KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial strains | ||
| Bacteroides thetaiotaomicron 1_1_6 | BEI | HM-23 |
| Bacteroides thetaiotaomicron VPI-5482 | ATCC | ATCC 29148 |
| Bacteroides thetaiotaomicron ATCC 29741 | ATCC | ATCC 29741 |
| Bacteroides finegoldii CL09T03C10 | BEI | HM-727 |
| Bacteroides finegoldii DSM 17564 | DSMZ | DSM 17564 |
| Bacteroides xylanisolvens sp. 1_1_30 | BEI | HM-22 |
| Bacteroides xylanisolvens sp. 2_1_22 | BEI | HM-18 |
| Bacteroides xylanisolvens CL03T12C04 | BEI | HM-722 |
| Bacteroides ovatus CL02T12C04 | BEI | HM-723 |
| Bacteroides ovatus ATCC 8483 | ATCC | ATCC 8483 |
| Bacteroides ovatus CL03T12C18 | BEI | HM-724 |
| Bacteroides ovatus sp. D2 | BEI | HM-28 |
| Bacteroides ovatus 3_8_47FAA | BEI | HM-222 |
| Bacteroides caccae ATCC 43185 | ATCC | ATCC 43185 |
| Bacteroides caccae CL03T12C61 | BEI | HM-728 |
| Bacteroides nordii CL02T12C05 | BEI | HM-721 |
| Bacteroides salyersiae CL02T12C01 | BEI | HM-725 |
| Bacteroides salyersiae DSM 18765 | DSMZ | DSM 18765 |
| Bacteroides fragilis 3_1_12 | BEI | HM-20 |
| Bacteroides fragilis CL05T00C42 | BEI | HM-711 |
| Bacteroides fragilis str. S13 L11 | Lab of Laurie E. Comstock | (Coyne et al., 2016) |
| Bacteroides fragilis str. 1007-1-F #7 | Lab of Laurie E. Comstock | (Coyne et al., 2016) |
| Bacteroides fragilis NCTC 9343 | ATCC | ATCC25825 |
| Bacteroides fragilis NCTC 638R | Lab of Laurie E. Comstock | (Coyne et al., 2016) |
| Bacteroides fragilis CL03T00C08 | BEI | HM-713 |
| Bacteroides fragilis str. DS-166 | Lab of Laurie E. Comstock | (Coyne et al., 2016) |
| Bacteroides fragilis str. S36L11 | Lab of Laurie E. Comstock | (Coyne et al., 2016) |
| Bacteroides fragilis CL07T00C01 | BEI | HM-709 |
| Bacteroides fragilis sp. 2_1_16 | BEI | HM-58 |
| Bacteroides cellulosilyticus CL02T12C19 | BEI | HM-726 |
| Bacteroides oleiciplenus DSM 22535 | DSMZ | DSM 22535 |
| Bacteroides eggerthii 1_2_48FAA | BEI | HM-201 |
| Bacteroides eggerthii DSM 20697 | DSMZ | DSM 20697 |
| Bacteroides uniformis CL03T00C23 | BEI | HM-715 |
| Bacteroides uniformis ATCC 8492 | ATCC | ATCC 8492 |
| Bacteroides uniformis sp. D20 | BEI | HM-189 |
| Bacteroides dorei sp. 9_1_42FAA | BEI | HM-27 |
| Bacteroides dorei CL02T00C15 | BEI | HM-717 |
| Bacteroides dorei DSM 17855 | DSMZ | DSM 17855 |
| Bacteroides dorei CL03T12C01 | BEI | HM-718 |
| Bacteroides dorei 5_1_36/D4 | BEI | HM-29 |
| Bacteroides vulgatus ATCC 8482 | ATCC | ATCC 8482 |
| Bacteroides vulgatus CL09T03C04 | BEI | HM-720 |
| Parabacteroides goldsteinii CL02T12C30 | BEI | HM-732 |
| Parabacteroides merdae CL03T12C32 | BEI | HM-730 |
| Parabacteroides merdae ATCC 43184 | ATCC | ATCC 43184 |
| Parabacteroides merdae CL09T00C40 | BEI | HM-729 |
| Parabacteroides johnsonii CL02T12C29 | BEI | HM-731 |
