REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
InVivoMAb CD25, Clone PC-61.5.3	BioXcell	Cat# BE0012, RRID:AB_1107619
AffiniPure Fab Fragment Goat Anti-Mouse IgM, μ chain specific	Jackson ImmunoResearch	Cat# 115-007-020; RRID:AB_2338477
B220 PE, Clone RA3-6B2	BD Bioscience	Cat# 553090; RRID:AB_244282
CD1d BV510, Clone 1B1	Biolegend	Cat# 563189, RRID:AB_2738056
CD3 BV605, Clone 17A2	Biolegend	Cat# 100237; RRID:AB_2562039
CD4 BV605, Clone RM4-5	Biolegend	Cat# 100548; RRID:AB_2563054
CD4 BV711, Clone RM4-5	Biolegend	Cat# 100550; RRID:AB_2562099
CD5 AF647, Clone 53-7.3	Biolegend	Cat# 100614; RRID:AB_2075301
CD8a BV605, Clone 53-6.7	Biolegend	Cat# 100744; RRID:AB_2562609
CD11b BV605, Clone M1/70	Biolegend	Cat# 101257; RRID:AB_2565431
CD11c BV605, Clone N418	Biolegend	Cat# 117334; RRID:AB_2562415
CD19 BV785, Clone 6D5	Biolegend	Cat# 115543; RRID:AB_11218994
CD19 BV785, Clone HIB19	Biolegend	Cat# 302240; RRID:AB_11218596
CD21 APC, Clone 7G6	Biolegend	Cat# 123412; RRID:AB_2085160
CD21 FITC, Clone 7G6	BD Biosciences	Cat# 553818, RRID:AB_395070
CD23 FITC, Clone B3B4	Biolegend	Cat# 101606; RRID:AB_312831
CD24 PE-Cy7, Clone M1/69	Biolegend	Cat# 101822; RRID:AB_756048
CD24 BV421, Clone M1/69	Biolegend	Cat# 101826; RRID:AB_2563508
CD24 PE/Cy7, Clone ML5	BD Biosciences	Cat# 311119, RRID:AB_2072734
CD25 BV510, Clone PC61	Biolegend	Cat# 102041, RRID:AB_2562269
CD38 BV605, HIT2	Biolegend	Cat# 303531, RRID:AB_2561527
CD43 PE/Cy7, Clone S7	BD Biosciences	Cat# 562866; RRID:AB_2737852
CD95 PE/Cy7, Clone Jo2	BD Biosciences	Cat# 557653, RRID:AB_396768
CD138 BV711, Clone 281-2	Biolegend	Cat# 142519; RRID:AB_2562571
CD138 BV605, Clone 281-2	Biolegend	Cat# 142515, RRID:AB_2562336
F4/80 BV605, Clone BM8	Biolegend	Cat# 123133; RRID:AB_2562305
TER-119/Erythroid cells BV605, Clone TER-119	Biolegend	Cat# 116239; RRID:AB_2562447
Ly6C/G BV605, Clone RB6-8C5	Biolegend	Cat# 108440; RRID:AB_2563311
TCRβ BV605, Clone H57-597	Biolegend	Cat# 109241; RRID:AB_2629563
Tim-1 PE, Clone RMT1-4	Biolegend	Cat# 119506; RRID:AB_2232887
CD249 PE, Clone BP-1	BD Biosciences	Cat# 553735; RRID:AB_395018
Blimp-1 AF647, Clone 5E7	Biolegend	Cat# 150004; RRID:AB_2565618
FoxP3 APC, Clone FJK-16	ThermoFisher Scientific	Cat# 17-5773-82; RRID:AB_469457
GL7 PerCP/CY5.5, Clone GL7	Biolegend	Cat# 144610, RRID:AB_2562979
IL-1beta (pro-form) APC, Clone NJTEN3	Thermo Fisher Scientific	Cat# 17-7114-80, RRID:AB_10670739
IL-6 PE, Clone MP5-20F3	Biolegend	Cat# 504504, RRID:AB_31533
IFN-γ APC, Clone XMG1.2	ThermoFisher Scientific	Cat# 17-7311-82; RRID:AB_469504
