Supplemental Table S1: Bacterial strains, vectors and primers used in this study

L. reuteri Strains / Description / Source
WT 6475 / L. reuteri ATCC PTA 6475, isolated from Finnish mother’s milk / BioGaia AB (Stockholm, Sweden)
WT 6475 pJP042 / L. reuteri ATCC PTA 6475_pJP042, Ermr, harboring the recombineering plasmid pJP042 / (van Pijkeren and Britton 2012)
6475::rsiR
(HMPREF0536_10683) / L. reuteri ATCC PTA 6475 rsiR::pORI28, Ermr, rsiR insertion mutant, used as a negative control for TNF suppression / (Hemarajata et al. 2013)
6475eriC-Stop
(HMPREF0536_10428) / L. reuteri ATCC PTA 6475 recombineered mutant with stop codon mutation in eriC / This study
E. coli Stellar™ / E. coli strain used in cloning and plasmid propagation / Clontech, Mountain View, CA
Vector / Description / Source
pCR®2.1 / Cloning vector, Cbr, Knr / Invitrogen, Carlsbad, CA
pVE6007 / Temperature-sensitive plasmid used as backbone for pPH-M1, Cmr / (Law et al. 1995)
pTRK847 / Plasmid carrying translational terminator T667 / A gift from T. R. Klaenhammer
pORI28 / Plasmid carrying ermR gene / (Leenhouts et al. 1996)
pMALC9 / Plasmid carrying him1C9 transposase gene, Cbr / (Akerley and Lampe 2002)
pMMOrf / Plasmid carrying inverted terminal repeats (ITRs) recognized by Himar1 transposase, Cbr / (Lampe et al. 1999)
pCR®2.1-NICEHim1 / Plasmid carrying the nisin-inducible Himar1 expression cassette, Cbr, Ermr / This study
pJP577 / Plasmid control for evaluation of transformation efficiency in recombineering, Cmr / (van Pijkeren and Britton 2012)
pPH-M1 / Himar1 transposase/transposon delivery vector, Cmr, Ermr / This study
Recombineering oligonucleotide / Sequence (5’ to 3’) / Gene targeted
o387stop / gaattagttgattgaactgattatagcgatgaaatgcctcttAtcAaGtctAcattgtttttctccaatttattaaaagtctacatgccattgtactaca, for stop codon mutation at codon 2, 4 and 5 / eriC
Primers / Primer sequence (5’ to 3’) / Gene targeted
nisF-Eco-AdF / CAGTGTGCTGGAATTACGAAGCTTTGGTATATTGAAAAGGAAGA, for cloning of nisRK element / nisRK
nisR-AatR / AAAATGTCTAGAAACCCGCTCGACGTCATCCTTAGAGATTAC, for cloning of nisRK element / nisRK
PnF-Eco-AdR / CCTTAAGGGCGAATTTTTACCGCGGGTTAAAATCATTAGAATA, for cloning of PnisA / PnisA
PnR / GTTTCTAGACATTTTGAGTGCCT for cloning of PnisA / PnisA
TF-AatF / TAATCTCTAAGGATGACGTCGGTCTTTAAGCTTCAACTAAAGCACCCATT, for cloning of T667 / T667
TR / GGCGTAATTGAAGCTTAAATAATTACTAATAAGAA, for cloning of T667 / T667
HimF-AatR / CTAGAAACCCGCTCGACGTCGGCTCCGAAGGAGATATACATCATG, for cloning of himar1C9 / himar1C9
HimR / AGCTTCAATTACGCCGGATCGATCCACTAGTTCTAGAGCGGTCT, for cloning of himar1C9 / himar1C9
pUCFSacIAdF / CCGCCACCGCGGTGGAGCTCCTGCATTAATGAATCGGCCAACGC, for cloning of ori from pUC19 / ori
pUCFSacIAdF / TTCATATTTATCAGGAGCTCAAAAGGATCTAGGTGAAGATCCTTTTTG, for cloning of ori from pUC19 / ori
ErmR-F / CCCTTGAATTAGTAAAGAGGTG, for screening of ermR / ermR
ErmR-R / GCAAACCCGTATTCCACGAT, for screening of ermR / ermR
Cat-F / GGCATATCAAATGAACTTTAATAAAATTGA, for screening of cat / cat
Cat-R / CGGCATTATCTCATATTATAAAAGCCAG, for screening of cat / cat
ErmR-RevF / GCTTATTAACGATTCATTATAACC, forward primer for inverse PCR / ermR
ErmR-RevR / ATCGTGGAATACGGGTTTGC, reverse primer for inverse PCR / ermR
KJP73 / GGAGAAAAACAATGTAGACTTGAT, for MAMA-PCR / eriC
KJP75 / gttggtgctgcagtattg, for screening of recombineered mutants / eriC
KJP76 / cgtttttttgctggttgc, for screening of recombineered mutants / eriC
qPCR Primer Name / Primer Sequence / Universal Probe Number
rpoB-F / cgtgatacttcattacgtgttcct / 77
rpoB-R / agtgaagactttaacatcttggatga
hdcA-F / gcactaacgataaccgtcgtc / 1
hdcA-R / cacccttattagcacaaacaatga
hdcB-F / tgcaagatcggatatcacaaa / 162
hdcB-F / ttgacgaattcaaccttctttaca
hdcP-F / tccctacggataccaagcac / 15
hdcP-R / agaggaacgctaagacaccaat