Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

Kim, Eiseul; Yang, Seung-Min; Lim, Bora; Park, Si Hong; Rackerby, Bryna; Kim, Hae-Yeong

doi:10.1186/s12866-020-01781-z

BMC Microbiology

Table 1 Information of primer pairs designed for this study

From: Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

Species	Target gene	Primer name	Sequence (5′–3′)	Product size (bp)	Primer conc.^b (μM)
IPC^a	16S–23S region	IPC-F	CAA CGC GAA GAA CCT TAC CAG	111	0.4
IPC^a		IPC-R	CCA ACA TCT CAA CGA CAC GAG C
L. gasseri	16S–23S region	Gasseri-F	TCA AGA GCT GTT AAG GCT GT	175	0.04
L. gasseri		Gasseri-R	CTA TCG CTT CAA GTG CTT TC
L. rhamnosus	16S–23S region	Rhamnosus-F	GCC GAT CGT TGA CGT TAG TTG G	137	0.04
L. rhamnosus		Rhamnosus-R	CAG CGG TTA TGC GAT GCG AAT
L. brevis	16S–23S region	Brevis-F	GGG CAA CGA AGC AAG ATC GC	260	0.08
L. brevis		Brevis-R	TTC CAA TCG TGT GCA CAC CA
L. sakei	16S–23S region	Sakei-F	TCG AAC GCA CTC TCG TTT AG	182	0.08
L. sakei		Sakei-R	CGA AAC CAT CTT TCA ACC CT
L. johnsonii	16S–23S region	Johnsonii-F	AGA GAG AAA CTC AAC TTG AAA TA	195	0.4
L. johnsonii		Johnsonii-R	CCT TCA TTA ACC TTA ACA GTT AA
L. jensenii	16S–23S region	Jensenii-F	AGT TCT TCG GAA TGG ACA TAG	148	0.4
L. jensenii		Jensenii-R	GCC GCC TTT TAA ACT TCT T
L. fermentum	Unique gene	Fermentum-F	GAC CAG CGC ACC AAG TGA TA	129	0.08
L. fermentum		Fermentum-R	AGC GTA GCG TTC GTG GTA AT
L. plantarum	Unique gene	Plantarum-F	GCT GGC AAT GCC ATC GTG CT	147	0.12
L. plantarum		Plantarum-R	TCT CAA CGG TTG CTG TAT CG
L. paracasei	Unique gene	Paracasei-F	CAA TGC CGT GGT TGT TGG AA	106	0.4
L. paracasei		Paracasei-R	GCC AAT CAC CGC ATT AAT CG
L. paraplantarum	Unique gene	Paraplantarum-F	TTA TTC AAG CCG TCG GAG TG	128	0.4
L. paraplantarum		Paraplantarum-R	TCG CTG GTG CTA ATG CAA TG
L. casei	Unique gene	Casei-F	CCA CAA TCC TTG GCT GTT CT	115	0.4
L. casei		Casei-R	GCT TGA GGC GAT TGT AAT CC
L. curvatus	16S–23S region	Curvatus-F	ACT CTC ATT GAA TTA GGA CGT T	132	0.4
L. curvatus		Curvatus-R	CCC GTG TTG GTA CTA TTT AAT
L. acidophilus	16S–23S region	Acidophilus-F	CCT TTC TAA GGA AGC GAA GGA T	129	0.4
L. acidophilus		Acidophilus-R	ACG CTT GGT ATT CCA AAT CGC
L. salivarius	16S–23S region	Salivarius-F	TAC ACC GAA TGC TTG CAT TCA	138	0.08
L. salivarius		Salivarius-R	AGG ATC ATG CGA TCC TTA GAG A
L. reuteri	16S–23S region	Reuteri-F	GAT TGA CGA TGG ATC ACC AGT	161	0.2
L. reuteri		Reuteri-R	CAT CCC AGA GTG ATA GCC AA
L. coryniformis	16S–23S region	Coryniformis-F	CAA GTC GAA CGC ACT GAC G	165	0.4
L. coryniformis		Coryniformis-R	ACA TTC AGG CCA TGT GGT CT
L. farciminis	Unique gene	Farciminis-F	ACG AAT CCG GCA GTC AAG AA	152	0.08
L. farciminis		Farciminis-R	AAG AAT CGC CAA GCT CTA GG
L. zymae	16S–23S region	Zymae-F	GCT AAA GCA AGC GCA CGA TT	132	0.08
