TABLE 2

Results of supervised classification of subgingival samples by using random forestsa

16S rRNA genus or ratioMetabolites or ratiobShotgun species or ratio
Disease class
 Mycoplasma 228.231–228.234_555–569 Capnocytophaga granulosa
    Order ML615J-28c697.907–697.909_220–226TM7
 Desulfovibrio 872.632–872.634_222–227 Porphyromonas gingivalis
 Filifactor 453.356–453.359_701–706TM7
 Porphyromonas 705.697–705.703_220–226 Porphyromonas gingivalis
 Eubacterium 689.111–689.113_218–222 Capnocytophaga granulosa
    Family Leptotrichiaceaec284.294–284.296_672–675 Streptococcus cristatus
 Desulfomicrobium 257.246–257.249_225–227TM7
    Family Tissierellaceaec185.113–185.115_217–222 Leptotrichia buccalis
 SHD-231698.306–698.308_221–227Order Neisserialesc
        1.5b1.61404b1.71429b
MPD
 Desulfovibrio 480.546–480.554_525–581 Shuttleworthia satelles
    Family Leptotrichiaceaec285.279–285.280_134–136 Tannerella forsythia
    Order: ML615J-28c272.294–272.297_370–376 Riemerellac
    Family Tissierellaceaec477.355–477.366_104–116 Selenomonas artemidis
 Butyrivibrio 497.357–497.366_765–803 Treponema denticola
 Pedobacter 382.156–382.159_330–362 Shuttleworthiac
 Megasphaera 611.354–611.358_462–473 Leptotrichia wadei
 Desulfomicrobium 285.277–285.280_149–177 Rothiac
 Porphyromonas 497.083–497.091_349–367 Actinomyces oris
 Paludibacter 475.096–475.105_713–757Family Aerococcaceaec
        1.25581b1.70175b0.89674b
  • a Shown are the top 10 features, as indicated by importance scores, predicting disease class (top) and MPD (bottom) from supervised classification analyses of subgingival samples.

  • b Ratio of estimated generalization error to baseline error of the classifier for subgingival samples.

  • c Not classifiable at a lower taxonomic level.