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 |