Antibodies |
|
|
|
Anti-Proliferating Cell Nuclear Antigen antibody |
Sigma-Aldrich |
Cat # P8825 RRID: AB_477413 |
Glypican-3 antibody |
Abbiotec |
Cat # 251482 RRID: AB_10641641 |
Neutrophil antibody [NIMP-R14]; Ly6G |
Abcam |
Cat# ab2557 RRID: AB_303154 |
Rabbit Anti-CD3, T Cell Antibody |
Sigma-Aldrich |
Cat# C7930 RRID: AB_259074 |
Ki67 antibody |
Abcam |
Cat# ab15580 RRID: AB_443209 |
RAT ANTI MOUSE F4/80 antibody |
Bio-Rad / AbD Serotec |
Cat# MCA497G RRID: AB_872005 |
Mouse Lipocalin-2/NGAL mAb (Clone 228418) |
R&D Systems |
Cat# MAB1857 RRID: AB_2136584 |
Cleaved Caspase-3 (Asp175) Antibody |
Cell Signaling Technology |
Cat# 9661 RRID: AB_2341188 |
Akt (pan) (C67E7) Rabbit mAb antibody |
Cell Signaling Technology |
Cat# 4691 RRID: AB_915783 |
Caspase-9 (C9) Mouse mAb antibody |
Cell Signaling Technology |
Cat# 9508 RRID: AB_2068620 |
Cytokeratin 19 Antibody (SPM561) |
Novus Biologicals |
Cat #: NBP2-34379 |
|
Chemicals, Peptides, and Recombinant Proteins |
|
|
|
Metronidazole |
Alfa Aesar |
Cat#: H6025814 |
Cholestyramine |
Sigma-Aldrich |
Cat#: C4650 |
Inulin |
Beneo |
Cat#: Orafti® HP |
FOS |
Beneo |
Cat#: Orafti®P95 |
Pectin |
Sigma-Aldrich |
Cat#: P9135 |
Sodium butyrate |
Sigma-Aldrich |
Cat#: 303410 |
Hops β-acid |
MDF lab; This paper |
N/A |
Cholic acid |
Sigma-Aldrich |
Cat #: C1129 |
Chenodeoxycholic acid |
Sigma-Aldrich |
Cat #: C9377 |
Lithocholic acid |
Sigma-Aldrich |
Cat #: L6250 |
Deoxycholic acid |
Sigma-Aldrich |
Cat#: D2510 |
Taurodeoxycholic acid sodium salt hydrate |
Sigma-Aldrich |
Cat #: T0875 |
Oil Red O |
Sigma-Aldrich |
Cat #: O0625 |
Lipopolysaccharides from Escherichia coli O128:B12 |
Sigma-Aldrich |
Cat #: L2887 |
Glycodeoxycholic Acid |
Cayman Chemical |
Item #: 20274 |
|
Critical Commercial Assays |
|
|
|
In Situ Cell Death Detection Kit, Fluorescein |
Sigma-Aldrich/Roche |
Cat# 11684795910 |
Reticulin silver plating staining kit |
Millipore-Sigma |
Cat# 1002510001 |
Total Bile Acid (TBA) assay |
Diazyme |
Cat# DZ042A-k |
Bilirubin assay |
Randox |
Cat # BR411 |
Alanine aminotransferase (ALT) assay |
Randox |
Cat # AL146 |
Aspartate aminotransferase (AST) assay |
Randox |
Cat # AS147 |
Mouse alpha-Fetoprotein (AFP) ELISA |
R&D Systems |
Cat# DY5369 |
Mouse Lipocalin-2 (Lcn2) ELISA |
R&D Systems |
Cat# DY1857 |
Mouse Keratinocyte-derived chemokine (KC) ELISA |
R&D Systems |
Cat# DY453 |
Mouse soluble intercellular adhesion molecule 1 (sICAM-1) ELISA |
R&D Systems |
Cat# DY796 |
Mouse Myeloperoxidase (MPO) ELISA |
R&D Systems |
Cat# DY3667 |
Mouse Neutrophil elastase (NE) ELISA |
R&D Systems |
Cat# DY4517 |
Mouse Serum Amyloid A (SAA) ELISA |
R&D Systems |
Cat# DY2948 |
Mouse Tumor necrosis factor alpha (TNFα) |
R&D Systems |
Cat# DY410 |
Mouse Interleukin-1 beta (IL-1β) ELISA |
R&D Systems |
Cat# DY401 |
Mouse Interleukin-6 (IL-6) ELISA |
R&D Systems |
Cat# DY406 |
Mouse Interferon-gamma (IFN-γ) ELISA |
R&D Systems |
Cat# DY485 |
Mouse Insulin ELISA |
Millipore-Sigma |
Cat# EZRMI-13K |
Total cholesterol assay |
Randox |
Cat# CH201 |
Triglycerides (TG) assay |
Randox |
Cat# TR210 |
Lactate Dehydrogenase (LDH) |
Randox |
Cat# LD3842 |
|
Deposited Data |
|
|
|
Transcriptome (RNA-sequencing) |
This paper |
European Nucleotide Archive, accession number PRJEB28449 |
16S sequencing |
This paper |
European Nucleotide Archive, accession number PRJEB28447 |
|
Experimental Models: Cell Lines |
|
|
|
Hepa-1c1c7 (mouse liver hepatoma) |
ATCC |
Hepa-1c1c7 CRL-2026 |
HEK-Blue-mTLR4 cells |
Invivogen |
Cat #: hkb-mtlr4 |
HEK-Blue mTLR5 cells |
Invivogen |
Cat#: hkb-mtlr5 |
|
Experimental Models: Organisms/Strains |
|
|
|
C57BL/6 WT mice |
Animal facility: The Pennsylvania State University (PSU), The university of Toledo (UT) and Georgia State University (GSU) |
N/A |
Germ-free C57BL/6 WT mice |
GSU |
N/A |
Tlr5 deficient (Tlr5KO) mice |
UT, PSU, and GSU |
N/A |
Germ-free Tlr5KO mice |
GSU |
N/A |
Tlr5KO (B6.129S1-Tlr5tm1Flv/J) mice |
The Jackson Laboratory |
Stock No: 008377 |
Lcn2 deficient (Lcn2KO) mice |
PSU |
N/A |
Tlr4 deficient (Tlr4KO) mice |
PSU |
N/A |
MyD88-deficient (MyD88KO) mice |
PSU |
N/A |
Tlr5/Tlr4 double knockout (Tlr5/Tlr4-DKO) mice |
PSU |
N/A |
Tlr5/Nlrc4 double knockout (Tlr5/Nlrc4-DKO) mice |
PSU |
N/A |
|
Oligonucleotides |
|
|
|
Table S3 |
Integrated DNA Technologies |
N/A |
|
Software and Algorithms |
|
|
|
GraphPad Prism 7.0 |
GraphPad |
https://www.graphpad.com/scientific-software/prism/ |
BD Accuri C6 Software |
BD Biosciences |
https://www.bdbiosciences.com/documents/BD_Accuri_C6_Software_User_Guide.pdf |
FlowJo software |
Becton Dickinson |
http://beckmanflow.com/?page_id=76/?pi_ad_id=113583631840 |
|
Other |
|
|
|
16 S sequencing |
QIIME, LEFSE and Picrust |
QIIME:http://qiime.org/
https://www.nature.com/articles/nmeth.f.303; LEFSE; https://bitbucket.org/biobakery/biobakery/wiki/lefse
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218848/; Picrust: http://picrust.github.io/picrust/
https://www.ncbi.nlm.nih.gov/pubmed/23975157
|