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Table 1 Most prevalent microorganisms detected by metagenomic sequencing of three cheese surface samples

From: Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

 

Reference genome

New(a)

Commercial cultures (b)

Number of reads (c)

Number of CDS (d)

Cumulated CDS length

Covered CDS (%) (e)

Covered sequence length (%) (f)

Mean genome coverage

Mapped reads (%) (g)

Sequences covered by perfect match reads (%) (h)

Cheese E

Arthrobacter arilaitensis GMPA29

1

1

2919327

3299

2875518

95.4

93.1

34.64

19.80

99.5

Psychrobacter immobilis PG1

1

0

1259254

2941

2824830

99.4

94.3

15.48

8.54

99.9

Vibrio litoralis B4

1

0

768119

3353

3158767

95.6

82.2

8.36

5.21

92.3

Pseudoalteromonas haloplanktis TAC125

0

0

384444

3454

3327182

94.1

70.4

4.00

2.61

93.1

Geotrichum candidum CLIB 918

0

1

378769

6925

10213537

98.3

38.6

1.30

2.57

95.5

Halomonas sp. 1 M45

1

0

221008

3526

3281784

95.6

77.1

2.31

1.50

93.5

Lactococcus lactis subsp. lactis Il1403

0

1

105179

2088

1869362

95.3

54.9

1.80

0.71

96.5

Debaryomyces hansenii CBS767

0

1

77071

6295

9107395

91.7

16.6

0.30

1.27

85.6

Cheese L

Pseudoalteromonas haloplanktis TAC125

0

0

1434355

3454

3327182

93.7

89.5

14.95

17.03

97.6

Halomonas sp. 1 M45

1

0

883652

3526

3281784

100.0

99.3

9.16

10.49

99.97

Psychrobacter celer 91

1

0

146974

2584

2414775

95.6

76.5

2.08

1.74

91.5

Lactococcus lactis subsp. cremoris A76

0

1

143400

2470

1969568

92.5

35.4

0.82

1.70

98.1

Penicillium camemberti FM 013

0

1

83277

14611

22234696

85.1

10.8

0.13

0.99

97.7

Vibrio litoralis B4

1

0

65937

3353

3158767

90.0

27.6

0.70

0.78

85.9

Providencia heimbachae GR4

1

0

53280

3824

3516737

83.6

26.7

0.51

0.63

55.3

Geotrichum candidum CLIB 918

0

1

45165

6925

10213537

95.0

12.7

0.15

0.54

95

Cheese G

Arthrobacter bergerei Ca106

1

1

2878361

3553

3110335

98.6

95.7

31.77

18.58

99.2

Lactobacillus delbrueckii subsp. bulgaricus ATCC11842

0

1

1179878

1508

1340406

98.7

95.4

29.44

7.62

99.8

Penicillium camemberti FM 013

0

1

633123

14611

22234696

99.4

54.2

1.00

4.09

96.5

Streptococcus thermophilus LMG 18311

0

1

597916

1827

1462709

98.3

86.1

13.62

3.86

99.4

Penicillium roqueforti FM 164

0

1

254435

12630

23447373

98.5

26.3

0.38

1.64

98.4

Pseudoalteromonas haloplanktis TAC125

0

0

146457

3454

3327182

93.5

57.8

1.53

0.95

92.3

Debaryomyces hansenii CBS767

0

1

80179

6295

9107395

94.2

17.6

0.31

0.52

97.1

Psychrobacter aquimaris ER15 174 BHI7

1

0

74153

2830

2734881

93.7

41.7

0.87

0.48

81.5

  1. (a) Genomes sequenced in the present study (1) or from the NCBI database (0).
  2. (b) Species known to be components of cheese making commercial cultures.
  3. (c) Number of reads mapped on CDS from the reference genome with three or less mismatches on 35 nucleotides.
  4. (d) Number of CDS in the genome. CDS corresponding to insertion sequences, prophages and potential repeated and transferable elements were removed.
  5. (e) Percentage of CDS covered with at least one read.
  6. (f) Percentage of sequence covered by at least one read (sequence is restrained to the selected CDS).
  7. (g) Number of reads aligned with this genome divided by the number of good quality reads.
  8. (h) Length of sequence covered by perfect match reads (with no mismatch on the 35 nt length alignment) divided by the length of the sequence covered by reads.
  9. For each cheese, the data presented correspond to the eight reference genomes with the highest numbers of mapped reads.
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BMC Genomics

ISSN: 1471-2164

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