50E-04 | 2.00E-04 | 2.00E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Gemella sanguinis | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 6.00E-04 | 4.00E-04 | |
| Gemella genus | 1.38E-02 | 1.01E-02 | 1.92E-02 | 8.58E-03 | 6.80E-03 | 3.07E-03 | |
| Abiotrophia defectivaad | 2.25E-02 | 1.14E-02 | 4.00E-03 | 9.49E-04 | 3.20E-03 | 2.08E-03 | |
| Granulicatella adiacens | 3.25E-03 | 2.93E-03 | 4.00E-03 | 1.92E-03 | 2.00E-04 | 2.00E-04 | |
| Granulicatella elegans | 5.00E-04 | 5.00E-04 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | |
| Granulicatella genuscd | 2.20E-02 | 1.10E-02 | 2.36E-02 | 5.73E-03 | 1.20E-03 | 7.35E-04 | |
| Streptococcus australis | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | 3.00E-03 | 1.90E-03 | |
| Streptococcus cristatus | 5.00E-03 | 3.70E-03 | 7.20E-03 | 3.51E-03 | 0.00E+ 00 | 0.00E+ 00 | |
| Streptococcus gordonii | 0.00E+ 00 | 0.00E+ 00 | 4.00E-04 | 4.00E-04 | 6.00E-04 | 6.00E-04 | |
| Streptococcus infantis | 7.50E-04 | 7.50E-04 | 4.00E-04 | 4.00E-04 | 8.00E-04 | 5.83E-04 | |
| Streptococcus intermedius | 3.75E-03 | 3.42E-03 | 2.04E-02 | 9.87E-03 | 1.16E-02 | 1.16E-02 | |
| Streptococcus mitis/ oralis/pneumoniae | 2.00E-03 | 5.77E-04 | 8.80E-03 | 5.23E-03 | 8.00E-04 | 3.74E-04 | |
| Streptococcus mutans | 2.50E-04 | 2.50E-04 | 2.32E-02 | 1.38E-02 | 3.86E-02 | 3.86E-02 | |
| Streptococcus parasanguinis | 1.75E-03 | 1.03E-03 | 2.00E-04 | 2.00E-04 | 2.40E-03 | 1.91E-03 | |
| Streptococcus salivarius | 7.50E-04 | 4.79E-04 | 4.40E-03 | 3.92E-03 | 6.40E-03 | 4.93E-03 | |
| Streptococcus sanguinis | 7.40E-02 | 2.77E-02 | 6.74E-02 | 1.35E-02 | 3.10E-02 | 1.59E-02 | |
| Streptococcus sp. AS14 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 3.20E-03 | 3.20E-03 | |
| Streptococcus sp. BS35b | 0.00E+ 00 | 0.00E+ 00 | 2.80E-03 | 2.80E-03 | 0.00E+ 00 | 0.00E+ 00 | |
| Streptococcus sp. GMD4S | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 1.20E-03 | 1.20E-03 | |
| Eubacterium infirmum | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.00E-03 | 2.00E-03 | |
| Eubacterium brachy | 2.50E-04 | 2.50E-04 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | |
| Ruminococcus torques | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | |
| Johnsonella ignava | 5.00E-04 | 2.89E-04 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | |
| Lachnoanaerobaculum saburreum | 2.50E-04 | 2.50E-04 | 0.00E+ 00 | 0.00E+ 00 | 4.00E-04 | 4.00E-04 | |
| Lachnospiraceae sp. HOT 107 | 2.50E-04 | 2.50E-04 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | |
| Oribacterium sp. HOT 078bcd | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 7.40E-03 | 4.20E-03 | |
| Stomatobaculum longum | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 1.40E-03 | 6.78E-04 | |
| Peptostreptococcus genus | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 4.00E-04 | 4.00E-04 | |
| Dialister invisus | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 1.48E-02 | 1.48E-02 | |
| Megasphaera micronuciformis | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 3.00E-03 | 2.14E-03 | |
| Mitsuokella genus | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | 2.00E-04 | 2.00E-04 | |
| Selenomonas artemidis | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 8.00E-04 | 8.00E-04 | |
| Selenomonas noxia | 2.25E-03 | 2.25E-03 | 1.40E-03 | 9.80E-04 | 2.00E-03 | 8.37E-04 | |
| Veillonella atypica | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 4.00E-04 | 4.00E-04 | |
| Veillonella parvula | 4.78E-02 | 2.98E-02 | 6.50E-02 | 1.63E-02 | 3.62E-02 | 2.30E-02 | |
| Veillonella genus | 2.06E-01 | 1.06E-01 | 2.44E-01 | 6.68E-02 | 9.50E-02 | 3.24E-02 | |
| Fusobacteria | Fusobacterium nucleatum | 0.00E+ 00 | 0.00E+ 00 | 1.00E-03 | 7.75E-04 | 5.20E-03 | 4.47E-03 |
| Fusobacterium periodonticum | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 6.00E-04 | 4.00E-04 | |
| Leptotrichia goodfellowii | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 6.00E-04 | 6.00E-04 | |
| Leptotrichia genus | 5.00E-04 | 2.89E-04 | 2.80E-03 | 2.56E-03 | 1.00E-03 | 1.00E-03 | |
| Proteobacteria | Rhodopseudomonas palustris | 5.00E-04 | 5.00E-04 | 1.80E-03 | 1.20E-03 | 2.00E-04 | 2.00E-04 |
