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Table 1 Assessment of genomes reconstructed from the shotgun-sequenced microbial community: assembly, binning, phylogeny, and genome completeness

From: Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life

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

  1. n/a, not available.