KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Cytokeratin-10 (Dilution 1:1000) | BioLegend | BioLegend Cat# 905401, RRID:AB_2565049 |
| Desmoglein 1 (Dilution 1:200) | Abcam | Abcam Cat# ab124798, RRID:AB_10974963 |
| Loricrin (Dilution 1:500) | BioLegend | BioLegend Cat# 905101, RRID:AB_2565046 |
| Alexafluor 594 conjugated goat-anti rabbit (Dilution 1:1000) | Thermo Fisher Scientific | Thermo Fisher Scientific Cat# A32740, RRID:AB_2762824 |
| Bacterial and Virus Strains | ||
| Staphylococcus epidermidis | This paper | EGM 2-01 |
| Staphylococcus hemolyticus | This paper | EGM 2-08 |
| Staphylococcus warneri | This paper | EGM 2-09 |
| Micrococcus luteus | This paper | EGM 2-04 |
| Corynebacterium aurimucosum | This paper | EGM 2-02 |
| S. aureus strain | Gift from Dr. Alexander Horswill, University of Colorado. (Miller et al., 2019) | AH3926 |
| Biological Samples | ||
| Primary human keratinocytes | Penn Skin Biology and Disease Resource-based Center | N/A |
| Primary mouse keratinocytes | Derived from mice described in experimental models | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Keratinocyte SFM media | Life technologies | Cat#17005042 |
| Keratinocyte growth supplement | Life technologies | Cat#S0015 |
| Medium 154 | Life technologies | Cat#M154500 |
| Antibiotic-Antimycotic (100X) | Life technologies | Cat#15240062 |
| 0.25% Trypsin-EDTA | Thermo Fisher Scientific | Cat# 25200056 |
| DMEM, high glucose | Thermo Fisher Scientific | Cat# 11965084 |
| Fetal Bovine Serum | Sigma-Aldrich | Cat# F6178 |
| Dialyzed Fetal Bovine Serum | Thermo Fisher Scientific | Cat# 26400044 |
| Collagen- Rat Tail | Collaborative | Cat# 354236 |
| Keratinocyte-SFM (1X), without calcium chloride | Life technologies | Cat# 37010022 |
| Y-27632 dihydrochloride, Rho kinase inhibitor | Abcam | Cat# ab120129; CAS Number: 129830-38-2 |
| Defined Trypsin Inhibitor | Thermo Fisher Scientific | Cat# R007100 |
| Sodium Pyruvate (100X) | Thermo Fisher Scientific | Cat# 11360070 |
| MEM Amino Acids Solution (50X) | Thermo Fisher Scientific | Cat # 11130051 |
| Tryptic soy broth | Fisher Scientific | Cat # DF0370 |
| Nutrient broth | Fisher Scientific | Cat# DF0003 |
| Dispase | Sigma | Cat# D4693-1G |
| RNAlater | Ambion, Inc. | Cat# AM7020 |
| Collagenase, Type IV, powder | Life technologies | Cat# 17104019 |
| Yeast cell lysis solution | Lucigen (from MasterPure Yeast DNA Purification kit) | Cat# MPY80200 |
| Protein precipitation reagent | ||
| ReadyLyse Lysozyme solution | Lucigen | Cat# R1810M |
| Metronidazole | Sigma Aldrich | Cat# 1442009 |
| Sulfamethoxazole | Sigma Aldrich | Cat# S7507 |
| Trimethoprim | Fisher Scientific | Cat# ICN19552701 |
| Cephalexin | DOT Scientific | Cat# DSV59000 |
| Enrofloxacin (Baytril ) | Sigma - Aldrich | Cat# 17849 |
| DMEM/F-12, + GlutaMAX supplement | Life technologies | Cat # 10565018 |
| Cholera Toxin | Sigma | Cat# C8052 |
| Insulin-Transferrin-Selenium-Ethanolamine (ITS -X) 100X | Life technologies | Cat# 51500056 |
| Adenine | Sigma | Cat# A9795 |
| Hydrocortisone | Calbiochem | Cat# 386698 |
| AHR ligand 6-formylindolo[3,2-b] carbazole (FICZ) | Sigma-Aldrich | Cat# SML1489 |
| AHR inhibitor (Sigma Aldrich, #CH-223191) | Sigma Aldrich | Cat#CH-223191 |
| Fugene® HD | Promega | Cat# E2311 |
| Peptidoglycan | Sigma Aldrich | Cat # 77140 |
| Ovalbumin | Sigma Aldrich | Cat# A5503 |
| Hoechst 33342 Solution (20 mM) | Thermo Scientific | Cat# 62249 |
| Critical Commercial Assays | ||
| RNeasy Mini Kit | Qiagen | Cat # 74104 |
| Qubit RNA BR and HS Kits | Thermo Fisher Scientific | Cat # Q10210 Cat# Q32852 |
