Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Bacteroides thetaiotaomicron) |
VPI 5482 [CIP 104206T, E50, NCTC 10582] |
ATCC | ATCC 29148 | |
| Strain, strain background (Bacteroides caccae) |
VPI 3452A [CIP 104201T, JCM 9498] |
ATCC | ATCC 43185 | |
| Strain, strain background (Bacteroides ovatus) |
[NCTC 11153] | ATCC | ATCC 8483 | |
| Strain, strain background (Bacteroides vulgatus) |
[NCTC 11154] | ATCC | ATCC 8482 | |
| Strain, strain background (Bacteroides uniformis) |
Not applicable | ATCC | ATCC 8492 | |
| Strain, strain background (Parabacteroides distasonis) |
[NCTC 11152] | ATCC | ATCC 8503 | |
| Strain, strain background (Bacteroides fragilis) |
VPI 2553 [EN-2; NCTC 9343] |
ATCC | ATCC 25285 | |
| Strain, strain background (Parabacteroides merdae) |
VPI T4-1 [CIP 104202T, JCM 9497] |
ATCC | ATCC 43184 | |
| Strain, strain background (Bacteroides eggerthii) |
Not applicable | DSMZ | DSM-20697 | |
| Strain, strain background (Bacteroides finegoldii) |
199 | DSMZ | DSM-17565 | |
| Strain, strain background (Bacteroides dorei) |
175 | DSMZ | DSM-17855 | |
| Strain, strain background (Bacteroides dorei) |
5_1_36/D4 | BEI | HM-29 | |
| Strain, strain background (Bacteroides sp.) |
1_1_6 | BEI | HM-23 | |
| Strain, strain background (Bacteroides sp.) |
9_1_42FAA | BEI | HM-27 | |
| Strain, strain background (Bacteroides sp.) |
D2 | BEI | HM-28 | |
| Strain, strain background (Bacteroides sp.) |
3_1_19 | BEI | HM-19 | |
| Strain, strain background (Bacteroides sp.) |
2_1_16 | BEI | HM-58 | |
| Strain, strain background (Parabacteroides sp.) |
20_3 (Deposited as Bacteroides sp., Strain 20_3) |
BEI | HM-166 | |
| Strain, strain background (Bacteroides sp.) |
2_1_22 | BEI | HM-18 | |
| Strain, strain background (Bacteroides fragilis) |
638R | Other | Gift from Seth Rakoff-Nahoum, Boston Children's Hospital |
|
| Strain, strain background (Lactobacillus plantarum) |
NCIMB 8826 [Hayward 3A, WCFS1] |
ATCC | BAA-793 | |
| Strain, strain background (Clostridium perfringens) |
NCTC 8237 [ATCC 19408, CIP 103 409, CN 1491, NCIB 6125, NCTC 6125, S 107] |
ATCC | ATCC 13124 | |
| Strain, strain background (Escherichia coli S17-1 λ pir) |
E. coli S17-1 λ pir | Other | Gift from Michael Fischbach, Stanford University |
|
| Strain, strain background (B. thetaiotaomicron VPI-5482 Δtdk) |
Bt WT | Other | Gift from Michael Fischbach, Stanford University |
|
| Strain, strain background (B. thetaiotaomicron VPI-5482 ΔtdkΔ2086) |
BtΔ2086 | This paper | See Materials and methods, ‘Construction of Bacteroides thetaiotaomicron knockout mutants’ |
|
| Strain, strain background (B. thetaiotaomicron VPI-5482 ΔtdkΔ1259) |
BtΔ1259 | This paper | See Materials and methods, ‘Construction of Bacteroides thetaiotaomicron knockout mutants’ |
|
| Strain, strain background (B. thetaiotaomicron VPI-5482 Δtdk Δ2086 pNBU2_erm_us1311_BT2086) |
BtΔ2086,2086+ | This paper | See Materials and methods, ‘Construction of Bacteroides thetaiotaomicron complementation strains’ |
|
| Strain, strain background (B. thetaiotaomicron VPI-5482 Δtdk Δ2086 pNBU2_erm_us1311_CTRL) |
