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Table 4 PCR primers used in this study

From: A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

Primer name

Platform

Library design

Variable region

Sequence

454_27YMF

454

F

V1-V3

CCATCTCATCCCTGCGTGTCTCCGACTCAGxxxxxxxxxx AGAGTTTGATYMTGGCTCAG

454_515R

   

CCTATCCCCTGTGTGCCTTGGCAGTCTCAGTTACCGCGGCKGCTGNCAC

454_F341

454

F

V3-V4

CCATCTCATCCCTGCGTGTCTCCGACTCAGxxxxxxxxxxCCTAYGGGRBGCASCAG

454_816R1

   

CCTATCCCCTGTGTGCCTTGGCAGTCTCAGGGACTACHVGGGTWTCTAAT

454_F515

454

F

V4-V5

CCATCTCATCCCTGCGTGTCTCCGACTCAGxxxxxxxxxxGTGNCAGCMGCCGCGGTAA

454_926R

   

CCTATCCCCTGTGTGCCTTGGCAGTCTCAGCCGYCAATTYMTTTRAGTTT

454_F515

454

F

V4-V6

CCATCTCATCCCTGCGTGTCTCCGACTCAGxxxxxxxxxxGTGNCAGCMGCCGCGGTAA

454_1061R

   

CCTATCCCCTGTGTGCCTTGGCAGTCTCAGCRRCACGAGCTGACGAC

454_F515

454

F

V4

CCATCTCATCCCTGCGTGTCTCCGACTCAGxxxxxxxxxxGTGNCAGCMGCCGCGGTAA

454_816R1

   

CCTATCCCCTGTGTGCCTTGGCAGTCTCAGGGACTACHVGGGTWTCTAAT

454_F515A

454

F

V4A

CCATCTCATCCCTGCGTGTCTCCGACTCAGxxxxxxxxxxGTGBCAGCMGCCGCGGTAA

454_805RA

   

CCTATCCCCTGTGTGCCTTGGCAGTCTCAGGACTACHVGGGTATCTAATCC

454_F787

454

F

V5-V9

CCATCTCATCCCTGCGTGTCTCCGACTCAGxxxxxxxxxxATTAGATACCCNGGTAG

454_1492R

   

CCTATCCCCTGTGTGCCTTGGCAGTCTCAGTACGGYTACCTTGTTAYGACTT

1Round515For

MS

DI

V4

CTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNGTGCCAGCMGCCGCGGTAA

1Round806Rev

   

GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGACTACHVGGGTWTCTAAT

1RounN515F

MS

DI

V4

CTACACTCTTTCCCTACACGACGCTCTTCCGATCTGTGCCAGCMGCCGCGGTAA

1Round806R

   

GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGACTACHVGGGTWTCTAAT

1Round341For

MS

DI

V4

CTACACTCTTTCCCTACACGACGCTCTTCCGATCTCCTAYGGGRBGCASCAG

1Round805RARev

   

GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGACTACHVGGGTATCTAATCC

1Round515AFor

MS

DI

V4

CTACACTCTTTCCCTACACGACGCTCTTCCGATCTGTGBCAGCMGCCGCGGTAA

1Round805RARev

   

GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGACTACHVGGGTATCTAATCC

DI_N5XXFor

MS

DI

V4

AATGATACGGCGACCACCGAGATCTACACxxxxxxxxACACTCTTTCCCTACACGACG

DI_N7xxRev

   

CAAGCAGAAGACGGCATACGAGATxxxxxxxxGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT

FG515for

MS

F

V4

AATGATACGGCGACCACCGAGATCTACACTATGGTAATTGTGTGCCAGCMGCCGCGGTAA

FG8xxrev

   

CAAGCAGAAGACGGCATACGAGATxxxxxxxxxxAGTCAGTCAGCCGGACTACHVGGGTWTAAT

Read 1 Seq Primer

MS

F

V4

TATGGTAATTGTGTGCCAGCMGCCGCGGTAA

Read 2 Seq Primer

MS

F

V4

AGTCAGTCAGCCGGACTACHVGGGTWTCTAAT

Index Seq Primer

MS

F

V4

ATTAGAWACCCBDGTAGTCCGGCTGACTGACT

454_F341

IT

F

V3-V4

CCATCTCATCCCTGCGTGTCTCCGACTCAGCxxxxxxxxxxCCTAYGGGRBGCASCAG

TtP1_Kn805rev

   

CCTCTCTATGGGCAGTCGGTGATGGACTACHVGGGTWTCTAAT

454_F515A

IT

F

V4

CCATCTCATCCCTGCGTGTCTCCGACTCAGxxxxxxxxxxGTGBCAGCMGCCGCGGTAA

TtP1_Kn805rev

   

CCTCTCTATGGGCAGTCGGTGATGGACTACHVGGGTATCTAATCC

454_F515

IT

F

V4

CCATCTCATCCCTGCGTGTCTCCGACTCAGACATACGCGTGTGNCAGCMGCCGCGGTAA

TtP1_Kn806rev

   

CCTCTCTATGGGCAGTCGGTGATGGGACTACHVGGGTWTCTAAT

PBv1F

PB

LA

V1-V9

ggtagxxxxxxxxxxxxxxxxAGAGTTTGATYMTGGCTCAG

PBv9R

   

ccatcxxxxxxxxxxxxxxxxTACGGYTACCTTGTTAYGACTT

  1. The variable region primer sequence is displayed in bold. The position of the multiplex identifier (MID) is shown as [x] and the respective sequences are shown in Tables 3, 5, 6, and 7. Degenerated bases in the sequence are represented as follows: M: C or A; B: not A; Y: C or T; R: A or G; W: A or T; H: not G; K: G or T; V: not T