| Bioanalyser RNA 6000 Pico Kit | Agilent | Cat# 5067-1513 |
| TruSeq Strandar RNA Sample Prep Kit | Illumina | Cat # 20020595 |
| NextSeq Mid Output Kit | Illumina | Cat # 20024905 |
| PureLink Genomic DNA Mini Kit (Invitrogen). | Invitrogen | Cat # K182001 |
| Dual-Luciferase® reporter assay system | Promega | Cat #E1910 |
| Deposited Data | ||
| RNA-Sequencing data from murine epithelia (24 total RNAseq samples were collected from 3 conditions (SPF, GF and COL) each from 4 female and 4 male replicate animals.) | This paper | BioProject: PRJNA683863 SRA: SRP297369 GEO accession #: GSE162925 |
| 16S rRNA gene sequencing Datasets | This paper | BioProject: PRJNA684321 SRA |
| Experimental Models: Cell Lines | ||
| HaCaT cells | Gift from Dr. John Seykora, University of Pennsylvania (Boukamp et al., 1988) | RRID:CVCL_0038 |
| Experimental Models: Organisms/Strains | ||
| C57BL6/J | The Jackson Laboratory | stock #000664 |
| Rag1 KO | The Jackson Laboratory | stock #002216 |
| Ahrfx | Gift from Dr. Jorge Henao-Mejia, University of Pennsylvania. Available from the Jackson Laboratory | stock #006203 |
| K14cre | The Jackson Laboratory | Stock #018964 |
| Oligonucleotides | ||
| Refer to Table S5 for Taqman Probes and PCR primers used in this paper | N/A | N/A |
| Recombinant DNA | ||
| pGL4.74 Renilla luciferase | Gift from Dr. Thomas R. Sutter (Sutter et al., 2011) | pGL4.74 |
| pGL4.23 Firefly luciferase reporter plasmid with xenobiotic response element (XRE) | pGL4.23 | |
| Genomic DNA from Microbial Mock Community B (Even, Low Concentration), v5.1L, for 16S rRNA Gene Sequencing | BEI Resources | HM-782D, v5.1L |
| Software and Algorithms | ||
| GraphPad Prism version 8.0.0 for Mac OS X | GraphPad Software, San Diego, California USA | www.graphpad.com |
| Image J, Version 10.2 | National Institute of Health | https://imagej.nih.gov/ij/ |
| Morpheus heat map viewer | Broad Institute | https://software.broadinstitute.org/morpheus/ |
| AlignerBoost | (Zheng and Grice, 2016) | https://github.com/Grice-Lab/AlignerBoost |
| STAR 2.5.3 | (Dobin et al., 2013) | http://code.google.com/p/rna-star/ |
| DESeq2 | (Love et al., 2014) | http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html webcite |
| biomaRt | (Durinck et al., 2009) | https://bioconductor.org/packages/release/bioc/html/biomaRt.html |
| topGO | (Alexa A, 2020) | https://bioconductor.org/packages/release/bioc/html/topGO.html |
| REVIGO | (Supek et al., 2011) | http://revigo.irb.hr/ |
| HmmUFOtu | (Zheng et al., 2018) | https://github.com/Grice-Lab/HmmUFOtu |
| PHYLOSEQ | (Desai, 1990) | https://bioconductor.org/packages/release/bioc/html/phyloseq.html |
| Other | ||
| 100μm cell strainer | Falcon | Cat# 352360 |
| Cell countess II | Invitrogen | Cat# A27977 |
| Lysing Matrix A tube | MP Biomedicals | Cat# 116910050-CF |
| FastPrep 24 | MP Biomedicals | Cat# 116004500 |
| 0.5 mm glass beads | Sigma-Aldrich | Cat# Z250465 |
| 6 mm ceramic beads | MP Biomedicals | Cat# 116540424-CF |
| Tewameter ®, TM300 | Courage+Khazaka, Cologne, Germany | https://www.courage-khazaka.de/en/16-wissenschaftliche-produkte/alle-produkte/172-tewameter-e |
| Scotch Heavy Duty Packaging Tape, 2”X800” | 3M | ID: 70005058279 |
| 12mm transwells with 0.4μm pore | Sigma-Aldrich | Cat# CLS3460 |
| EVOM2 Epithelial Voltmeter with STX2 electrode | World Precision Instruments | https://www.wpiinc.com/var-2754-epithelial-volt-ohm-teer-meter |
| Blood agar plates | Remel | Cat# R01201 |
| Tissue Culture dishes 35mm, 60mm, 100mm dia. | Cell Star | Cat#s 627160, 628160, 664160 |