Table 1.
Genomes reconstructed from the oral metagenome of a 3-week-old premature infant.
| Binned | Closed | |||||||
|---|---|---|---|---|---|---|---|---|
| Genome | 1 | 2 | 3 | 4 | 5 | 6 | 2 | CP007711b |
| Organism | Pseudomonas aeruginosa | Mycoplasma sp. ‘Mnola' | Streptococcus parasanguinis | Enterobacter cloacae | Staphylococcus epidermidis | Trichomonas vaginalis | Ca. M. girerdii str. UC-B3 | Ca. M. girerdii str. VCU-M1 |
| Fold coverage | 151.8 | 79.7 | 17.2 | 4.7 | 5.5 | ~0.2a | 76.1 | 67–9516 |
| Scaffolds ≥1 kb | 71 | 23 | 95 | 1,013 | 62 | 149 | 1 | 1 |
| Size (bp) | 6,722,245 | 613,365 | 2,204,765 | 1,550,266 | 92,937 | 268,614 | 629,409 | 618,983 |
| N50 | 212,032 | 71,441 | 48,153 | 1,504 | 1,401 | 1,817 | n/a | n/a |
| L50 | 9 | 3 | 16 | 370 | 22 | 48 | n/a | n/a |
| G + C (%) | 66.1 | 28.6 | 41.5 | 55.1 | 32.6 | 31.4 | 28.6 | 28.6 |
| Genetic code | 11 | 4 | 11 | 11 | 11 | 1 | 4 | 4 |
| CheckM completeness (% of marker sets) | 99.68 | 98.08 | 100.00 | 36.95 | 0.00 | n/d | 98.08 | 98.08 |
| Relative abundance (% of genomes) | 58.57 | 30.77 | 6.64 | 1.81 | 2.12 | 0.08 | n/d | n/a |
| Absolute abundance (% of bases) | 66.58 | 3.19 | 2.48 | 0.48 | 0.03 | 2.31 | n/d | n/a |
| Index of replication (iRep) | 1.72 | 1.42 | 1.35 | n/d | n/d | n/d | 1.42 | n/a |
| Domain; Phylum | Bacteria; Proteobacteria | Bacteria; (Tenericutes) | Bacteria; Firmicutes | Bacteria; Proteobacteria | Bacteria; Firmicutes | Eukaryota; Metamonada | Bacteria; (Tenericutes) | Bacteria; (Tenericutes) |
| Genes | 6,512 | 629 | 2,182 | 2,364 | 123 | n/d | 609 | 611 |
| rRNAs (rrn copies predicted) | 5S, 16S, 23S (4) | 5S, 16S, 23S (1) | 5S, 16S, 23S (4) | 5S, 16S, 23S (~7–8) | 5S, 16S, 23S (~4–6) | 5.8S, 18S, 28S (~250)27 | 5S, 16S, 23S (1) | 5S, 16S, 23S (1) |
| tRNAs (amino acids decoded) | 58 (21) | 31 (20) | 31 (16) | 14 (10) | none detected | none detected | 31 (20) | 31 (20) |
| Other ncRNAs | n/d | RNAse P RNA | n/d | n/d | n/d | n/d | RNAse P RNA | n/d |
| ORFs | 6,450 | 595 | 2,148 | 2,347 | 120 | n/d | 574 | 577 |
| Frameshifts | n/d | n/d | n/d | n/d | n/d | n/d | 10 | 4 |
| Pseudogenes | n/d | n/d | n/d | n/d | n/d | n/d | 1 | 1 |
| CRISPR-Cas | none detected | none detected | none detected | present | n/d | n/a | none detected | none detectedc |
aEstimated using reference-based mapping; bAccession number of the vaginal strain, provided here for reference; cOur own finding, which differs from that of Fettweis et al.16 as described in the Supplementary Methods; n/a, not applicable; n/d, not determined; (Tenericutes) branches within the phylum Firmicutes7.