| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| PE anti-mouse SiglecF (Clone E50-2240) | BD Pharmigen™ | Cat# 562068; RRID: AB_10896143 |
| FITC anti-mouse CD4 (Clone GK1.5) | Biolegend | Cat# 100406; RRID: AB_312691 |
| FITC anti-mouse CD11c (Clone N418) | Biolegend | Cat# 117306; RRID: AB_313775 |
| PE anti-mouse CD44 (Clone IM7) | BD Pharmigen™ | Cat# 553134; RRID: AB_394649 |
| PE anti-mouse IL-17A (Clone TC11-18H0.1) | Biolegend | Cat# 506904; RRID: AB_315464 |
| PerCP-Cy™5.5 anti-mouse TCR β chain (Clone H57-597) | BD Pharmigen™ | Cat# 560657; RRID: AB_1727575 |
| PE-Cy™7 anti-mouse CD11b (Clone M1/70) | BD Pharmigen™ | Cat# 552850; RRID: AB_394491 |
| PE/Cyanine7 anti-mouse CD62L (Clone MEL-14) | Biolegend | Cat# 104418; RRID: AB_313103 |
| APC anti-mouse Ly6G (Clone 1A8) | Biolegend | Cat# 127613; RRID: AB_1877163 |
| APC anti-mouse CD45 (Clone 30-F11) | Biolegend | Cat# 103112; RRID: AB_312977 |
| PerCP anti-mouse CD45 (Clone 30-F11) | Biolegend | Cat# 103129; RRID: AB_893343 |
| APC/Cyanine7 anti-mouse I-A/I-E (Clone M5/114.15.2) | Biolegend | Cat# 107627; RRID: AB_1659252 |
| eFluor450 anti-mouse FoxP3 (Clone FJK-16s) | eBioscience™ | Cat# 48-5773-82; RRID: AB_1518812 |
| eFluor450 anti-mouse IL-13 (Clone 13A) | eBioscience™ | Cat# 48-7133-80; RRID: AB_11219690 |
| Brilliant Violet 421™ anti-mouse F4/80 (Clone BM8) | Biolegend | Cat# 123131; RRID: AB_10901171 |
| APC/Cyanine7 anti-mouse TCR β chain (Clone H57-597) | Biolegend | Cat# 109220; RRID: AB_893624 |
| PE/Cyanine7 anti-mouse IFNγ (Clone XMG1.2) | Biolegend | Cat# 505825; RRID: AB_1595591 |
| APC anti-mouse TNFα (Clone MP6-XT22) | BD Pharmigen™ | Cat# 561062; RRID: AB_2034022 |
| Bacterial and virus strains | ||
| Bacteroides fragilis (BFM04319) | Isolated from stool of a human subject with asthma in this study by plating stool anaerobically on brain-heart-infusion media supplemented to 0.1% porcine mucin. | NA |
| Bacteroides fragilis (VPI2553) | Received as a gift from the laboratory of Jeffrey I. Gordon. Can be acquired from ATCC. | Cat# 25285 |
| Biological samples | ||
| Human stool samples were obtained from both an adult (ages 18-40 years) and a pediatric population (ages 6-10 years). | The study cohorts came from the Microbiome in Asthma Research Study (MARS) | NA |
| Chemicals, peptides, and recombinant proteins | ||
| Fetal Bovine Serum | Thermo Fisher Scientific (GIBCOTM) | Cat# 26140-079 |
| BD Difco™ Bacto™ Brain Heart Infusion | Fisher Scientific | Cat# DF0037-07-0 |
| Mucin from porcine stomach | Millipore Sigma | Cat# M1778 |
| L-Cysteine hydrochloride anhydrous | Millipore Sigma | Cat# C1276 |
| BD Difco™ Dehydrated Culture Media: Noble Agar | Fisher Scientific | Cat# DF0142-17-0 |
| DL-Histidine monohydrochloride monohydrate | Millipore Sigma | Cat# H7875 |
| Hematin porcine | Millipore Sigma | Cat# H3281 |
| Resazurin sodium salt | Millipore Sigma | Cat# R7017 |
| Albumin from chicken egg white | Millipore Sigma | Cat# A5503 |
| Imject™ Alum Adjuvant | Thermofisher Scientific | Cat# 77161 |
| Phenol/Chloroform/Isoamyl Alcohol (25:24:1 Mixture, pH 6.7/8.0, Liq.) | Fisher Scientific | Cat# BP1752I-400 |
| BioSpec Products 0.1 MM Zirconia/Silica Beads | Fisher Scientific | Cat# NC0362415 |
| Low Carbon Steel Balls (5/32'') | McMaster-Carr | Cat# 96455K73 |
| AMPure XP Reagent, 5 mL | Beckman Coulter | Cat# A63880 |
| HEPES (Fine White Crystals/Molecular Biology), Fisher BioReagents™ | Fisher Scientific | Cat# BP310-500 |
| Liberase™ DL Research Grade | Millipore Sigma (Roche) | Cat# 5466202001 |
| DNase I | Millipore Sigma (Roche) | Cat# 10104159001 |
