| Antibodies |
| Alexa Fluor 488 goat anti-rabbit IgG |
Life Technologies |
Cat#A11008 |
| Mucin 2 antibody (H-300) |
Santa Cruz Biotechnology |
Cat#sc-15334 |
| Chemicals, Peptides, and Recombinant Proteins |
| 4-nitrophenyl N-acetyl-β-D-glucosaminide |
Sigma-Aldrich |
Cat#N9376 |
| 4-nitrophenyl α-D-galactopyranoside |
Sigma-Aldrich |
Cat#N0877 |
| 4-nitrophenyl β-D-glucopyranoside |
Sigma-Aldrich |
Cat#N7006 |
| 4-nitrophenol |
Sigma-Aldrich |
Cat#73560 |
| Acetic acid |
Acros Organics |
Cat#222140010 |
| Adenine |
Sigma-Aldrich |
Cat#A2786 |
| Alanine |
Sigma-Aldrich |
Cat#A7469 |
| Alcian blue |
Sigma-Aldrich |
Cat#A5268 |
| Alginate |
Sigma-Aldrich |
Cat#180947 |
| Ammonium chloride |
Sigma-Aldrich |
Cat#A0171 |
| Ammonium sulfate |
Thermo Fisher Scientific |
Cat#A702 |
| Arginine |
Sigma-Aldrich |
Cat#A8094 |
| Asparagine |
Sigma-Aldrich |
Cat#A4159 |
| Aspartic Acid |
Sigma-Aldrich |
Cat#A93100 |
| Barley β-glucan (Barliv Betafiber) |
Cargill |
Cat#BBF-100 |
| Beef extract |
Sigma-Aldrich |
Cat#B4888 |
| Biotin |
Sigma-Aldrich |
Cat#B4501 |
| Boric acid |
Sigma-Aldrich |
Cat#B6768 |
| Calcium chloride |
Sigma-Aldrich |
Cat#C1016 |
| Calcium pantothenate |
Sigma-Aldrich |
Cat#P2250 |
| Cellulose |
International Fiber Corporation |
Solka-Floc |
| Chloroform |
Sigma-Aldrich |
Cat#496189 |
| Chondroitin sulfate |
Federal Laboratories |
Cat#CSP1K |
| cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail |
Sigma-Aldrich |
Cat#000000004693159001 |
| Copper(II) sulfate pentahydrate |
Sigma-Aldrich |
Cat#C7631 |
| Corn starch/amylopectin |
Sigma-Aldrich |
Cat#10120 |
| Cyanocobalamin |
Sigma-Aldrich |
Cat#V2876 |
| Cysteine |
Sigma-Aldrich |
Cat#C7352 |
| Cytosine |
Sigma-Aldrich |
Cat#C3506 |
| DAPI |
Sigma-Aldrich |
Cat#D9542 |
| Dextran |
Sigma-Aldrich |
Cat#31389 |
| Dipotassium phosphate |
Thermo Fisher Scientific |
Cat#BP363-500 |
| EDTA |
Sigma-Aldrich |
Cat#ED4SS |
| Ethanol |
Decon Labs |
Cat#2701 |
| Fiber-Free diet |
Teklad/Envigo |
Cat#TD.130343 |
| Folic acid |
Sigma-Aldrich |
Cat#F7876 |
| Fructose |
Sigma-Aldrich |
Cat#F0127 |
| Galactose |
Sigma-Aldrich |
Cat#G0625 |
| Glucomannan |
Konjac Foods |
Konjac Glucomannan Powder |
| Glucose |
Sigma-Aldrich |
Cat#158968
|
| Glutamine |
Sigma-Aldrich |
Cat#G8540 |
| Glutaraldehyde |
Electron Microscopy Sciences |
Cat#16537 |
| Guanine |
Sigma-Aldrich |
Cat#G11950
|
| Guar gum galactomannan |
Sigma-Aldrich |
Cat#G4129 |
| Glutamic Acid |
Sigma-Aldrich |
Cat#G1501 |
| Hematin |
Sigma-Aldrich |
Cat#H3281 |
| Histidine |
Sigma-Aldrich |
Cat#H8000 |
| Hydrochloric Acid |
Sigma-Aldrich |
Cat#320331 |
| Inulin |
Cargill |
Oliggo-Fiber Instant Inulin |
| Iron(II) sulfate heptahydrate |
Sigma-Aldrich |
Cat#215422 |
| Isobutyric acid |
Alfa Aesar |
Cat#79-31-2 |
| Isoleucine |