| Parabacteroides distasonis sp. 3_1_19 | BEI | HM-19 |
| Parabacteroides distasonis 31_2 | BEI | HM-169 |
| Parabacteroides distasonis CL03T12C09 | BEI | HM-733 |
| Parabacteroides distasonis ATCC 8503 | ATCC | ATCC 8503 |
| Parabacteroides distasonis CL09T03C24 | BEI | HM-734 |
| Parabacteroides distasonis sp. 20_3 | BEI | HM-166 |
| Bt VIP Δ3942 | This study | N/A |
| Bv ATCC Δ1163 | This study | N/A |
| Bv ATCC Δ1163 Δ0574 | This study | N/A |
| Bv ATCC Δ1163 Δ2719 | This study | N/A |
| Bv ATCC Δ0574 | This study | N/A |
| Bv ATCC Δ2719 | This study | N/A |
| Bv ATCC Δ1163 att1:: pNBU2-erm_TetR-p1T_DP-GH023_BVU_1163 | This study | N/A |
| Bv ATCC Δ1163 Δ0574 att1:: pNBU2-erm_TetR-p1T_DP-GH023_BVU_1163 | This study | N/A |
| Bv CL09 Δ1163 | This study | N/A |
| Bv CL09 Δ2719 | This study | N/A |
| Bv CL09 Δ1163 Δ2719 | This study | N/A |
| Escherichia coli DH5a λ pir | (Pal et al., 2005) | N/A |
| Escherichia coli S17-1 λ pir | (Simon et al., 1983) | N/A |
| Escherichia coli BL21 (DE3) | Novagen | C600003 |
| Chemicals and recombinant proteins | ||
| Brain Heart Infusion | BD Bioscience | Cat# 237500 |
| Sodium formate | Sigma-Aldrich | Cat# 107603 |
| Sodium acetate | Sigma-Aldrich | Cat# S2889 |
| Sodium D-lactate | Sigma-Aldrich | Cat# 71716 |
| Sodium L-lactate | Sigma-Aldrich | Cat# 71718 |
| Sodium propionate | Sigma-Aldrich | Cat# P1880 |
| Sodium malonate dibasic | Sigma-Aldrich | Cat# 63409 |
| Sodium succinate dibasic hexahydrate | Sigma-Aldrich | Cat# S9637 |
| Sodium butyrate | Sigma-Aldrich | Cat# 303410 |
| Sodium butyrate (13C4) | Cambridge Isotope Laboratories | Cat# CLM-10426-0.1 |
| Glucose | Sigma-Aldrich | Cat# G7021 |
| Fructose | Sigma-Aldrich | Cat# F3510 |
| Mannose | Sigma-Aldrich | Cat# M6020 |
| N-Acetylglucosamine | Sigma-Aldrich | Cat# A3286 |
| Galactose | Sigma-Aldrich | Cat# G5388 |
| Arabinose | Sigma-Aldrich | Cat# A3131 |
| Xylose | Sigma-Aldrich | Cat# X3877 |
| Fucose | Sigma-Aldrich | Cat# F2252 |
| Rhamnose | Sigma-Aldrich | Cat# R3875 |
| Ribose | Sigma-Aldrich | Cat# D5251 |
| N-Acetylgalactosamine | Sigma-Aldrich | Cat# A2795 |
| 3-Sialyllactose (3-SL) | GLYCOM | Cat# GlyCare™ 3SL |
| Lacto-N-neotetraose (LNnT) | GLYCOM | Cat# GlyCare™ LNnT |
| 2-fucosyllactose (2-FL) | GLYCOM | Cat# GlyCare™ 2FL |
| Pullulan | Sigma-Aldrich | Cat# P4516 |
| Levan | Sigma-Aldrich | Cat# L8647 |
| Xylan | Sigma-Aldrich | Cat# X4252 |
| Xyloglucan (Tamarind) | Megazyme | Cat# P-XYGLN |
| Arabinan (Sugar beet) | Megazyme | Cat# P-ARAB |
| Arabinogalactan (Larch Wood) | Megazyme | Cat# P-ARGAL |
| Chondroitan sulfate | Sigma-Aldrich | Cat# R7500 |
| Inulin | Beneo | Cat# Orafti P95 |
| Pectin | Sigma-Aldrich | Cat# P9135 |
| Mannan | Sigma-Aldrich | Cat# M7504 |
| Glucomannan | Megazyme | Cat# p-GLCML |
