| Antibodies |
| Rabbit polyclonal anti-Muc2 (Muc2C3) |
Johansson et al, 2008 |
N/A |
| Rabbit polyclonal anti-apo-Muc2 (PH497) |
Hansson et al., 1994 |
N/A |
|
|
|
| Bacterial and Virus Strains |
| Bifidobcterium longum NCC2705 |
Nestlé |
N/A |
|
|
|
| Chemicals, Peptides, and Recombinant Proteins |
| GuHCl 8M |
Thermo Scientific |
24115 |
| DTT |
Sigma-Aldrich |
D9163 |
| Iodoacetamide |
Sigma-Aldrich |
I6125 |
| LysC |
Wako |
125-05061 |
| Trypsin |
Promega |
V5111 |
| Mouse Muc2 SpikeTides™_L Proteotypic Peptides |
JPT |
N/A |
| Fat adjusted diet |
Envigo |
TD.96132 |
| Autoclavable Mouse Breeder Diet |
LabDiet |
5021 |
| Isoflurane |
Kronans apotek |
N01AB06 |
| 2X cOmplete Protease Inhibitor Cocktail |
Roche |
11873580001 |
| Lysing matrix E |
MPBio |
116914100 |
| Sodium isovalerate-1-13C |
Sigma-Aldrich |
487643 |
| Isobutyric acid-1-13C |
Sigma-Aldrich |
606138 |
| Sodium butyrate-13C4
|
Sigma-Aldrich |
488380 |
| Propionic acid-d6
|
Sigma-Aldrich |
490644 |
| Sodium acetate-1-13C,d3
|
Sigma-Aldrich |
298042 |
| Succinic acid 13C4
|
Cambride Isotope Laboratories |
CLM-1571 |
| Sodium lactate 13C3
|
Cambride Isotope Laboratories |
CLM-1579 |
| N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide |
Sigma-Aldrich |
394882 |
| Ampicillin |
Sigma-Aldrich |
A9518-100G |
| Metronidazole |
Sigma-Aldrich |
M3761-5G |
| Vancomycin |
Sigma-Aldrich |
V2002-5G |
| Neomycin |
Sigma-Aldrich |
|
|
N6386-100G |
|
| Black 10μm polystyrene Polybead microspheres |
Polysciences |
24294 |
| Crimson 1μm Fluospheres |
Thermo Fisher Scientific |
F8816 |
| Calcein violet AM |
Thermo Fisher Scientific |
C34858 |
| Hoechst-34580 |
Sigma-Aldrich |
63493 |
| Oligofructose-enriched inulin (Orafti Synergy 1) |
Alsiano/Beneo |
http://www.beneo.com |
| Difco Reinforced Clostridial Medium |
BD |
218081 |
|
|
|
| Critical Commercial Assays |
| Bayer Contour Next blood glucose strips |
Kronans apotek |
732781 |
| Ultra Sensitive Mouse Insulin ELISA kit |
Crystal Chem Inc. |
90080 |
| RNeasy Mini kit |
Qiagen |
74106 |
| High Capacity cDNA Reverse Transcription Kit |
Thermo Fisher Scientific |
4368814 |
| HotStarTaq Master mix Kit |
Qiagen |
203445 |
| pGEM®-T Vector Systems |
Promega |
A3600 |
| One Shot MAX Efficiency DH10B T1 cells |
Invitrogen |
12331-013 |
| QIAprep Spin Miniprep Kit |
Qiagen |
27106 |
| 1x SYBR Green Master Mix |
Thermo Fisher Scientific |
4309155 |
| 5PRIME HotMasterMix |
Quantabio |
733-2474 |
| NucleoSpin Gel and PCR Clean-up kit |
Macherey-Nagel |
740609 |
| Quant-iT PicoGreen dsDNA Assay kit |
Thermo Fisher Scientific |
P11496 |
| Agencourt AMPure XP |
Beckman Coulter |
A63880 |
|
|
|
| Deposited Data |
| Proteomics data raw data |
This paper |
ProteomeXchange PXD006129 |
| Microbiota 16S rDNA gene sequences |
This paper |
ENA archivePRJEB20367 |
| Greengenes reference database |
DeSantis et al., 2006 |
http://greengenes.lbl.gov |
| Experimental Models: Organisms/Strains |
| Male C57BL/6J mice |
Charles River Germany |
000664 |Black 6 |
| Male heterozygous Ob/WT mice B6.Cg-Lepob/J |
Charles River Italy |