| ACK Lysing Buffer | Thermofisher (Gibco) | Cat# A1049201 |
| PMA | Sigma-Aldrich | Cat# P1585 |
| Ionomycin from Streptomyces conglobatus | Sigma-Aldrich | Cat# I9657 |
| eBioscience™ Monensin Solution (1000X) | Thermofisher (Invitrogen) | Cat# 00-4505-51 |
| eBioscience™ Brefeldin A Solution (1000X) | Thermofisher (Invitrogen) | Cat# 00-4506-51 |
| RNAlater™ Stabilization Solution | Thermofisher (Invitrogen) | Cat# AM7021 |
| TRIzolTM Reagent | Thermofisher (Invitrogen) | Cat# 15596018 |
| Fluorescein isothiocyanate–dextran | Millipore Sigma (Sigma-Aldrich) | Cat# 46944 |
| Thomas Scientific GelRed Nucleic Acid Gel Stain, 10,000X in Water, 0.1mL | Fisher Scientific (Thomas Scientific) | Cat# NC9938951 |
| Critical commercial assays | ||
| Illumina DNA Prep (Nextera) | Illumina | Cat# FC-121-1030 |
| Bacteria Counting Kit, for flow cytometry (SYTO-BC) | Thermofisher (Invitrogen) | Cat# B7277 |
| QIAquick 96 PCR Purification Kit | Qiagen | Cat# 28183 |
| Quant-iT™ dsDNA Assay Kits, broad range (BR) | Thermofisher (Invitrogen) | Cat# Q33130 |
| RNAeasy Mini Kit | Qiagen | Cat# 74104 |
| Quant-it™ RiboGreen RNA Assay Kit and RiboGreen RNA Reagent, RediPlate™ 96 RiboGreen™ RNA Quantitation Kit | Thermofisher (Invitrogen) | Cat# R11490 |
| NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® | Illumina | Cat# E7645L |
| Power SYBR™ Green PCR Master Mix | Thermofisher (Applied Biosystems) | Cat# 4367659 |
| LEGENDplex™ Mouse Inflammation Panel (13-plex) with V-bottom Plate | Biolegend | Cat# 740446 |
| DNeasy Blood & Tissue Kit (50) | Qiagen | Cat# 69504 |
| DNA/RNA Oxidative Damage (High Sensitivity) ELISA Kit | Cayman Chemicals | Cat# 589320 |
| BD Microtainer™ Capillary Blood Collector and BD Microgard™ Closure | Fisher Scientific (BD) | Cat# 02-675-185 |
| Epredia™ Shandon™ Kwik-Diff™ Stains | Fisher Scientific (Epredia) | Cat# 99-907-01 |
| AllPrep PowerFecal DNA/RNA Kit | Qiagen | Cat# 80244 |
| cDNA Synthesis: EasyScript Plus™ cDNA Synthesis Kit | Lambda Biotech | Cat# G236 |
| Calprotectin ELISA Assay Kit | Eagle Biosciences | Cat# CAL35-K01 |
| Deposited data | ||
| Sequencing Data | This paper | European Nucleotide Archive Accesion Number: PRJEB45298 |
| Experimental models: Organisms/strains | ||
| Mouse: Germ-free C57BL/6J: WT C57BL/6J | Bred in house | N/A |
| Oligonucleotides | ||
| See Table S8 for a list of oligonucleotides | N/A | N/A |
| Software and algorithms | ||
| R version 4.2.1 or higher | R Development Core Team, 2011 | https://www.r-project.org/ |
| FlowJo v10 | BD | RRID: SCR_008520, https://www.flowjo.com/solutions/flowjo/downloads |
| BD FACSDivaTM software | BD Bioscience | RRID: SCR_001456 |
| DADA2 (version 1.10.1 in R) | Callahan et al., 201628 | https://benjjneb.github.io/dada2/ |
| vegan (version 2.5.7 in R) | Oksanen et al., 202376 | https://github.com/vegandevs/vegan |
| phyloseq (version 1.28.0 in R) | McMurdie and Holmes, 201377 | https://joey711.github.io/phyloseq/ |
| DESEQ2 (version 1.24.0 in R) | Love et al., 201478 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| cooccur (version 1.3 in R) | Griffith et al., 201679 | https://rdrr.io/cran/cooccur/man/cooccur.html |
| Bbtools | Bushnell et al. 201780 | sourceforge.net/projects/bbmap/ |
| SPAdes version 3.11.0 | Bankevich et al., 201281 | https://cab.spbu.ru/software/spades/ |
| prokka (version 1.14.6) | Seemann, T. 201482 | https://github.com/tseemann/prokka |
| gnominator (version 1.0 in R) | This paper | Zenodo: https://doi.org/10.5281/zenodo.7522060 |
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