Table 3 Bacterial Strains and Plasmids used in this study.

   E. coli EC101

Cloning host, repA⁺ km^r

²⁹

   E. coli EC101-pNZ-M.BbrII + M.BbrIII

EC101 harbouring pNZ8048 derivative containing bbrIIM and bbrIIIM, Cm^r

²⁵

   B. breve UCC2003

Isolate from nursling stool

²¹

   B. breve UCC2003-nagA1-(I)

UCC2003 pBS423Δrep first crossover integrant via nagA1 deletion fragment I, Spec^r

This study

   B. breve UCC2003-nagA1-(II)

UCC2003 pBS423Δrep first crossover integrant via nagA1 deletion fragment II, Spec^r

This study

   B. breve UCC2003-nagA2-(I)

UCC2003 pBS423Δrep first crossover integrant via nagA2 deletion fragment I, Spec^r

This study

   B. breve UCC2003-nagA1-(I)-pRTB101

B. breve UCC2003-nagA1-(I) harbouring pRTB101, Spec^r, Cm^r

This study

   B. breve UCC2003-nagA1-(II)-pRTB101

B. breve UCC2003-nagA1-(II) harbouring pRTB101 Spec^r, Cm^r

This study

   B. breve UCC2003-nagA2-(I)-pRTB101

B. breve UCC2003-nagA2-(I) harbouring pRTB101 Spec^r, Cm^r

This study

   B. breve UCC2003ΔnagA1

nagA1 846 bp inframe deletion mutant of UCC2003

This study

   B. breve UCC2003ΔnagA2

nagA2 969 bp inframe deletion mutant of UCC2003

This study

   B. breve UCC2003ΔnagA1ΔnagA2

nagA1, nagA2 double deletion mutant of UCC2003

This study

   UCC2003PK1

B. breve UCC2003 harbouring pPKCM Cm^r

²¹

   UCC2003ΔnagA1 + 2PK1

B. breve UCC2003ΔnagA1ΔnagA2 harbouring pPKCM Cm^r

This study

   B. bifidum ATCC29521(PRL2010)

B. bifidum type strain

ATCC

   B. bifidum PAM5

B. bifidum ATCC29521 harbouring pAM5 Tet^r

This study

   pBS423Δrep

4.4 kb, E. coli- vector, ΔpMB1, ori pTB4 ori repA Spec^r

³⁰

   pRTB101

7.3 kbp, E. coli-Bifidobacterium shuttle vector, pMB1 ori pTB4 ori repA

³⁰

   pPKCM

pCIBA089-pSK-Cm^r

³¹

   pAM5

pBC1-puC19-Tet^r

³²