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Table 5 Coverage findings described in the literature for the gene primer pairs analysed in the present study

From: In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea

Present study

Other studies

Results present study

Results other studies

Ref.

Primer pair

Mean length (bps)

Primer pair name

Bacterial SC (%)

Archaeal SC (%)

Bacterial coverage (%)

Archaeal coverage (%)

KP_F044-KP_R023

100–300

S-D-Bact-0337-a-S-20/S-D-Bact-0518-a-A-17

87.52

0.00

80.90

0.00

[17]

KP_F044-KP_R021

100–300

S-D-Bact-0337-a-S-20/S-D-Bact-0515-a-A-19

92.46

0.00

85.80

0.00

[17]

KP_F046-KP_R023

100–300

S-D-Bact-0341-a-S-17/S-D-Bact-0518-a-A-17

87.52

0.00

81.30

0.00

[17]

KP_F046-KP_R021

100–300

S-D-Bact-0341-a-S-17/S-D-Bact-0515-a-A-19

92.46

0.00

86.20

0.00

[17]

KP_F046-OP_R045

100–300

S-D-Bact-0341-a-S-17/ N/A

87.52

0.00

81.50

0.00

[17]

KP_F047-KP_R021

100–300

S-D-Bact-0341-b-S-17/ S-D-Bact-0515-a-A-19

92.59

0.00

91.20a

0.00a

[16]

KP_F056-KP_R032

100–300

S-D-Bact-0564-a-S-15/S-D-Bact-0785-b-A-18

96.23

8.76

89.00a; 83.40b

14.60a; 0.00b

[16]

S-D-Bact-0564-a-S-15/S-D-Bact-0785-b-A-18

88.10

14.40

[17]

KP_F058-KP_R053

100–300

S-D-Bact-0784-a-S-19/S-D-Bact-1061-a-A-17

84.40

0.00

78.60

0.00

[17]

KP_F077-KP_R071

100–300

U341F – 534R

95.58

59.79

98.00

~ 91.00

[19]

KP_F078-OP_R010

100–300

515F – 806 R (original)

95.32

62.89

86.80

52.90

[22]

S-*-Univ-0515-a-S-19/N/A

86.10

52.00

[17]

KP_F078-KP_R037

100–300

S-*-Univ-0515-a-S-19/S-D-Bact-0787-a-A-20

87.39

0.52

77.10

0.00

[17]

KP_F018-KP_R002

100–300

S-D-Arch-0349-a-S-17/S-D-Arch-0519-a-A-16

0.00

95.88

0.00a; 0.00b

76.80a; 74.50b

[16]

KP_F020-KP_R032

100–300

S-D-Arch-0519-a-S-15/S-D-Bact-0785-b-A-18

95.58

99.48

89.10a; 83.40b

88.00a; 76.50b

[16]

519F – 785R

88.80

88.90

[22]

KP_F020-KP_R035

100–300

S-D-Arch-0519-a-S-15/S-D-Bact-0785-a-A-21

95.45

98.97

87.10a

86.50a

[16]

OP_F014-OP_R014

100–300

515F – 806 R (modified)

95.32

88.14

87.70

85.70

[22]

515F – 806R

96.20

96.39

[25]

OP_F066-OP_R073

100–300

N/A/ N/A

98.31

92.78

88.90

75.30

[17]

KP_F044-KP_R032

301–600

S-D-Bact-0337-a-S-20/S-D-Bact-0785-b-A-18

94.28

0.00

84.30

0.00

[17]

KP_F046-OP_R010

301–600

S-D-Bact-0341-a-S-17/ N/A

93.89

0.00

83.30

0.10

[17]

KP_F047-KP_R035

301–600

S-D-Bact-0341-b-S-17/S-*-D-Bact-0785-a-A-21

94.15

0.00

86.20a; 43.10b

0.50a; 0.00b

[16]

341F -805R

96.69

83.59

[25]

341F -785R

96.51

82.96

[21]

S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21

86.00

0.50

[17]

KP_F049-KP_R033

301–600

S-D-Bact-0347-a-S-19/S-D-Bact-0785-a-A-19

76.59

0.00

76.50a

0.00a

[16]

KP_F056-KP_R074

301–600

S-D-Bact-0564-a-S-15/S-Univ-1100-a-A-15

97.27

7.73

92.70a; 76.20b

8.00a; 0.00b

[16]

OP_F021-OP_R050

301–600

N/A / N/A

91.68

1.03

86.50

0.50

[17]

KP_F020-KP_R013

301–600

S-D-Arch-0519-a-S-15/S-D-Arch-1041-a-A-18

0.00

95.88

0.00a

76.60a

[16]

KP_F032-KP_R063

>600

S-D-Bact-0008-b-S-20/S-D-Bact-1492-a-A-16

60.47

0.00

17.30

0.00

[17]

KP_F033-KP_R060

>600

S-D-Bact-0008-c-S-20/S-D-Bact-1391-a-A-17

74.90

0.00

78.00a

0.10a

[16]

KP_F033-KP_R050

>600

S-D-Bact-0008-c-S-20/S-D-Bact-1046-a-A-19

72.56

0.00

81.30a

0.00a

[16]

KP_F047-KP_R053

>600

S-D-Bact-0341-b-S-17/S-D-Bact-1061-a-A-17

93.11

0.00

91.90a; 58.90b

0.00a; 0.00b

[16]

KP_F051-KP_R057

>600

S-D-Bact-0515-a-S-16/S-D-Bact-1100-a-A-15

82.70

0.00

77.30

0.00

[17]

KP_F018-KP_R078

>600

S-D-Arch-0349-a-S-17/S-*-Univ-1392-a-A-15

0.00

93.30

0.00a

65.80a

[16]

KP_F059-KP_R078

>600

S-D-Bact-0785-a-S-18/S-*-Univ-1392-a-A-15

93.63

96.39

74.10a

72.30a

[16]

  1. The coverage findings from the other investigations are those obtained when zero mismatches were accepted
  2. F forward, KP Klindworth primer, OP oral primer, R reverse, Ref references, SC coverage at the species level
  3. aSilva database, bGlobal Ocean Sampling database