Long-term colonization exceeding six years from early infancy of Bifidobacterium longum subsp. longum in human gut

Oki, Kaihei; Akiyama, Takuya; Matsuda, Kazunori; Gawad, Agata; Makino, Hiroshi; Ishikawa, Eiji; Oishi, Kenji; Kushiro, Akira; Fujimoto, Junji

doi:10.1186/s12866-018-1358-6

Table 2 Primers used in this study

From: Long-term colonization exceeding six years from early infancy of Bifidobacterium longum subsp. longum in human gut

Primer Name	Target	Sequence (5′ - 3′)	Reference
Amplification and sequencing of 16S rRNA gene for Bifidobacterium
BI8	16S rRNA gene	GGGTTYCGATTCTGGCTCAGGATG	[34]
15R		AAGGAGGTGATCCARCCGCA
520R		ACCGCGGCTGCTGGC
Subspecies-specific PCR for Bifidobacterium longum
BiINF-1	Bifidobacterium longum subsp. infantis	TTCCAGTTGATCGCATGGTC	[35]
BiINF-2		GGAAACCCCATCTCTGGGAT	[35]
BiLON-1	Bifidobacterium longum subsp. longum	TTCCAGTTGATCGCATGGTC	[35]
BiLON-2		GGGAAGCCGTATCTCTACG	[35]
MLST for Bifidobacterium longum subsp. longum strains
Blon-clpC-F	clpC	CCTGAAGAAGGTGCTGAAGG	[22]
Blon-clpC-R		TTCTCCTGCTTGTCGCGCAGT	[22]
Blon-dnaG-F	dnaG	GTTGCCGTAGATTTGGGCTTGG	[22]
Blon-dnaG-R		ATGACTTCGGTGTTCCGCAC	[22]
Blon-dnaJ-F	dnaJ	GCTGAGCAAGAAGGAAGATCGC	[22]
Blon-dnaJ-R		TGAACTTCTTGCCGTCCACGG	[22]
Blon-fusA-F	fusA	CACCATCAAGGAGAAGCTGG	[22]
Blon-fusA-R		ACGAGCTTGCCGTAGAACG	[22]
Blon-gyrB-if1	gyrB	AAGTGCGCCGTCAGGGCTT	[22]
Blon-gyrB-R		GTGTTCGCGAAGGTGTGCAC	[22]
Blon-purF-F2	purF	CGGCTGAACTCGAAGAC	This study
Blon-purF-R2		GTTGAGCGCTTCCTTGAG	This study
Blon-rpoB-F	rpoB	AGACCGACAGCTTCGATTGG	[22]
Blon-rpoB-R		AACACGATGGCGGACTGCTT	[22]
AFLP analysis
MseI adapter 1	Restriction site of MseI	TACTCAGGACTCAT	[22]
MseI adapter 2		GACGATGAGTCCTGAG	[22]
MspI adapter 1	Restriction site of MspI	CTCGTAGACTGCGTACA	[22]
MspI adapter 2		CGTGTACGCAGTCTAC	[22]
Preselective MseI	MseI adapter	GATGAGTCCTGAGTAA	[22]
Preselective MspI	MspI adapter	GACTGCGTACACGGA	[22]
Selective MseI-T	MseI adapter	GATGAGTCCTGAGTAAT	[22]
Selective MspI-A	MspI adapter	FAM^a-GACTGCGTACACGGAA	[22]
Quantification of fecal Bifidobacteirum
g-Bifid-F	Genus Bifidobacterium	CTCCTGGAAACGGGTGG	[17]
g-Bifid-R		GGTGTTCTTCCCGATATCTACA	[17]
BiADOg-1a	Bifidobacterium adolescentis group^b	CTCCAGTTGGATGCATGTC	[17]
BiADOg-1b		TCCAGTTGACCGCATGGT
BiADO-2		CGAAGGCTTGCTCCCAGT
Bflact2	Bifidobacterium animalis subsp. lactis	GTGGAGACACGGTTTCCC	[17]
Bflact5		CACACCACACAATCCAATAC	[17]
BiBIF-1	Bifidobacterium bifidum	CCACATGATCGCATGTGATTG	[17]
BiBIF-2		CCGAAGGCTTGCTCCCAAA	[17]
BiBRE-1	Bifidobacterium breve	CCGGATGCTCCATCACAC	[17]
BiBRE-2		ACAAAGTGCCTTGCTCCCT	[17]
BiCATg-1	Bifidobacterium catenulatum group^c	CGGATGCTCCGACTCCT	[17]
BiCATg-2		CGAAGGCTTGCTCCCGAT	[17]
BiDEN-1	Bifidobacterium dentium	ATCCCGGGGGTTCGCCT	[17]
BiDEN-2		GAAGGGCTTGCTCCCGA	[17]
BiINF-1	Bifidobacterium longum subsp. infantis	TTCCAGTTGATCGCATGGTC	[17]
BiINF-2		GGAAACCCCATCTCTGGGAT	[17]
BiLON-1	Bifidobacterium longum subsp. longum	TTCCAGTTGATCGCATGGTC	[17]
BiLON-2		GGGAAGCCGTATCTCTACG	[17]

^a6-carboxyfluorescein
^bThe B. adolescentis group includes B. adolescentis genotypes A and B
^cThe B. catenulatum group includes B. catenulatum and Bifidobacteium pseudocatenulatum

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ISSN: 1471-2180

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