IL-10 PE, Clone JES5-16E3	Biolegend	Cat# 505008; RRID:AB_315362
IL-10 APC, Clone JES3-19F1	BD Biosciences	Cat# 554707, RRID:AB_398582
IL-17 PE (TC11-18H10.1)	Biolegend	Cat# 506904; RRID:AB_315464
Purified GL7 monoclonal antibody, Clone GL7	ThermoFisher Scientific	Cat# 14-5902-82, RRID:AB_467715
Goat anti-rat IgM secondary Antibody Alexa 647	ThermoFisher Scientific	Cat# A-21248, RRID:AB_2535816
Rabbit anti-Histone H3 (acetyl K27) antibody	Abcam	Cat# ab4729; RRID:AB_2118291
Rabbit anti-Histone H3 antibody	Abcam	Cat# ab1791; RRID:AB_302613
Goat Anti-Rabbit IgG – H&L Polyclonal antibody, HRP conjugated	Abcam	Cat# ab6721; RRID:AB_955447
Chemicals, Peptides, and Recombinant Proteins
Lipopolysaccharide (LPS)	Sigma Aldrich	Cat# L4391
CpG Class B (ODN 2006)	Invitrogen	Cat# L34961
Methylated bovine serum albumin (mBSA)	Sigma Aldrich	Cat# A1009
Immunisation Grade Bovine Type II Collagen	Chondrex	Cat# 20021
Incomplete Freund’s adjuvant (IFA)	Sigma Aldrich	Cat# F5506
Phorbol-12-myristate-13 acetate (PMA)	Sigma Aldrich	Cat# P8139
Ionomycin	Sigma Aldrich	Cat# I0634
DAPI	Sigma Aldrich	Cat# D9542
Brefeldin A	Biolegend	Cat# 420601
2-Mercaptoethanol	ThermoFisher Scientific	Cat# 31350010
RNase-Free DNase set	QIAGEN	Cat# 79254
Sodium Butyrate (for culture)	Sigma Aldrich	Cat# B5887
Sodium Butyrate (for supplementation)	Sigma Aldrich	Cat# 303410
Butyric acid (for HPLC)	Sigma Aldrich	Cat# B103500
L-para-chlorophenylalanine (4-Chloro-DL-phenylalanine)	Sigma Aldrich	Cat# C6506
5-Hydroxyindole-3-acetic acid	Sigma Aldrich	Cat# H8878
L-Kynurenine	Sigma Aldrich	Cat# K8625
Kynurenic Acid	Sigma Aldrich	Cat# K3375
Sodium Acetate (for supplementation)	Sigma Aldrich	Cat# S2889
Sodium Propionate (for supplementation)	Sigma Aldrich	Cat# P1880
Propionic acid	Sigma Aldrich	Cat# P1385
Valeric acid	Sigma Aldrich	Cat# 240370
2-Methylbutyric acid	Sigma Aldrich	Cat# 193070
Isobutyric acid	Sigma Aldrich	Cat# I1754
2-Ethylbutyric acid	Sigma Aldrich	Cat# 109959
Isovaleric acid	Sigma Aldrich	Cat# 129542
Lactic Acid	Sigma Aldrich	Cat# 69785
Acetic Acid	Sigma Aldrich	Cat# 45754
3-Methyl-indole	Sigma Aldrich	Cat# M51458
Indole	Sigma Aldrich	Cat# I3408
Indole-3-Carboxaldehyde	Sigma Aldrich	Cat# I29445
Tryptamine	Sigma Aldrich	Cat# 196747
Tryptophan	Sigma Aldrich	Cat# 193747
Indole-3-acetic acid	Sigma Aldrich	Cat# I5148
Indole-3-propionic acid	Sigma Aldrich	Cat# 57400
N-(3-Dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride E7750	Sigma Aldrich	Cat# E7750
2-Nitrophenylhydrazine hydrochloride	Apollo Scientific	Cat# OR1939
Diethyl Ether	Fisher Chemical	D/2450/17