| Rhodopseudomonas genus | 2.50E-04 | 2.50E-04 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | |
| Lautropia mirabilisd | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 3.00E-03 | 2.05E-03 | |
| Thiomonas genus | 0.00E+ 00 | 0.00E+ 00 | 4.00E-04 | 4.00E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Kingella denitrificans | 2.50E-04 | 2.50E-04 | 2.00E-04 | 2.00E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Kingella oralis | 1.25E-03 | 9.46E-04 | 1.40E-03 | 7.48E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Kingella genus | 1.38E-02 | 1.15E-02 | 5.60E-03 | 1.57E-03 | 2.40E-03 | 2.16E-03 | |
| Neisseria elongata | 1.25E-03 | 9.46E-04 | 3.00E-03 | 1.48E-03 | 1.60E-03 | 1.60E-03 | |
| Neisseria flavescens | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 4.00E-04 | 2.45E-04 | |
| Neisseria macacae | 0.00E+ 00 | 0.00E+ 00 | 4.00E-04 | 4.00E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Neisseria meningitidis | 2.50E-04 | 2.50E-04 | 4.00E-04 | 4.00E-04 | 8.00E-04 | 5.83E-04 | |
| Neisseria sicca | 4.00E-03 | 2.04E-03 | 1.40E-03 | 7.48E-04 | 4.00E-04 | 2.45E-04 | |
| Neisseria subflava | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | |
| Neisseria genus | 5.17E-01 | 1.61E-01 | 3.15E-01 | 1.10E-01 | 1.05E-01 | 6.38E-02 | |
| Campylobacter gracilis | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | 3.80E-03 | 3.56E-03 | |
| Campylobacter showae | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 4.00E-04 | 4.00E-04 | |
| Cardiobacterium hominis | 1.50E-03 | 6.45E-04 | 8.00E-04 | 3.74E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Cardiobacterium valvarum | 2.50E-04 | 2.50E-04 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | |
| Enterobacter cloacae | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | |
| Escherichia coli | 5.00E-04 | 2.89E-04 | 1.00E-03 | 1.00E-03 | 4.00E-04 | 2.45E-04 | |
| Escherichia genus | 0.00E+ 00 | 0.00E+ 00 | 4.00E-04 | 4.00E-04 | 2.00E-04 | 2.00E-04 | |
| Pantoea genus | 2.50E-04 | 2.50E-04 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | |
| Actinobacillus genus | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | |
| Aggregatibacter genus | 0.00E+ 00 | 0.00E+ 00 | 6.00E-04 | 6.00E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Haemophilus parainfluenzae | 7.50E-04 | 4.79E-04 | 2.00E-04 | 2.00E-04 | 1.10E-02 | 3.00E-03 | |
| Pasteurella genus | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | |
| Acinetobacter genus | 2.00E-03 | 2.00E-03 | 6.00E-04 | 4.00E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Pseudomonas genus | 0.00E+ 00 | 0.00E+ 00 | 8.00E-04 | 8.00E-04 | 1.20E-03 | 9.70E-04 | |
| Vibrio choleraecd | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 7.80E-03 | 3.72E-03 | |
| Treponema | Treponema socranskii | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 6.00E-04 | 4.00E-04 |
| Naumovozyma | Naumovozyma genus | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | 0.00E+ 00 | 0.00E+ 00 |
| Yeast | Candida genus | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | 0.00E+ 00 | 0.00E+ 00 |
| Viruses | Hpunalikevirus Vibrio phage kappa (DNA) | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 1.26E-02 | 1.26E-02 |
| Mastadenovirus Human adenovirus E (DNA) | 0.00E+ 00 | 0.00E+ 00 | 1.04E-02 | 1.02E-02 | 0.00E+ 00 | 0.00E+ 00 | |
| Bromovirus Brome mosaic virus (RNA) | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 6.00E-04 | 6.00E-04 | |
| Endornavirus Bell pepper endornavirus (RNA) | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Narnavirus Saccharomyces 20S RVA narnavirus (RNA) | 0.00E+ 00 | 0.00E+ 00 | 8.00E-04 | 8.00E-04 | 0.00E+ 00 | 0.00E+ 00 | |
| Potyvirus Dasheen mosaic virusd (RNA) | 0.00E+ 00 | 0.00E+ 00 | 4.00E-04 | 2.45E-04 | 6.82E-02 | 3.45E-02 | |
| Alpharetrovirus Avian myelocytomatosis virus (RNA) | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 2.00E-04 | 2.00E-04 | |
| Gammaretrovirus Murine osteosarcoma virus (RNA) | 7.50E-04 | 4.79E-04 | 4.80E-03 | 2.65E-03 | 8.00E-03 | 4.64E-03 | |
| Tobamovirus Cucumber green mottle mosiac virus (RNA) | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 0.00E+ 00 | 1.80E-03 | 1.80E-03 |
p ≤ 0.05, a = CF vs CC, b = CF vs DC, c = CC vs DC, d = all groups.