Table 1 - Designing and validation of genus-specific primers for human gut flora study

Table 1. Positions of genus specific primer sequences with respect to E. coli 16S rRNA.

Genus	Primer Sequence	Primer Position vs E. coli 16S rRNA†	PCR Product	Annealing Temp‡
Bacteroides	GGGGTTCTGAGAGGAAG ACCCCCCATTGTACCAC	S-G- Bacto- 0297- S- 17 S-G- Bacto-1245- A- 17	950 bp	5 2.0
Bifidobacterium	CGCTGGCGGCGTGCTTAACACAT CGCGATTACTAGCGACTCCGCCTTCA	S-G- Bif- 0008- S- 23 S-G- Bif- 1306- b- A- 26	1300 bp	60.0
Lactobacillus	TGCCTAATACATGCAAGTCGA GTTTGGGCCGTGTCTCAGT	S-G-Lacb-0018-S-21 S-G-Lacb-336-A-19	318 bp	52.0
Ruminococcus	CCTCTGACCGCTCTTTAATCGGAGCTTTCCTTC CCAGTTATCGGTCCCACCTTCGGCAGCT	S-G-Rum-0998-S-33 S-G-Rum-1447-A-28	482 bp	61.0
Peptostreptococcus productus	AACTCCGGTGGTATCAGATG GGGGCTTCTGAGTCAGGTA	S-G-PSP-0212-S-20 S-G-PSP-0503-A-19	270 bp	51.0
Peptococcus	GGTGCCGCAGTAAACACAATAAGT AAGGCCCGGGAACGTATTCA	S-G-Pep-0830-S-24 S-G-Pep-1369-A-20	539 bp	53.0
Clostridium	CTCAACTTGGGTGCTGCATTT ATTGTAGTACGTGTGTAGCCC	S-G-Clos-0586-S-21 S-G-Clos-1205-A-20	619 bp	53.0
Campylobacter	AGGGAATATTGCGCAATGGGGGAAA TTACTAGCGATTCCGGCTTCATGC	S-G-Camp-0466-S-25 S-G-Camp-1435-A-24	969 bp	55.0
E. coli	ECO-1 GACCTCGGTTTAGTTCACAGA ECO-2 CACACGCTGACGCTGACCA	Mal B promoter gene	585 bp	53.0
Staphylococcus aureus	mecA-1 AAAATCGATGGTAAAGGTTGGC mecA-2 AGTTCTGCAGTACCGGATTTGC	Methicillin resistance gene	533 bp	51.0

† Primer positions are represented according to the OPD nomenclature (Alm et al. 1996). As per nomenclature; ‘S': Small subunit rRNA, A hyphen (S-). Each character or group of characters in the primer name is set off with a hyphen to facilitate computer –aided manipulations. G: Genus; A: antisense template strand; S; DNA sense strand; 4 digit number in the middle represents the position of the primer with respect to E. coli and the last two digit number depicts the number of nucleotides present in the primer; e.g. (S-G-Bif-1306-A-26). Bacto: Bacteroides; Bif: Bifidobacterium; Rum: Ruminococcus; Lacb: Lactobacillus; Pep: Peptoccoccus; PSP: Peptostreptococcus productus; Clos: Clostridium. Primer sets for Bacto (Menaja et al. 1996); PSP (Wang et al. 1996); E. coli (Wang et al. 1996); and S. aureus (Louie et al. 2002) used in the present study are cited in the literature.
‡: Annealing temperatures are based on standardized conditions.