Acetonitrile	Sigma Aldrich	271004
Sodium acetate-13C2	Sigma Aldrich	282014
Sodium butyrate-13C4	Sigma Aldrich	488380
Sodium propionate-d5	Cambridge Isotope Labs	DLM-1601
Critical Commercial Assays
Negative CD43- Isolation Kit	Miltenyi Biotec	Cat# 130-049-801
Picopure™ RNA isolation kit	ThermoFisher Scientific	Cat# KIT0204
iScript™ cDNA synthesis kit	Biorad	Cat# 1708891
iQ™ SYBR® green supermix	Biorad	Cat# 1708882
Nextera DNA library preparation kit	Illumina	Cat# FC-121-1030
MinElute PCR purification kit	QIAGEN	Cat# 28004
Pierce™ BCA Protein Assay Kit	ThermoFisher Scientific	Cat# 23225
QIAamp DNA Mini Kit	QIAGEN	Cat# 51306
BioPulverizer Lysing Matrix E	MP Biomedical Europe	Cat# 116914050
Taq PCR Core kit	QIAGEN	Cat# 201225
ZymoBIOMICS Microbial Community DNA Standard	Zymo Research	Cat# D6305
Agencourt AMPure XP	Beckman Coulter	Cat# A63881
Qubit dsDNA HS Assay Kit-500 assays	ThermoFisher Scientific	Cat# Q32854
NEBNext Library Quant Kit for Illumina	New England BioLabs	Cat# E7630L
High Sensitivity D1000 ScreenTape	Agilent	Cat# 5067-5584
Agilent High Sensitivity DNA Reagents	Agilent	Cat# 5067-4627
MiSeq Reagent Kit v2 (500-cycles)	Illumina	Cat# MS-102-2003
PhiX Control v3	Illumina	Cat# FC-110-3001
Deposited Data
16 s Data	This paper	PRJNA603680
Raw and analyzed ATAC-seq data – Ahrfl/-Mb1cre/+ and Mb1cre/+ CD19+CD21hiCD24hi B cells isolated ex vivo from control and butyrate treated mice	This paper and Piper et al., 2019	E-MTAB-7525
Raw and analyzed RNA-seq data - Ahrfl/-Mb1cre/+ and Mb1cre/+ CD19+CD21hiCD24hi B cells isolated ex vivo from control and butyrate treated mice	This paper and Piper et al., 2019	E-MTAB-7345
Experimental Models: Organisms/Strains
Mouse, B6(Cg)-Il10tm1.1Karp/J	Prof. Christopher Karp	RRID:IMSR_JAX:014530
Mouse, C57BL/6J	Envigo	N/A
Mouse, DBA/1J	Envigo	N/A
Mouse, B6.C(Cg)-Cd79atm1(cre)Reth/EhobJ	Jackson laboratory	RRID:IMSR_JAX:020505
Mouse, B6.129-Ahrtm1Bra/J	Jackson laboratory	RRID:IMSR_JAX:002831
Mouse, Ahr−/−Mb1cre/cre	Prof. Brigitta Stockinger	N/A
Mouse, Ahrfl/flR26R FP635fl/fl	Prof. Brigitta Stockinger	N/A
Mouse, Mb1cre/+	Generated in house from above strains	N/A
Mouse, Ahrfl/-Mb1cre/+	Generated in house from above strains	N/A
Mouse, B6.129S2-Ighmtm1Cgn/J	Jackson laboratory	RRID:IMSR_JAX:002288
Mouse, 129(B6)-Il10tm1Cgn/J	Prof. Fiona Powrie	RRID:IMSR_JAX:004368
Mouse, B6.SJL-PtprcaPepcb/BoyJ	Prof. Derek Gilroy	RRID:IMSR_JAX:002014
Oligonucleotides
qPCR primers	ThermoFisher Scientific; This paper	N/A
Actb
Fwd 5′-AGATGACCCAGATCATGTTTGAG-3′
Rev 5′-AGGTCCAGACGCAGGATG-3′