Sigma-Aldrich |
Cat#I2752 |
| Isopropanol |
Sigma-Aldrich |
Cat#278475 |
| Isovaleric acid |
Alfa Aesar |
Cat#503-74-2 |
| Laboratory Autoclavable Rodent Diet - 5010 |
LabDiet |
Cat#0001326 |
| Larch arabinogalactan |
Megazyme |
Cat#P-ARGAL |
| Leucine |
Sigma-Aldrich |
Cat#L8000 |
| Lysine |
Sigma-Aldrich |
Cat#L5501 |
| Lysozyme |
Thermo Fisher Scientific |
Cat#BP535-1 |
| Magnesium chloride anhydrous |
Sigma-Aldrich |
Cat#M8266 |
| Magnesium sulfate anhydrous |
Sigma-Aldrich |
Cat#M7506 |
| Magnesium sulfate heptahydrate |
Sigma-Aldrich |
Cat#M5921 |
| Manganese(II) sulfate monohydrate |
Mallinkrodt |
Cat#6192 |
| Mannose |
Acros Organics |
Cat#150600 |
| Menadione |
Sigma-Aldrich |
Cat#M5625 |
| Methanol anhydrous |
Thermo Fisher Scientific |
Cat#A412-1 |
| Methionine |
Sigma-Aldrich |
Cat#M9625 |
| Mucin from porcine stomach |
Sigma-Aldrich |
Cat#M1778 |
| N-acetyl glucosamine |
Sigma-Aldrich |
Cat#A3286 |
| Nicotinic acid |
Sigma-Aldrich |
Cat#N4126 |
| Osmium tetroxide |
Electron Microscopy Sciences |
Cat#19100 |
| p-Aminobenzoic acid |
Sigma-Aldrich |
Cat#A9878 |
| Pancreatic digest of casein |
BioWorld |
Cat#30620060-1 |
| Phenol |
Sigma-Aldrich |
Cat#P4557 |
| Phenol:Chloroform:Isoamyl Alcohol (pH 8.05) |
Thermo Fisher Scientific |
Cat# 15593031 |
| Phenol:Chloroform:Isoamyl Alcohol (pH 4.3) |
Fisher Scientific |
Cat#BP1754I-400 |
| Phenylalanine |
Sigma-Aldrich |
Cat#P2126 |
| p-nitrophenyl α-L-fucopyranoside |
Sigma-Aldrich |
Cat#N3628 |
| p-nitrophenyl β-D-xylopyranoside |
Sigma-Aldrich |
Cat#N2132 |
| Polygalacturonic acid |
Sigma-Aldrich |
Cat#P3850 |
| Potassium 4-nitrophenyl sulfate |
Sigma-Aldrich |
Cat#N3877 |
| Potassium chloride |
Sigma-Aldrich |
Cat#P9333 |
| Potassium dihydrogen phosphate |
Thermo Fisher Scientific |
Cat#P284 |
| Potato pectic galactan |
Megazyme |
Cat#P-PGAPT |
| Proline |
Sigma-Aldrich |
Cat#P5607 |
| Propionic acid |
Acros Organics |
Cat#149300010 |
| Propylene oxide |
Electron Microscopy Sciences |
Cat#20412 |
| Pyridoxine HCl |
Sigma-Aldrich |
Cat#P9755 |
| Resazurin |
Acros Organics |
Cat#418900010 |
| Retrievagen A |
BD Biosciences |
Cat#550524 |
| Rhamnogalacturonic acid |
Megazyme |
Cat#P-RHAM1 |
| Riboflavin |
Sigma-Aldrich |
Cat#R7649 |
| RNAprotect |
Qiagen |
Cat#76506 |
| SDS |
Sigma-Aldrich |
Cat#L3771 |
| Serine |
Sigma-Aldrich |
Cat#84959 |
| Sodium acetate |
Sigma-Aldrich |
Cat#S2889 |
| Sodium bicarbonate |
Sigma-Aldrich |
Cat#S5761 |
| Sodium chloride |
Sigma-Aldrich |
Cat#S7653 |
| Sodium citrate |
Sigma-Aldrich |
Cat#S1804 |
| Sodium hydroxide |
Sigma-Aldrich |
Cat#S8045 |
| Sodium lactate |
Thermo Fisher Scientific |
Cat#S326-500 |
| Sodium molybdate dihydrate |
JT Baker Chemical Company |
Cat#3764 |
| Sugar beet arabinan |
Megazyme |
Cat#p-ARAB |