L. zymae		Zymae-R	TCG GCA GTG TGA CAT GGA G
L. pentosus	Unique gene	Pentosus-F	GCG GTA TCG ATT CGA TTG GT	145	0.08
L. pentosus		Pentosus-R	TGA TGT CAA TCG CCT CTT GG
L. crustorum	16S–23S region	Crustorum-F	GGA ATA GCC CAA ACC AGA G	145	0.2
L. crustorum		Crustorum-R	ACT GAA TGG AGT GGG TCA GA
L. mucosae	16S–23S region	Mucosae-F	ACG GAC TTG ACG TTG GTT TAC	156	0.4
L. mucosae		Mucosae-R	GTG ATA GCC GAA ACC ACC TT
L. buchneri	16S–23S region	Buchneri-F	CAA GTC GAA CGC GTC TCC AT	189	0.08
L. buchneri		Buchneri-R	CCG AAG CCG TCT TTT AAA CC
L. helveticus	Unique gene	Helveticus-F	CTA CTT CGC AGG CGT TAA CT	132	0.08
L. helveticus		Helveticus-R	GTA CTT GAT GCT CGC ATA CC
L. amylovorus	Unique gene	Amylovorus-F	CAA GCA CGA TTG GCA AGA TG	126	0.4
L. amylovorus		Amylovorus-R	ATT GGA TTC CGC TTC TGT GG
L. heilongjiangensis	16S–23S region	Heilongjiangensis-F	GCT TCA TGA ATC GGA TCT AA	133	0.4
L. heilongjiangensis		Heilongjiangensis-R	TAA ACT ACG ATC ATG TGA AAG TA
L. parabuchneri	Unique gene	Parabuchneri-F	AGC GTC GTG ATT CCT GAT AC	137	0.08
L. parabuchneri		Parabuchneri-R	CGA CTC TCC GAT CGT TGT TA
L. acidipiscis	Unique gene	Acidipiscis-F	AGC GGT TCG ATG GCT TAT AC	125	0.08
L. acidipiscis		Acidipiscis-R	TCC AAG TCC GAC ACC AGT CA
L. sanfranciscensis	Unique gene	Sanfranciscensis-F	TGG AAC TGA TAC GCG GAT GT	130	0.08
L. sanfranciscensis		Sanfranciscensis-R	GGC CAA TTC CTC CAA TAA CG
L. ruminis	16S–23S region	Ruminis-F	TTG CAT TCA CCG AAA GAA GC	129	0.4
L. ruminis		Ruminis-R	CAT AAA CAT CAT GCG GTG TTC
L. agilis	16S–23S region	Agilis-F	TCG TAG CTT GCT ACA CCG ATT G	137	0.4
L. agilis		Agilis-R	CAT AAT GAC CAT GCG ATC ATC A
L. delbrueckii	16S–23S region	Delbrueckii-F	CAT GTG CAG ACA TGC TAT CCT T	192	0.4
L. delbrueckii		Delbrueckii-R	CTC TGA AGT GCC ATG TCT CAG T
L. amylophilus	16S–23S region	Amylophilus-F	CGA GTT CTG GTT AAG AGT AGC G	174	0.4
L. amylophilus		Amylophilus-R	CGC CAT CTT TCA AAC ATC TAT C
L. kunkeei	16S–23S region	Kunkeei-F	GAA CGA GCT CTC CCA AAT TGA	161	0.4
L. kunkeei		Kunkeei-R	GAA CCA TGC GGT TCC AAC TA
L. acetotolerans	16S–23S region	Acetotolerans-F	GAT TAC CTT CGG GTA TGA AGT T	131	0.2
L. acetotolerans		Acetotolerans-R	TCA TGT GAT CTC TCC TTT TAT CC
L. lindneri	Unique gene	Lindneri-F	CGG CGT TCT CGA GGA CCA TA	170	0.4
L. lindneri		Lindneri-R	CAT CCG GCG TCC TTC ATA GC
L. gallinarum	Unique gene	Gallinarum-F	AAC TGG CGG TTA TCG TAG AC	118	0.2
L. gallinarum		Gallinarum-R	CAC AGC AGG AAC CAT TTT AG
L. amylolyticus	16S–23S region	Amylolyticus-F	TTC GGT AGT GAC GTT TCG GA	134	0.2
L. amylolyticus		Amylolyticus-R	TCA AGC AAG TGC CAT GCA G

^aIPC, internal positive control
^bconc., concentration

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