| Isoleucine | Sigma-Aldrich | Cat# I2752 |
| Leucine | Sigma-Aldrich | Cat# L8000 |
| Valine | Sigma-Aldrich | Cat# V0500 |
| Maltose | Sigma-Aldrich | Cat# M5895 |
| Sucrose | Sigma-Aldrich | Cat# S7903 |
| Palatinose | Sigma-Aldrich | Cat# P2007 |
| Isopropyl β-D-1-thiogalactopyranoside | Sigma-Aldrich | Cat# I6758 |
| 4-chloro-phenylalanine | Sigma-Aldrich | Cat# C6506 |
| 5,5′-dithiobis (2-nitrobenzoic acid) | Sigma-Aldrich | Cat# D8130 |
| Acetyl coenzyme A | Sigma-Aldrich | Cat# A2181 |
| Propionyl coenzyme A | Sigma-Aldrich | Cat# P5397 |
| Butyryl coenzyme A | Sigma-Aldrich | Cat# B1508 |
| Succinyl coenzyme A | Sigma-Aldrich | Cat# S1129 |
| Hexanoyl coenzyme A | Sigma-Aldrich | Cat# H2012 |
| Decanoyl coenzyme A | Sigma-Aldrich | Cat# D5269 |
| Palmitoyl coenzyme A | Sigma-Aldrich | Cat# P9716 |
| BCECF, AM (2’,7’-Bis-(2 Carboxyethyl)-5-(and-6)-Carboxyfluorescein, Acetoxymethyl Ester) | Thermo Fisher Scientific | Cat# B1151 |
| Nigericin | Sigma-Aldrich | Cat# N7143 |
| Valinomycin | Sigma-Aldrich | Cat# V0627 |
| Propidium Iodide | Thermo Fisher Scientific | Cat# P3566 |
| BT_3942-His tag | This study | N/A |
| BVU_0767-His tag | This study | N/A |
| Antibodies | ||
| Anti-HA | Santa Cruz | Cat# sc-7392 |
| Anti-E. coli RpoA | BioLegend | Cat# 663104 |
| Critical commercial assays | ||
| SuperScript VI Reverse Transcriptase | Thermo Fisher Scientific | Cat# 18090200 |
| Fast SYBR Green Master Mix | Applied Biosystem/ Thermo Fisher Scientific | Cat# 4385617 |
| Ribo-Zero rRNA Removal Kit | Epicenter | Cat# RZH1046 |
| PureLink Genomic DNA mini kit | Thermo Fisher Scientific | Cat# K182002 |
| GeneArt Seamless Cloning and Assembly Enzyme Kit | Thermo Fisher Scientific | Cat# A14606 |
| Zymo DNA Clean and Concentrator Kits | Zymo Research | Cat# D4013 |
| ZymoBIOMICS DNA Miniprep Kit | Zymo Research | Cat# D4301 |
| NEBNext Ultra DNA Library Prep Kit | New England Biolabs | Cat# E7370 |
| AMPure XP beads | Beckman Coulter Inc. | Cat# A63880 |
| NEBNext Library Quant Kit for Illumina | New England Biolabs | Cat# E7630 |
| Platinum SuperFi PCR Master Mix | Thermo Fisher Scientific | Cat# 12358250 |
| Direct-zol RNA Miniprep Plus Kit | Zymo Research | Cat# R2072 |
| HisPur Ni-NTA Resin | Thermo Fisher Scientific | Cat# 88221 |
| Halt Protease Inhibitor Cocktail | Thermo Fisher Scientific | Cat# PI87786 |
| NuPAGE 4 to 12%, Bis-Tris Mini Protein Gel | Thermo Fisher Scientific | Cat# NP0322BOX |
| Deposited data | ||
| The raw RNA_Seq and Tn_Seq data | NCBI BioProject ID | PRJNA640947 |
| Tn-Seq_B. thetaiotaomicron VPI-5482/Glucose | NCBI BioProject ID | PRJNA640947 |
| Tn-Seq_B. vulgatus ATCC 8482/Glucose | NCBI BioProject ID | PRJNA640947 |
| Tn-Seq_Bv ΔBVU_1163/Galactose | NCBI BioProject ID | PRJNA640947 |