| Tamarind xyloglucan |
Carbomer |
Cat#4-00634 |
| Thiamine HCl |
Sigma-Aldrich |
Cat#T4625 |
| Thioctic acid |
Sigma-Aldrich |
Cat#T5625 |
| Threonine |
Sigma-Aldrich |
Cat#T8625 |
| Thymine |
Sigma-Aldrich |
Cat#T0895 |
| Tris |
Thermo Fisher Scientific |
Cat#BP152 |
| TritonX-100 |
Sigma-Aldrich |
Cat#T9284 |
| TRIzol |
Invitrogen |
Cat#15596026 |
| Tryptone |
Thermo Fisher Scientific |
Cat#BP1421 |
| Tyrosine |
Sigma-Aldrich |
Cat#T3754 |
| Uracil |
Sigma-Aldrich |
Cat#U1128 |
| Valeric acid |
Alfa Aesar |
Cat#109-52-4 |
| Valine |
Sigma-Aldrich |
Cat#V0500 |
| Wheat arabinoxylan |
Megazyme |
Cat#P-WAXYL |
| Xylene |
Sigma-Aldrich |
Cat#296333 |
| Xylene Substitute |
Sigma-Aldrich |
Cat#A5597 |
| Xylose |
Sigma-Aldrich |
Cat#X3877 |
| Yeast extract |
Fluka Analytical |
Cat#70161 |
| Zinc sulfate heptahydrate |
JT Baker Chemical Company |
Cat#4382 |
| Critical Commercial Assays |
| AccuPrimeTaq DNA Polymerase, high fidelity kit |
Thermo Fisher Scientific |
Cat#12346086 |
| Affymetrix Mouse Gene ST 2.1 strips |
Affymetrix |
Cat#902120 |
| Arcturus PicoPure DNA Extraction Kit |
Arcturus |
Cat#KIT0103 |
| DNeasy Blood & Tissue Kit |
Qiagen |
Cat#69506 |
| epMotion 5075 TMX |
Eppendorf |
Cat#960020033 |
| High-sensitivity DNA analysis kit |
Agilent |
Cat#5067-4626 |
| KAPA SYBRFAST qPCR kit |
KAPA Biosystems |
Cat#KK4600 |
| KAPA Library Quantification Kit for Illumina platforms |
KAPA Biosystems |
Cat# KK4824 |
| Mouse Lipocalin-2/NGAL DuoSet ELISA kit |
R & D Biosystems |
Cat#DY1857 |
| Pierce Microplate BCA Protein Assay Kit |
Thermo Fisher Scientific |
Cat#PI23252 |
| PowerSoil Isolation Kit |
MoBio Laboratories |
Cat#12888 |
| Qubit RNA Assay Kit |
Thermo Fisher Scientific |
Cat#Q32852
|
| Ribo-Zero rRNA Removal Kits (Bacteria) |
Illumina |
Cat#MRZB12424 |
| RNeasy Protect Bacteria Mini Kit |
Qiagen |
Cat #74524 |
| SequalPrep Normalization Plate Kit, 96-well |
Thermo Fisher Scientific |
Cat#A1051001 |
| TURBO DNase kit |
Ambion |
Cat#AM1907 |
| Deposited Data |
| 16S rRNA gene sequences and metadata |
NCBI BioProjectID NCBI SRA; |
PRJNA300261;SRP065682 |
| Mouse microarray data |
NCBI Geo |
GSM2084849–55 |
| RNA-Seq data |
NCBI BioProjectID |
PRJNA310052, PRJNA310058, PRJNA310062 |
| Experimental Models: Organisms/Strains |
|
Akkermansia muciniphila: DMS 22959, type strain |
DSMZ |
Cat#DMS 22959 |
|
Bacteroides caccae: DSM 19024, type strain |
DSMZ |
Cat#DSM 19024 |
|
Bacteroides ovatus: DSM 1896, type strain |
DSMZ |
Cat#DSM 1896 |
|
Bacteroides thetaiotaomicron: DSM 2079, type strain |
DSMZ |
Cat#DSM 2079 |
|
Bacteroides uniformis: ATCC 8492, type strain |
ATCC |
Cat#ATCC 8492 |
|
Barnesiella intestinihominis: YIT11860 |
DSMZ |
Cat#DSM 21032 |
|
Citrobacter rodentium: DBS100 |
David Schauer, Massachusetts Institute of Technology |