Cyp1a1	QIAGEN	Cat#QT00105756
Il10	ThermoFisher Scientific; Yanaba et al., 2009	N/A
Fwd 5′-GGTTGCCAAGCCTTATCGGA-3′
Rev 5′-ACCTGCTCCACTGCCTTGCT-3′
Software and Algorithms
GraphPad Prism 6	Graphpad Software	https://www.graphpad.com
Flowjo v10.5.0	Flowjo, LLC	https://www.flowjo.com
Limma	Ritchie et al., 2015	https://bioconductor.org/packages/release/bioc/html/limma.html
STAR	Dobin et al., 2013	https://github.com/alexdobin/STAR
HTSeq	Anders et al., 2015	https://htseq.readthedocs.io/en/release_0.11.1/install.html#install
Kallisto	Bray et al., 2016	https://pachterlab.github.io/kallisto/download
EdgeR	Robinson et al., 2010	https://bioconductor.org/packages/release/bioc/html/edgeR.html
Signaling pathway impact analysis	Tarca et al., 2009	https://bioconductor.org/packages/release/bioc/html/SPIA.html
Venny 2.1	Oliveros, J.C. (2007-2015) Venny. An interactive tool for comparing lists with Venn’s diagrams.https://bioinfogp.cnb.csic.es/tools/venny/index.html	https://bioinfogp.cnb.csic.es/tools/venny/
Illumina Casava 1.7	Illumina	https://www.illumina.com
Picard Tools	N/A	https://broadinstitute.github.io/picard/
MACS2 v2.1.1.20160309	Zhang et al., 2008	https://github.com/taoliu/MACS
Integrative Genomics Viewer (IGV)	James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011).	https://software.broadinstitute.org/software/igv/
Multiple Experiment Viewer (MeV_4_8)	Saeed et al., 2003	http://mev.tm4.org/#/welcome
Mothur V1.35.13	Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41	https://www.mothur.org/
R-studio version 3.6.0		https://rstudio.com/
Phyloseq		https://joey711.github.io/phyloseq/
Other
RPMI-1640 media	Sigma Aldrich	Cat# R8758
Red blood cell lysis buffer	Sigma Aldrich	Cat# R7757
Foetal calf serum (FCS)	Biosera	Cat# FB1001/500
Noraml Goat Serum	Vector	Cat# S1000
LIVE/DEAD™ Fixable Blue	Invivogen	Cat# L34961
Vectashield Mounting Medium with DAPI	Vector	Cat# H-1200
Formalin solution, nerutral buffered, 10%	Sigma Aldrich	Cat# HT501320
Penicillin/Streptomycin	Sigma Aldrich	Cat# P0781
eBioscience™ Intracellular fixation & permeabilization buffer set	ThermoFisher Scientific	Cat# P078188-8824-00
Brilliant stain buffer	BD Biosciences	Cat# 563794
eBioscience™ FoxP3 / Transcription Factor Staining Buffer Set	ThermoFisher Scientific	Cat# 00-5523-00
M. tuberculosis H37 Ra, desiccated	BD	Cat# 231141
Cell Lysis Buffer (10x)	Cell Signaling Technology	Cat# 9803
PierceTMECL Western Blotting Substrate	ThermoFisher Scientific	Cat# 32106
SPME Fiber Assembly 75mm CAR/PDMS, Fused Silica 23Ga	Sigma Aldrich	Cat# 57344-U