TABLE 1 

Bacterial strains and plasmids used in this study

Strain or plasmidDescriptionSource or reference
Strains
    E. coli
        EPI300F mcrA Δ(mrr-hsdRMS-mcrBC) φ80dlacZΔM15 ΔlacX74 recA1 endA1 araD139 Δ(ara leu)7697 galU galK rpsL (Smr) nupG trfA dhfrEpicentre
        HB101F mcrB mrr hsdS20(rB mB) recA13 leuB6 ara-14 proA2 lacY1 galK2 xyl-5 mtl-1 rpsL20 (Smr) glnV4440
    B. thetaiotaomicron
        VPI 5482B. thetaiotaomicron type strain; the VPI 5482 type strain is the same as ATCC 2914823
        BtUW24Derivative of VPI 5482 with deletion of BT_2275 (tdk); used in conjunction with pExchange-tdk to construct deletion mutants30
        BtUW25Derivative of Δtdk with deletion of BT_0238 (anSME); unable to grow on chondroitin sulfate as sole carbon source15
        BtUW4B. thetaiotaomicron BtUW25 carrying anSME-complementing clone from BT3 genomic library designated BT3_chuR2This study
        BtUW7B. thetaiotaomicron BtUW25 carrying anSME-complementing clone from BT3 genomic library designated BT3_chuR5This study
        BtUW8B. thetaiotaomicron BtUW25 carrying anSME-complementing clone from BT3 genomic library designated BT3_chuR6This study
        BtUW11B. thetaiotaomicron BtUW25 carrying anSME-complementing clone from BT3 genomic library designated BT3_chuR9This study
        BtUW12B. thetaiotaomicron BtUW25 carrying anSME-complementing clone from BT3 genomic library designated BT3_chuR10This study
        BtUW14B. thetaiotaomicron BtUW25 carrying anSME-complementing clone from CLGM3 metagenomic library designated CLGM3_chuR1This study
        BtUW15B. thetaiotaomicron BtUW25 carrying anSME-complementing clone from CLGM3 metagenomic library designated CLGM3_chuR2 (clone 2)This study
        BtUW16B. thetaiotaomicron BtUW25 carrying anSME-complementing clone from CLGM3 metagenomic library designated CLGM3_chuR3This study
        BtUW17B. thetaiotaomicron BtUW25 carrying anSME-complementing clone from CLGM3 metagenomic library designated CLGM3_chuR4This study
        BtUW18B. thetaiotaomicron BtUW25 carrying anSME-complementing clone from CLGM3 metagenomic library designated CLGM3_chuR5 (clone 5)This study
        BtUW20B. thetaiotaomicron BtUW25 carrying anSME-complementing clone from CLGM3 metagenomic library designated CLGM3_chuR8This study
        BtUW21B. thetaiotaomicron BtUW25 carrying anSME-complementing clone from CLGM3 metagenomic library designated CLGM3_chuR9This study
Plasmids
    pRK2013Mobilizer plasmid; ColE1 replication origin and Kmr41
    pAFD1E. coli-Bacteroides shuttle vector with pUC replication origin42
    pJC8Cosmid vector with RK2 replication origin; NCBI accession no. KC14951329
    pJET1.2Commercial vector for PCR product cloning; NCBI accession no. EF69405643
    pCC1FOSCommercial fosmid vector; NCBI accession no. EU140751Epicentre
    pKL13Derivative of pCC1FOS; ermF and repA for selection and replication in Bacteroides, respectively; oriT for conjugation from E. coli into B. thetaiotaomicron; NCBI accession no. KU746975This study