KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD3 | Fisher Scientific | 11-0032-82 (Clone: 17A2); RRID:AB_2572431 |
| IL-17a | Fisher Scientific | 25-7177-82 (Clone: ebio17b7); RRID:AB_10732356 |
| CD4 | Biolegend | 100428 (Clone: GK1.5); RRID:AB_493647 |
| IFNy | Fisher Scientific | 45-7311-80 (Clone: XMG1.2); RRID:AB_906239 |
| Foxp3 | Fisher Scientific | BDB563902 (Clone: R16–715); RRID:AB_2630318 |
| Gr1 | Biolegend | 108408 (Clone: RB6–8C5); RRID:AB_313373 |
| CD11b | VWR (Biolegend) | 101228-BL (Clone: M1/70); RRID:AB_893232 |
| TER119 | Biolegend | 116212 (Clone: TER-119); RRID:AB_313713 |
| B220 | Fisher Scientific (Invitrogen) | 5014055 (Clone: RA3–6B2); RRID:AB_11220275 |
| CD44 | VWR (Tonbo) | 10050–486 (Clone: IM-7); RRID:AB_2621572 |
| CD69 |
VWR (Biolegend) | 104511-BL (Clone: H1.2F3); RRID: AB_493565 |
| LIVE/DEAD Fixable Dead Cell Stain Kit | Life technologies | L34957 |
| Bacterial and Virus Strains | ||
| Bacteroides thetaiotaomicron | DSM | 2079 |
| Clostridium asparagiforme | DSM | 15981 |
| Clostridium sporogenes | ATCC | 15579 |
| Clostridium symbiosum | DSM | 934 |
| Akkermansia muciniphila | DSM | 22959 |
| Alistipes shahii | DSM | 19121 |
| Bacillus subtilis 168 | DSM | 402 |
| Bacteroides acidifaciens | DSM | 15896 |
| Bacteroides caccae | DSM | 19029 |
| Bacteroides eggerthii | DSM | 20697 |
| Bacteroides finegoldii | DSM | 17565 |
| Bacteroides fragilis | DSM | 2151 |
| Bacteroides ovatus | DSM | 1896 |
| Bacteroides stercoris | DSM | 19555 |
| Bacteroides uniformis | DSM | 6597 |
| Bacteroides vulgatus | DSM | 1447 |
| Bacteroides xylanisolvens | DSM | 18836 |
| Bifidobacterium longum subsp longum | DSM | 20219 |
| Blautia producta | DSM | 3507 |
| Clostridium innocuum | DSM | 1286 |
| Clostridium scindens | DSM | 5676 |
| Collinsella aerofaciens | DSM | 3979 |
| Delftia acidovorans | ATCC | 25012 |
| Dorea formicigenerans | DSM | 3992 |
| Dorea longicatena | DSM | 13814 |
| Edwardsiella tarda | ATCC | 23685 |
| Eggerthella lenta 1-3-56 | DSM | 110906 |
| Eggerthella lenta | DSM | 2243 |
| Eggerthella sinensis | DSM | 16107 |
| Eggerthella sp. | DSM | 11767 |
| Enterococcus faecalis | DSM | 2570 |
| Escherichia coli BW25113 | DSM | 27469 |
| Eubacterium eligens | DSM | 3376 |
| Eubacterium hallii | DSM | 3353 |
| Eubacterium rectale | DSM | 17629 |
| Faecalibacterium prausnitzii | DSM | 17677 |
| Fusobacterium nucleatum subsp. nucleatum | DSM | 15643 |
| Gordonibacter pamelae | DSM | 110924 |
| Lactococcus lactis | DSM | 20481 |
| Lactonifactor longoviformis | DSM | 17459 |
| Parabacteroides distasonis | DSM | 20701 |
| Parabacteroides merdae | DSM | 19495 |
| Prevotella copri | DSM | 18205 |
| Providencia rettgeri | DSM | 4542 |
| Ruminococcus obeum | DSM | 25238 |
| Biological Samples | ||
| Stool samples from healthy and rheumatoid arthritis patients | This paper | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Methotrexate (Pharmaceutical Grade) for mouse experiments | Fresenius Kabi | Product # 102250 |
| Methotrexate for in vitro and ex vivo studies | Sigma Aldrich | M9929–100MG |
| Folic acid | Fisher Scientific | BP25195 |
| Leucovorin | Spectrum Chemicals | LE117–100MG |
| Dextran sodium sulfate | Alfa Aesar | Cat no. 9011-18-1 |
| Critical Commercial Assays | ||
| ZymoBIOMICS 96 MagBead DNA Kit | Zymo | D4302 |
| KAPA HiFi Hot Start PCR kit | Kapa Biosystems | KK2502 |
| SequalPrep Normalization Plate | Life Technologies | A10510–01 |
| Qiagen MinElute Gel Extraction Kit | Qiagen | 28604 |
| Qiagen MinElute PCR Purification Kit | Qiagen | 28004 |
| Nextera DNA Flex Library Kit | Illumina | 20018705 |
| Nextera Compatible Unique Dual Indices - Set A primers | Illumina | 20027213 |
| Deposited Data | ||
| 16S rRNA, shotgun, and RNA-seq data | NCBI SRA | PRJNA656577 |
| Metabolomics data | This paper | Table S6C |
| Experimental Models: Cell Lines | ||
| Experimental Models: Organisms/Strains | ||
| Germ free C57BL/6 | UCSF Gnotobiotics Core | N/A |
| Oligonucleotides | ||
| Recombinant DNA | ||
| Software and Algorithms | ||
| R (v3.6.2) | Packages for analytical parts: phyloseq, tidyverse, ape, vegan, nlme, stats, DEseq2, edgeR, GrowthCurveR, MaSaLin2, ggtree, clusterprofiler, dada2, UpSetR, pubmedR | https://www.r-project.org/ |
| QIIME (v1.91) | Caporaso et al., 2010 | http://qiime.org/ |
| QIIME2 (v2020.2) | Boylen et al., 2019 | https://qiime2.org/ |
| UniPro UGENE (v33) | Okonechnikov et al., 2012 | http://ugene.net/ |
| Trimmomatic (v0.32) | Bolger et al., 2014 | http://www.usadellab.org/cms/?page=trimmomatic |
| SortMeRNA (v2.1) | Kopylova et al., 201 | https://github.com/biocore/sortmerna |
| Bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| BlastKOALA | Kanehisa et al., 2016 | https://www.kegg.jp/blastkoala/ |
| Fastp (v0.20.0) | Chen et al., 2018 | https://github.com/OpenGene/fastp |
| MetaPhlAn2(v2.7.7) | Truong et al., 2015 | https://huttenhower.sph.harvard.edu/metaphlan |
| HUMAnN2 (v0.11.1) | Franzosa et al., 2018 | https://huttenhower.sph.harvard.edu/humann |
| Other | ||