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. Author manuscript; available in PMC: 2023 Sep 27.
Published in final edited form as: Cell Rep. 2023 Aug 21;42(8):113009. doi: 10.1016/j.celrep.2023.113009

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER

Antibodies

Goat polyclonal anti-IgA Southern Biotech Cat#OB1040–01
Goat anti-mouse IgA:HRP BioRad Cat#STAR137P
Rabbit polyclonal anti-mouse Muc2 Santa Cruz Biotechnology Cat#sc-15334
Alexa Fluor 488 goat anti-rabbit IgG Invitrogen Cat#A-11008

Bacterial and Virus Strains

Bacteroides thetaiotaomicron VPI-5482 wildtype Gift from Deutschbauer lab AMD595
RB-Tn mutant isolated from monocolonized mice with barcoded transposon insertion in BT1876 Gift from Deutschbauer lab AMD595-derived RB-Tn library3
RB-Tn mutant isolated from monocolonized mice with barcoded transposon insertion in BT1874 This work Tn_BT1874
RB-Tn mutant isolated from monocolonized mice with barcoded transposon insertion in BT1876 This work Tn_BT1876
RB-Tn mutant isolated from monocolonized mice with barcoded transposon insertion in the intergenic region between BT1872 and BT1873 This work Tn_BT1872–83
RB-Tn mutant isolated from monocolonized mice with barcoded transposon insertion in BT1872 This work Tn_BT1872
RB-Tn mutant isolated from monocolonized mice with barcoded transposon insertion in BT1874 and BT3132 This work Tn_BT1874/BT3132
RB-Tn mutant isolated from monocolonized mice with barcoded transposon insertion in BT3133 This work Tn_BT3133
WT Bt with a copy of BT1871 integrated into the Bt genome at the attN1 site under the BT1311 (rpoD) constitutive promoter. This work WT + BT1871OE
Bt mutant isolated from feces after 6-week monoassociation of Bt; carries a tandem repeat of the BT1871 locus (see Figure 7). This work MZ65

Chemicals, Peptides, and Recombinant Proteins

Brain Heart Infusion Broth Fisher Cat#DF0037178
Agar Fisher Cat#DF0145–17-0
Hemin Fisher Cat#51280–5G
Glucose Sigma Cat#158968–500G
Galactose Sigma Cat#G0750–500G
Sucrose Fisher Cat#AAJ64270A1
Raffinose Fisher Cat#AC195670250
Melibiose Sigma Cat#M5500–100G
Erythromycin Fisher Cat#AC227330050
Phosphate Buffered Saline Sigma Cat#P3813–10PAK
Glycerol Fisher Cat#BP2291
Ambion TRIzol Reagent Fisher Cat#15–596-018
Chloroform Fisher Cat#AC390760010
Isopropanol Fisher Cat#BP2618500
Ethanol Fisher Cat#BP2818500
DNAse Fisher Cat#18068015
Tris Fisher Cat#BP152–10
EDTA Fisher Cat#PR-V4231
NaCl Fisher Cat#S640–10
SDS Sigma Cat#L3771–25G
Phenol:Chloroform:Isoamyl Alcohol Fisher Cat#AM9732
Proteinase K Sigma Cat#3115852001
HCl Sigma Cat#A144–212
Methanol Fisher Cat#A452SK-4
Methoxyamine Sigma Cat#226904
Pyridine Sigma Cat#270970
Derivatizing reagent (BSTFA +1% TMCS) Sigma Cat#B-023
Ethyl acetate Sigma Cat#650528
ELISA diluent R&D Systems Cat#DY995
Acetic acid Fisher Cat#A38–500
Xylene Fisher Cat#X3S-4
Lysozyme Fisher Cat#89833
Sodium citrate Fisher Cat#S279–500
DAPI Sigma Cat#D8417–5MG
ProLong Gold Anti-Fade mounting medium Fisher Cat#P10144
iTaq Universal SYBR Green Supermix BioRad Cat#1725124