BtΔ2086,CTRL+ | This paper | See Materials and methods, ‘ Construction of Bacteroides thetaiotaomicron complementation strains’ |
|
| Recombinant DNA reagent | pExchange-tdk (plasmid) |
PMID: 18611383 | ||
| Recombinant DNA reagent | pNBU2_erm_us1311 (plasmid) |
PMID: 25574022 | ||
| Sequence-based reagent (knockout primer pairs) |
BT2086_UF | Eurofins Genomics | GAA AGA AGA TAA CAT TCG AGT CGA CAT CCA AAC CCA GTG TGA ACT |
|
| Sequence-based reagent (knockout primer pairs) |
BT2086_UR | Eurofins Genomics | CAT ATT ACT TCC AAA TTA AAT AGT TGA TAC TC |
|
| Sequence-based reagent (knockout primer pairs) |
BT2086_DF | Eurofins Genomics | GAG TAT CAA CTA TTT AAT TTG GAA GTA ATA TGT AGT CGA TAG TTA GTT ATG TGG TAA G |
|
| Sequence-based reagent (knockout primer pairs) |
BT2086_DR | Eurofins Genomics | CCA CCG CGG TGG CGG CCG CTC TAG AAG CAG ACG TTA TCC TGG TTT C |
|
| Sequence-based reagent (knockout primer pairs) |
BT1259_UF | Eurofins Genomics | GAA AGA AGA TAA CAT TCG AGT CGA CGG ATG ATT ATT GCC CCA TTT TG |
|
| Sequence-based reagent (knockout primer pairs) |
BT1259_UR | Eurofins Genomics | CGT ACA CAT AAT TTC GAT TTT TAG TTA TAG |
|
| Sequence-based reagent (knockout primer pairs) |
BT1259_DF | Eurofins Genomics | CTA TAA CTA AAA ATC GAA ATT ATG TGT ACG TAA ATT GAT AGC AGC TTG CTG C |
|
| Sequence-based reagent (knockout primer pairs) |
BT1259_DR | Eurofins Genomics | CCA CCG CGG TGG CGG CCG CTC TAG ACG TTT TTC TAC CGG ACG AAT C |
|
| Sequence-based reagent (complementation primer pairs) |
us1311-BT-For-NdeI | Eurofins Genomics | GGG TCC ATA TGA AGA AAA AAC TTA CGG GTG TTG C |
|
| Sequence-based reagent (complementation primer pairs) |
BT-Rev-XbaI | Eurofins Genomics | CTA GTC TAG ACT ACA TCA CCG GAG TTT CGA A |
|
| Sequence-based reagent (diagnostic primer) |
pExchange_seq_UF | Eurofins Genomics | CGG TGA TCT GGC ATC TTT CT | |
| Sequence-based reagent (diagnostic primer) |
pExchange_seq_DR | Eurofins Genomics | AAC GCA CTG AGA AGC CCT TA | |
| Sequence-based reagent (diagnostic primer) |
BT2086_seq_F1 | Eurofins Genomics | CAA CTG TCC GGG TGA ATA TAA AG | |
| Sequence-based reagent (diagnostic primer) |
BT2086_seq_F2 | Eurofins Genomics | GAA GTT TTC GTT GGG TGA ATG | |
| Sequence-based reagent (diagnostic primer) |
BT1259_seq_F1 | Eurofins Genomics | AGA AGG TAC ATC GCC TGT AC | |
| Sequence-based reagent (diagnostic primer) |
BT1259_seq_F2 | Eurofins Genomics | TAC TAT TCA CGC ACC ACA CC | |
| Sequence-based reagent (diagnostic primer) |
pNBU2_UNIV-F | Eurofins Genomics | TAA CGG TTG TGG ACA ACA AG | |
| Sequence-based reagent (diagnostic primer) |
pNBU2_UNIV-R | Eurofins Genomics | CAC AAT ATG AGC AAC AAG GAA TCC | |
| Sequence-based reagent (qRT-PCR primer) |
qBTBSH_F | Eurofins Genomics | GCGTGCGGGACACAATAAAG | |
| Sequence-based reagent (qRT-PCR primer) |
qBTBSH_R | Eurofins Genomics | TAGCCTGTTGCGATTACGCT | |
| Sequence-based reagent (qRT-PCR primer) |
qBT16s_F | Eurofins Genomics | GTGAGGTAACGGCTCACCAA | |
| Sequence-based reagent (qRT-PCR primer) |
qBT16s_R | Eurofins Genomics | CTGCCTCCCGTAGGAGTTTG |