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Table 2 Comparison of reconstructed genomes and 16S rRNA gene sequences with reference databases

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

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

  1. 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.