Critical Commercial Assays

DNeasy PowerSoil Kit. Qiagen Cat#47016
Rapid Barcoding Kit Oxford Nanopore Technologies Cat#SQK-RBK004
Transcriptor First Strand cDNA Synthesis Kit Roche Cat#35081963001
Invitrogen IgG (Total) Mouse Uncoated ELISA Kit Invitrogen Cat#88–50400-88

Deposited Data

RNAseq raw data from Bt at different time points This work https://www.ncbi.nlm.nih.gov/sra (accession: PRJNA797447)
Shotgun sequencing raw data from evolution experiment fecal samples This work https://www.ncbi.nlm.nih.gov/sra (accession: PRJNA797447)
Long-read sequencing raw data from isolate MZ65 This work https://www.ncbi.nlm.nih.gov/sra (accession: PRJNA797447)

Experimental Models: Organisms/Strains

Mouse: germ-free wild-type C57BL/6J University of Chicago
Gnotobiotic Core Facility
N/A

Oligonucleotides

Custom Ribo-Zero Plus Probes SeqCenter See Table S1A
qPCR primers Miyoshi et al., 201750 See Table S1B

Software and Algorithms

bcl2fastq Illumina Version 2.20.0.422
MinKNOW Oxford Nanopore Technologies Version 4.3.4
Guppy Oxford Nanopore Technologies Version 5.0.11
Flye https://github.com/fenderglass/Flye Version 2.651
Pilon https://github.com/broadinstitute/pilon Version 1.2352
MassHunter Quantitative
Analysis software
Agilent Technologies Version B.10
R software https://www.r-project.org/ Version 4.2.153
vegan R software https://cran.r-project.org/web/packages/vegan/index.html Version 2.6–454
pairwiseAdonis R software https://github.com/pmartinezarbizu/pairwiseAdonis Version 0.4
DESeq2 R software https://bioconductor.org/packages/release/bioc/html/DESeq2.html Version 1.36.055
anvi’o https://anvio.org/ Version 7.156
fgsea R package https://bioconductor.org/packages/release/bioc/html/fgsea.html Version 3.1757
Graphpad Prism https://www.graphpad.com/features Version 9
Prodigal https://github.com/hyattpd/Prodigal Version 2.6.358
bowtie2 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Version v2.3.5.159
samtools http://www.htslib.org/ Version 1.1160
gggenes https://github.com/wilkox/gggenes/tree/master Version 0.4.1
blastn https://blast.ncbi.nlm.nih.gov/Blast.cgi Version 2.5.0
minimap2 https://github.com/lh3/minimap2 Version 2.1761
IGV https://igv.org/ Version 2.11.162
LAS_X Leica Leica N/A

Other

Standard mouse chow LabDiets 5K67
Anaerobic chamber Coy Laboratory Products N/A
GENSYS 40-Vis spectrophotometer Thermo Scientific N/A
Mini-BeadBeater-96 BioSpec Products N/A
BioAnalyzer Agilent N/A
NextSeq2000 Illumina N/A
IsoCage P Bioexclusion cages Tecniplast N/A
Agencourt AMPure XP beads Beckman Coulter Cat#A63882
Flow Cell (R9.4.1) Oxford Nanopore Technologies Cat#FLO-MIN106D
MinION Oxford Nanopore Technologies N/A
Beadruptor tubes Fisher Cat#15–340-154
Bead Mill 24 Homogenizer Fisher Cat#15–340-163
Mass spectrometry autosampler vial Microliter Cat#09–1200
Biotage SPE Dry 96 Dual Biotage Cat#3579M
Thermomixer C Eppendorf Cat#2231001005
Agilent 7890A GC system Agilent N/A
Agilent 5975C MS detector Agilent N/A
HP-5MSUI column Agilent Cat#19091S-433UI
CFX384 Real-Time System BioRad N/A
Leica SP8 laser scanning confocal microscope Leica N/A