KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| 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 |