Table 4.
ONT R10.4 output classification of the 4.5 kb rrn reads in characterizing the ZymoBIOMICS gut microbiome standard.
| Genus | Species | NCBI RRN | EMU | RDP | SILVA | Theoretical |
|---|---|---|---|---|---|---|
| Akkermansia | Akkermansia muciniphila | 0.97 | ||||
| Bacteroides | Bacteroides fragilis | 15.55 | 15.53 | 15.77 | 4 | 9.94 |
| Bifidobacterium | Bifidobacterium adolescentis | 1.68 | 1.66 | 1.67 | 1.15 | 8.78 |
| Clostridioides | Clostridioides difficile | 4.52 | 4.38 | 4.41 | 4.13 | 2.62 |
| Clostridium | Clostridium perfringens | <0.01 | ||||
| Enterococcus | Enterococcus faecalis | <0.01 | ||||
| Escherichia | Escherichia coli | 8.12 | 8.08 | 8 | 3.56 | 12.12 |
| Faecalibacterium | Faecalibacterium prausnitzii | 9.43 | 9.32 | 2.28 | 17.63 | |
| Faecalibacterium | uncultured Faecalibacterium sp. | 6.92 | ||||
| Fusobacterium | Fusobacterium nucleatum | 4.25 | 4.21 | 4.1 | 5.3 | 7.49 |
| Klebsiella | Klebsiella pneumoniae | 9.2 | ||||
| Limosilactobacillus | Limosilactobacillus fermentum | 1.03 | 1.01 | 1 | 9.63 | |
| Methanobrevibacter | Methanobrevibacter smithii | 0.07 | ||||
| Mycoplasma | Mycoplasma arthritidis | 0.51 | ||||
| Myroides | Myroides odoratimimus | 18.33 | ||||
| Prevotella | Prevotella corporis | 12.64 | 17.8 | 8.52 | 19.46 | 4.98 |
| Prevotella | Prevotella melaninogenica | 4.83 | ||||
| Prevotella | Prevotella sp. S4-BM14 | 9.05 | ||||
| Roseburia | Roseburia hominis | 1.73 | 1.71 | 0.92 | 1.7 | 9.89 |
| Streptococcus | Streptococcus pneumoniae | 7.85 | ||||
| Veillonella | Veillonella rogosae | 0.69 | 6.79 | 3.72 | 3.18 | 15.87 |
| Veillonella | uncultured Veillonella sp. | 0.9 | ||||
| Veillonella | Veillonella atypica | 6.58 | ||||
| Veillonella | Veillonella dispar | 17.25 | 0.59 | 0.33 | ||
| Veillonella | Veillonella parvula | 11.56 | 28.63 | 18.41 | 21.27 | |
| Veillonella | Veillonella sp. oral clone VeillD5 | 1.01 | ||||
| Veillonella | Veillonella sp. SY-2 | 11.33 | ||||
| Salmonella enterica | <0.01 | |||||
| uncultured bacterium adhufec225 | 0.2 |
Relative abundances are shown as the average across four replicates after applying sample abundance threshold filtering. Four databases were tested: NCBI RRN database (NCBI RRN), Ribosomal Database Project (RDP), the EMU database (EMU), and Silva-138 database (Silva-138). The values for the relative abundance of the Mock are obtained through the supplier's website and attached documents. Taxa absent using specific taxonomy databases are shown as missing values in their respective cells.