| sTn-Seq_B. vulgatus CL09/Galactose | NCBI BioProject ID | PRJNA640947 |
| RNA-Seq_ B. thetaiotaomicron VPI-5482/Glucose/Acetate | NCBI BioProject ID | PRJNA640947 |
| RNA-Seq_ B. thetaiotaomicron VPI-5482/Glucose/Succinate | NCBI BioProject ID | PRJNA640947 |
| RNA-Seq_ B. thetaiotaomicron VPI-5482/Glucose/Butyrate | NCBI BioProject ID | PRJNA640947 |
| RNA-Seq_ B. thetaiotaomicron VPI-5482/Galactose | NCBI BioProject ID | PRJNA640947 |
| RNA-Seq_ B. vulgatus ATCC 8482/Glucose/Acetate | NCBI BioProject ID | PRJNA640947 |
| RNA-Seq_ B. vulgatus ATCC 8482/Glucose/Succinate | NCBI BioProject ID | PRJNA640947 |
| RNA-Seq_ B. vulgatus ATCC 8482/Glucose/Butyrate | NCBI BioProject ID | PRJNA640947 |
| RNA-Seq_ B. vulgatus ATCC 8482/GlNAC/Butyrate | NCBI BioProject ID | PRJNA640947 |
| RNA-Seq_ B. vulgatus ATCC 8482/Galactose/Butyrate | NCBI BioProject ID | PRJNA640947 |
| RNA-Seq_ B. vulgatus ATCC 8482/Xylose/Butyrate | NCBI BioProject ID | PRJNA640947 |
| RNA-Seq_ B. vulgatus CL09 /Glucose/Butyrate | NCBI BioProject ID | PRJNA640947 |
| Oligonucleotides | ||
| Primers used in this study | This study | Table S1 |
| Recombinant DNA | ||
| pRK231 | (Smith et al., 1992) | N/A |
| pKNOCK-bla-ermGb | (Koropatkin et al., 2008) | N/A |
| pKNOCK-bla-ermGb_pheS* | This study | N/A |
| pSAM_BcellWH2 | (Wu et al., 2015) | N/A |
| pFD340 | (Smith et al., 1992) | N/A |
| pNBU2-bla-ermGb | (Koropatkin et al., 2008) | N/A |
| pWH2-Term6 | This study | N/A |
| pBT_3942 | This study | N/A |
| pBVU_0767 | This study | N/A |
| pBv_1163 | This study | N/A |
| pBv_1163-HA | This study | N/A |
| pBt_1163 | This study | N/A |
| pBv_3193 | This study | N/A |
| pBt_3193 | This study | N/A |
| pBt_3193-HA | This study | N/A |
| pN_1163 | This study | N/A |
| pN_3193 | This study | N/A |
| pBv_TTAG-1163 | This study | N/A |
| pBv_TTAG_down-1163 | This study | N/A |
| pBt_TTTA-1163 | This study | N/A |
| pBt_TTTA_up-1163 | This study | N/A |
| pNBU2-erm_TetR-p1T_DP-GH023 | (Lim et al., 2017) | Addgene Cat #90324 |
| pTetR_p1T_ BVU_1163 | This study | N/A |
| pET-28a | Novagen | Cat# 69864-3 |
| pET-28a_BT_3942-His | This study | N/A |
| pET-28a_BVU_0767-His | This study | N/A |
| Software and algorithms | ||
| Prism9 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| MEGA | https://www.megasoftware.net/ | |
| MATLAB/ R2017b | MathWorks | https://www.mathworks.com |
| Heatmapper | (Babicki et al., 2016) | http://www.heatmapper.ca |
| DAVID 6.8 | (Huang et al., 2009) | https://david.ncifcrf.gov/ |
| Other | ||
| Anaerobic Chamber | Coy manufacturing | Vinyl Anaerobic Chamber |
| Microplate plate absorbance reader | BioTek Instruments | Synergy HTX multi-mode reader |
| QuantStudio Real-time PCR system | Applied Systems | 3 |
| Focused-ultrasonicators | Covaris | M220 |