Table 1.
Assessment of genomes reconstructed from the shotgun-sequenced microbial community: assembly, binning, phylogeny, and genome completeness
| Genome | Near-complete genome | Phylum | Bin | Genome size (bp) | Genome relative abundance (%) | N50 (bp) | Number of ORFs | Predicted% single copy genes |
|---|---|---|---|---|---|---|---|---|
|
Escherichia coli - strain A/B - plasmid |
Yes |
n/a |
14 |
3,225 |
41.67 |
3,225 |
5 |
n/a |
|
Escherichia coli - strain A - phage |
|
n/a |
5 |
3,920 |
16.57 |
3,920 |
4 |
n/a |
|
Enterococcus faecalis - plasmid |
Yes |
n/a |
14 |
5,231 |
5.98 |
5,231 |
5 |
n/a |
|
Streptococcus anginosus |
Yes |
Firmicutes |
7 |
2,108,491 |
5.14 |
537,826 |
2,252 |
100.0 |
|
Escherichia coli - strain A |
|
Proteobacteria |
5, 21 |
5,662,200 |
4.91 |
5,304 |
7,405 |
48.1 |
|
Actinomyces urogenitalis - phage |
|
n/a |
12 |
2,996 |
4.85 |
2,996 |
4 |
n/a |
|
Veillonella dispar |
Yes |
Firmicutes |
11 |
2,445,194 |
3.99 |
53,688 |
2,693 |
100.0 |
|
Veillonella sp. - species A - phage |
|
n/a |
22 |
20,453 |
3.49 |
20,453 |
32 |
n/a |
|
Veillonella sp. - species B - phage |
|
n/a |
23 |
16,533 |
2.43 |
16,533 |
30 |
n/a |
|
Actinomyces urogenitalis |
Yes |
Actinobacteria |
12, 13 |
2,604,957 |
2.28 |
3,337 |
3,035 |
92.6 |
|
Clostridium butyricum |
Yes |
Firmicutes |
1 |
4,350,784 |
2.17 |
103,127 |
4,094 |
100.0 |
|
Veillonella sp. - species A - plasmid |
Yes |
n/a |
16 |
47,631 |
1.20 |
47,631 |
56 |
n/a |
|
Veillonella sp. - species A |
|
Firmicutes |
3, 16 |
2,664,763 |
1.03 |
4,180 |
3,427 |
37.0 |
|
Enterococcus faecalis |
Yes |
Firmicutes |
4 |
2,960,721 |
0.76 |
235,714 |
2,906 |
100.0 |
|
Staphylococcus sp. - plasmid B |
Yes |
n/a |
Unbinned |
2,539 |
0.65 |
2,539 |
2 |
n/a |
|
Staphylococcus sp. - plasmid A |
Yes |
n/a |
Unbinned |
2,556 |
0.54 |
2,556 |
3 |
n/a |
|
Staphylococcus sp. - phage |
|
n/a |
Unbinned |
2,423 |
0.42 |
2,423 |
5 |
n/a |
|
Escherichia coli - strain B |
|
Proteobacteria |
14 |
633,084 |
0.37 |
4,041 |
873 |
3.7 |
|
Varibaculum cambriense
|
Yes |
Actinobacteria |
20 |
2,247,641 |
0.37 |
240,417 |
1,954 |
100.0 |
|
Streptococcus parasanguinis - plasmid |
Yes |
n/a |
23 |
8,975 |
0.31 |
8,975 |
7 |
n/a |
|
Veillonella sp. - species B |
|
Firmicutes |
18, 19 |
639,180 |
0.27 |
2,044 |
879 |
29.6 |
|
Clostridium bartlettii |
Yes |
Firmicutes |
8, 9 |
2,685,446 |
0.18 |
12,095 |
2,633 |
92.6 |
|
Negativicoccus succinicivorans |
Yes |
Negativicoccus |
17, 25 |
1,508,898 |
0.10 |
15,236 |
1,686 |
100.0 |
|
Staphylococcus sp. |
|
Firmicutes |
6, 22 |
1,509,765 |
0.09 |
9,200 |
1,634 |
33.3 |
|
Propionibacterium sp. |
|
Propionibacterium |
15 |
336,576 |
0.07 |
1,117 |
565 |
18.5 |
|
Streptococcus parasanguinis |
Yes |
Firmicutes |
23, 24 |
2,822,032 |
0.06 |
3,494 |
3,647 |
77.8 |
|
Leuconostoc sp. |
|
Firmicutes |
2 |
566,369 |
0.06 |
1,603 |
874 |
25.9 |
| Streptococcus sp. | Firmicutes | 10 | 1,915,777 | 0.05 | 11,008 | 2,114 | 55.6 |
n/a, not available.