N/A |
|
Citrobacter rodentium: DBS120 |
David Schauer, Massachusetts Institute of Technology |
N/A |
|
Clostridium symbiosum: DSM 934, type strain, 2 |
DSMZ |
Cat#DSM 934 |
|
Collinsella aerofaciens: DSM 3979, type strain |
DSMZ |
Cat#DSM 3979 |
|
Desulfovibrio piger: ATC 29098, type strain |
ATCC |
Cat#ATC 29098 |
|
Escherichia coli HS |
ATCC |
N/A |
|
Eubacterium rectale: DSM 17629, A1-86 |
DSMZ |
Cat#DSM 17629 |
|
Faecalibacterium prausnitzii: DSM 17677, A2-165 |
DSMZ |
Cat#DSM 17677 |
|
Marvinbryantia formatexigens: DSM 14469, type strain, I-52 |
DSMZ |
Cat#DSM 14469 |
|
Roseburia intestinalis: DSM 14610 type strain, L1-82 |
DSMZ |
Cat#DSM 14610 |
| Sequence-Based Reagents |
| 16S rRNA gene Illumina sequencing primers |
Kozich et al. 2013 |
Table S2B |
| qPCR primers |
This paper |
Table S3A |
| Software and Algorithms |
| Arraystar |
DNAStar |
http://www.dnastar.com/t-sub-products-genomics-arraystar.aspx |
| Gen5 |
Biotek |
http://www.biotek.com/products/microplate_software/gen5_data_analysis_software.html |
| ImageJ |
Schneider et al., 2012 |
http://imagej.net/ |
| Microsoft Excel |
Microsoft |
https://products.office.com/en-us/excel |
| Mothur v1.33.3 |
Schloss et al., 2009 |
http://www.mothur.org/ |
| Multi-array average (RMA) method |
Irizarry et al, 2003 |
http://www.bioconductor.org/ |
| Prism v5.04 |
GraphPad Software |
http://www.graphpad.com/scientific-software/prism/ |
| QIAGEN’s Ingenuity Pathway Analysis |
Qiagen |
http://www.ingenuity.com/products/ipa |
| R |
The R Foundation |
https://www.r-project.org/ |
| R - Limma package |
Ritchie et al., 2015 |
https://bioconductor.org/packages/release/bioc/html/limma.html |
| R - Plyr package |
Wickham, 2011 |
https://CRAN.R-project.org/package=plyr |
| UCHIME |
Edgar et al., 2011 |
http://drive5.com/usearch/manual/uchime_algo.html |
| Other |
| Acid-washed glass beads (212–300 μm) |
Sigma-Aldrich |
Cat#G1277 |
| Anaerobic chamber |
Coy manufacturing |
Vinyl Type A + Type B |
| Biostack automated plate handling device |
Biotek Instruments |
BIOSTACK2WR |
| Bioluminescence reader |
Xenogen |
IVIS200 |
| Breathe-Easy polyurethane membrane |
Biversified Biotech |
Cat#BEM-1 |
| Flat bottom 96-well plates |
Costar |
|
| General Laboratory Homogenizer |
Omni International |
|
| Microdissection instrument |
Arcturus |
Veritas Microdissection Instrument |
| Millex-GV Syringe Filter Unit, 0.22 μm, PVDF, 4 mm, ethylene oxide sterilized |
EMD Millipore |
Cat#SLGV004SL |
| Mini-BeadBeater-816 |
Biospec Products |
Cat#607 |
| Powerwave HT absorbance reader |
Biotek Instruments |
PowerWaveHT |
| Synergy HT absorbance reader |
Biotek Instruments |
Synergy HT |
| Upright fluorescence microscope |
Olympus |
BX60 |
| Transmission electron microscope |
Philips |
Philips CM-100 |
