Table 2.
Comparison of reconstructed genomes and 16S rRNA gene sequences with reference databases
| Genome | Genome size (bp) | Closest relative with sequenced genome | Closest relative genome size (bp) | % ORFs orthologous to reference | Average% amino acid ID of orthologs | EMIRGE 16S rRNA gene match | EMIRGE 16S% ID |
|---|---|---|---|---|---|---|---|
|
Escherichia coli - strain A/B - plasmid |
3,225 |
Salmonella enterica subsp. enterica serovar Newport str. SL254 plasmid |
684 |
20.0 |
93.9 |
n/a |
n/a |
|
Escherichia coli - strain A - phage |
3,920 |
n/a |
n/a |
n/a |
n/a |
n/a |
n/a |
|
Enterococcus faecalis - plasmid |
5,231 |
Enterococcus faecalis 62 plasmid |
1,295 |
100.0 |
100.0 |
n/a |
n/a |
|
Streptococcus anginosus |
2,108,491 |
Streptococcus anginosus 1 2 62CV uid62163 |
1,821,055 |
67.7 |
95.2 |
S. anginosus |
99.8 |
|
Escherichia coli - strain A |
5,662,200 |
Escherichia coli S88 uid62979 |
5,032,268 |
47.7 |
97.5 |
E. coli O83:H1 str. NRG 85 |
99.9 |
|
Actinomyces urogenitalis - phage |
2,996 |
n/a |
n/a |
n/a |
n/a |
n/a |
n/a |
|
Veillonella dispar |
2,445,194 |
Veillonella dispar ATCC 17748 |
2,118,767 |
60.0 |
91.6 |
V. dispar |
99.3 |
|
Veillonella sp. - species A - phage |
20,453 |
n/a |
n/a |
n/a |
n/a |
n/a |
n/a |
|
Veillonella sp. - species B - phage |
16,533 |
n/a |
n/a |
n/a |
n/a |
n/a |
n/a |
|
Actinomyces urogenitalis |
2,604,957 |
Actinomyces urogenitalis DSM 15434 |
2,702,812 |
67.1 |
98.7 |
A. urogenitalis |
99.9 |
|
Clostridium butyricum |
4,350,784 |
Clostridium butyricum 5521 |
4,540,699 |
73.5 |
96.5 |
C. butyricum |
99.3 |
|
Veillonella sp. - species A - plasmid |
47,631 |
Caldicellulosiruptor kristjanssonii 177R1B plasmid |
3,674 |
3.6 |
38.8 |
n/a |
n/a |
|
Veillonella sp. - species A |
2,664,763 |
Veillonella dispar ATCC 17748 |
2,118,767 |
47.1 |
95.6 |
Veillonella sp. oral taxon 158 |
91.2 |
|
Enterococcus faecalis |
2,960,721 |
Enterococcus faecalis OG1RF |
2,739,625 |
79.1 |
98.8 |
E. faecalis OG1RF |
98.7 |
|
Staphylococcus sp. - plasmid B |
2,539 |
Staphylococcus haemolyticus JCSC1435 plasmid |
402 |
100.0 |
99.8 |
n/a |
n/a |
|
Staphylococcus sp. - plasmid A |
2,556 |
Macrococcus caseolyticus JCSC5402 plasmid |
997 |
33.3 |
80.3 |
n/a |
n/a |
|
Staphylococcus sp. - phage |
2,423 |
n/a |
n/a |
n/a |
n/a |
n/a |
n/a |
|
Escherichia coli - strain B |
633,084 |
Escherichia coli S88 uid62979 |
5,032,268 |
52.7 |
82.3 |
n/a |
n/a |
|
Varibaculum cambriense
|
2,247,641 |
Mobiluncus mulieris ATCC 35239
|
2,533,633 |
56.0 |
53.9 |
V. cambriense
|
99.2 |
|
Streptococcus parasanguinis - plasmid |
8,975 |
Enterococcus faecium Aus0004 plasmid |
1,192 |
14.3 |
32.4 |
n/a |
n/a |
|
Veillonella sp. - species B |
639,180 |
Veillonella dispar ATCC 17748 |
2,118,767 |
62.5 |
86.7 |
V. parvula DSM 2008 |
90.3 |
|
Clostridium bartlettii |
2,685,446 |
Clostridium bartlettii DSM 16795 |
2,972,256 |
81.7 |
98.1 |
Clostridium sp. MDA2315 |
99.4 |
|
Negativicoccus succinicivorans |
1,508,898 |
Bacillus coagulans 36D1 |
3,552,226 |
45.0 |
43.4 |
N. succinicivorans |
98.0 |
|
Staphylococcus sp. |
1,509,765 |
Staphylococcus epidermidis ATCC 12228 |
2,499,279 |
78.3 |
98.4 |
S. epidermidis ATCC 12228 |
96.2 |
|
Propionibacterium sp. |
336,576 |
Propionibacterium 5 U 42AFAA |
2,532,807 |
46.4 |
82.4 |
Propionibacterium sp. H456 |
99.4 |
|
Streptococcus parasanguinis |
2,822,032 |
Streptococcus parasanguinis ATCC 15912 |
2,153,652 |
45.0 |
94.3 |
S. parasanguinis |
98.9 |
|
Leuconostoc sp. |
566,369 |
Leuconostoc citreum KM20 |
1,796,284 |
66.7 |
96.0 |
n/a |
n/a |
| Streptococcus sp. | 1,915,777 | Streptococcus M334 | 2,207,013 | 67.6 | 93.9 | n/a | n/a |
Reconstructed genomes were compared with the genomes of isolate strains. Reconstructed 16S rRNA genes were searched against sequences in the RDP and GreenGenes databases to aid classification. n/a, not available.