000632 | B6 ob |
| Female heterozygous Ob/WT mice B6.Cg-Lepob/J |
Charles River Italy |
000632 | B6 ob |
| Male C57BL/6J mice |
own breeding |
N/A |
|
|
|
| Oligonucleotides |
| V4 region 515F and 806R primers |
Kozich et al., 2013 |
N/A |
| Dmbt1 F 5′-GGGGATCTCCACTGTTATCTTTGA-3′ |
Sigma-Aldrich |
N/A |
| Dmbt1 R 5′-AGAATCTGTTCCATCTGTGGGA-3′ |
Sigma-Aldrich |
N/A |
|
|
|
| Recombinant DNA |
| pGEM-T-Dmbt1 |
This paper |
N/A |
|
|
|
| Software and Algorithms |
| MaxQuant |
Cox, et al 2008 |
http://www.biochem.mpg.de/5111795/maxquant |
| Perseus |
Tyanova, et al 2016 |
http://www.biochem.mpg.de/5111810/perseus |
| Prism (version 7.0b) |
GraphPad |
https://www.graphpad.com/scientific-software/prism/ |
| QIIME (version 1.9.1). |
Caporaso et al., 2010a |
http://qiime.org |
| Mouse mucin sequence database |
in-house database |
http://www.medkem.gu.se/mucinbiology/databases/ |
| PEAR |
Zhang et al., 2014 |
http://www.exelixis-lab.org/web/software/pear |
| UCLUST |
Edgar, 2010 |
http://www.drive5.com/usearch/ |
| Imaris (version 7.6.3) |
Bitplane |
http://www.bitplane.com |
| Zen (version 2.3) |
Carl Zeiss |
http://www.zeiss.com |
| PyNAST |
Caporaso et al., 2010b |
http://pynast.sourceforge.net |
| FastTree |
Price et al., 2010 |
http://www.microbesonline.org/fasttree |
| ChimeraSlayer |
Haas et al., 2010 |
http://microbiomeutil.sourceforge.net/#A_CS |
| Other |
| Nanosep 10K Omega |
Pall, Life Sciences |
OD010C35 |
| EchoMRI Body Composition Analyzers for Live Small Animals |
Echo Medical Systems |
http://www.echomri.com |
| EASY-nLC system 1000 |
Thermo Scientific |
LC120 |
| reverse-phase column (150 × 0.075 mm inner diameter, C18-AQ 3 μm |
in-house packed |
N/A |
| QExactive Hybrid Quadrupole-Orbitrap Mass Spectrometer |
Thermo Scientific |
IQLAAEGAAPFALGMAZR |
| StageTip C18 columns |
Rappsilber et al., 2007 |
N/A |
| TissueLyser II |
Qiagen |
85300 |
| QiaCube |
Qiagen |
9001885 |
| NanoDrop ND-1000 spectrophotometer |
Thermo Scientific |
http://www.nanodrop.com/Products.aspx |
| CFX96 Real-Time PCR Detection System |
Bio-Rad |
C1000 |
| Illumina MiSeq |
Illumina |
https://www.illumina.com/systems/sequencing-platforms/miseq.html |
| Fast-Prep-24 Classic |
MPBio |
116004500 |
| Gas Chromatograph-Mass Spectrometer |
Agilent Technologies |
7890A + 5975C series |
| Anaerobic COY chamber |
COY Laboratory Products |
http://coylab.com/products/anaerobic-chambers/vinyl-anaerobic-chambers/ |
| Horizontal perfusion chamber |
Gustafsson et al., 2012 |
N/A |
| Perfusion chamber heating blocks |
Gustafsson et al., 2012 |
N/A |
| Dual automatic temperature controller |
Warner instruments |
TC-344B |
| DDS syringe pump |
Harvard apparatus |
70-3333 |
| LED light source |
Photonic optics |
F3000 |
| Stereo-microscope |
Lecia |
MZ75 |
| Digimatic micrometer |
Mitutoyo |
350-261-30 |
| Digimatic interface |
Mitutoyo |
264-014-10 |
| Borosilicate glass capillaries |
Sutter instrument |
BF120-60-10 |
| Flaming/Brown Micropipette Puller |
Sutter instrument |
P-97 |
| Laser scanning confocal imaging system |
Carl Zeiss |
LSM700 |
