Table 3.

The details of culture positive specimens with conflicting results

Specimen Type	Culture Results	Metagenomic Results (no. of species within the genus)
Sputum (P25)c a	Coliforms	Porphyromonas pasteri b Streptococcus species. (9) Prevotella species (10)
Throat Swab (P29)a	Moraxella spp	Prevotella species (9) Prevotella melaninogenica b
Pus Swab (P70)	Coagulase negative Staphylococcus species	Streptococcus b Filifactor alocis Prevotella intermedia
Pus Swab (P75)	Acinetobacter spp	Prevotella bivia b Peptoniphilus indolicus Finegoldia magna Dialister micraerophilus Veillonella montpellierensis Streptococcus anginosus Ureaplasma parvum
Pus Swab (P97)	Coliform Organisms	(−)

^aSamples in which all species detected in metagenomics workflow are not displayed due to the large number of species identified. See Additional file 2 for all species identified per sample

^bspecies of highest abundance

^cfungal species detected