Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Monocyte + Macrophage antibody [MOMA-2] | abcam | Cat#ab33451 |
| Anti-Actin, α-Smooth Muscle – FITC antibody, Mouse monoclonal | Sigma-Aldrich | Cat#3777 |
| Monoclonal Anti-FITC-Biotin antibody produced in mouse | Sigma-Aldrich | Cat#B0287 |
| Rabbit Anti-Rat IgG H&L (Biotin) | abcam | Cat#ab6733 |
| Bacterial and virus strains | ||
| Bifidobacterium dentium | ATCC | Cat#27678 |
| Collinsella aerofaciens | ATCC | Cat#25986 |
| Bacteroides caccae | ATCC | Cat#43185 |
| Bacteroides finegoldii | DSM | Cat#17565 |
| Bacteroides stercoris | ATCC | Cat#43183 |
| Bacteroides thetaiotaomicron VPI-5482 | ATCC | Cat#29148 |
| Bacteroides xylanisolvens | DSM | Cat#18836 |
| Phocaeicola dorei | DSM | Cat#17855 |
| Blautia hansenii | ATCC | Cat#27752 |
| Blautia luti | DSM | Cat#14534 |
| Blautia producta | Lab isolate | N/A |
| Clostridioides difficile CD196 | Jan Peter van Pijkeren (University of Wisconsin-Madison) |
N/A |
| Clostridium scindens | Lab isolate | N/A |
| Clostridium sporogenes | ATCC | Cat#15579 |
| Clostridium symbiosum | ATCC | Cat#14940 |
| Coprococcus comes | ATCC | Cat#27758 |
| Dorea formicigenerans | ATCC | Cat#2755 |
| Dorea longicatena | DSM | Cat#13814 |
| Enterocloster asparagiformis | DSM | Cat#15981 |
| Enterocloster bolteae | ATCC | Cat#BAA-613 |
| Erysipelatoclostridium ramosum | ATCC | Cat#25582 |
| Hungatella hathewayi | DSM | Cat#13479 |
| Megamonas funiformis | DSM | Cat#19343 |
| Mitsuokella multacida | ATCC | Cat#27723 |
| Ruminococcus torques | ATCC | Cat#27756 |
| Fusobacterium nucleatum | ATCC | Cat#23726 |
| Fusobacterium varium | ATCC | Cat#8501 |
| Victivallis vadensis | ATCC | Cat#BAA-548 |
| Citrobacter youngae | ATCC | Cat#29220 |
| Edwardsiella tarda | ATCC | Cat#23685 |
| Escherichai coli I-11 | Lab isolate | N/A |
| Escherichia coli K12 | ATCC | Cat#29425 |
| Escherichia coli MS 200–1 | Emily Balskus (Harvard University) |
N/A |
| E. coli MS 200–1 with ΔallB::tetA-sacB | This manuscript | FER039 |
| E. coli MS 200–1 with Δ(ygeW-arcC)::tetA-sacB | This manuscript | FER041 |
| E. coli MS 200–1 with ΔygeV::tetA-sacB | This manuscript | FER063 |
| T-SACK | Thomason et al. 88 | N/A |
| Biological samples | ||
| Human peripheral plasma | Human study | N/A |
| Human stool samples | Human study | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Adenine | Alfa Aesar | Cat#A14906 |
| Allantoin | Alfa Aesar | Cat#A15571.30 |
| Hypoxanthine | Thermo Fisher Scientific |
Cat#A11481.06 |
| Uric Acid | Sigma-Aldrich | Cat#U0881 |
| Oxonic acid potassium salt | Thermo Fisher Scientific |
Cat#J60400.14 |
| Phenol:Chloroform:Isoamyl alcohol | Invitrogen / Thermo Fisher Scientific | Cat#15593–049 |
| 0.1 mm zirconia/silic beads | BioSpec Products | Cat#11079101z |
| Bacterial media formulation, detailed preparation | This manuscript, Methods S1 | N/A |
| Oil Red O | Sigma-Aldrich | Cat#O0625 |
| Streptavidin/HRP | Agilent Technologies | Cat#P0397 |
| DAB, Liquid | Agilent Technologies | Cat#K3467 |
| Hematoxylin Solution, Mayer’s | Sigma-Aldrich | Cat#MHS16 |
| Tissue-Tek O. C.T. compound | Sakura Finetek, Tokyo, Japan | Cat# 4583 |
| D9-Choline | Cambridge Isomiddlee Laboratories | Cat#DLM-549–1 |
| D9-TMAO | Cambridge Isomiddlee Laboratories | Cat#DLM-4779-PK |
| Acetic acid-d4 | Sigma-Aldrich | Cat#233315 |
| Propionic acid-d6 | Sigma-Aldrich | Cat#490644 |
| Butyric acid-d7 | CDN Isomiddlees | Cat#D-0171 |
| N-tert-Butyldimethylsilyl-N-methyltrifluoroacetamide | Sigma-Aldrich | Cat#394882 |
| SsoAdvanced SYBR Green Supermix | BioRad Laboratories, Inc. | Cat#1725271 |
| Critical commercial assays | ||
| Monarch Total RNA Miniprep Kit | New England Biolabs Inc. |
Cat#T2010S |
| Broad Range Qubit | Invitrogen / Thermo Fisher Scientific | Cat#Q32853 |
| Nucleospin Gel and PCR Clean-up Kit | Macherey-Nagel GmbH & Co. | Cat#740609.250 |
| Trichrome Stain Kit | Abcam | Cat#ab150686 |
| Cholesterol E | FUJIFILM Wako | Cat#999–02601 |
| HDL-Cholesterol E | FUJIFILM Wako | Cat#997–01301 |
| Multi-Calibrator Lipids | FUJIFILM Wako | Cat#464–01601 |
| L-Type Triglyceride M Enzyme Color A | FUJIFILM Wako | Cat#461–08992 |
| L-Type Triglyceride M Enzyme Color B | FUJIFILM Wako | Cat#461–09092 |
| QCL-1000 Endpoint Chromogenic LAL Assay | Lonza | Cat#50–647U |
| Deposited data | ||
| Mouse Metagenomics data | This study | PRJNA904303 |
| Bacterial RNA-Seq data | This study | PRJNA911264 |
| COPRO-Seq data | This study | PRJNA903666 |
| Human Metagenomics data | Wu et al. 36 | EGAS00001004480 |
| Experimental models: Cell lines | ||
| Experimental models: Organisms/strains | ||
| AXB10/PgnJ | The Jackson Laboratory | Cat#001681 |
| BXD5/TyJ | The Jackson Laboratory | Cat#000037 |
| BTBR T+tf/J | The Jackson Laboratory | Cat#002282 |
| BXA8/PgnJ | The Jackson Laboratory | Cat#001704 |
| Germ-free C57BL/6J | Germ-free mice raised in the gnotobiotic facility at the University of Wisconsin–Madison |
N/A |
| Germ-free ApoE KO | Germ-free mice raised in the gnotobiotic facility at the University of Wisconsin–Madison |
N/A |
| Oligonucleotides | ||
| qPCR primer 401F | Walker et al. 98 | N/A |
| qPCR primer 611R | Walker et al. 98 | N/A |
| 5’- ATATTGAACATTGAGTTAAAAACCAATCTGTATTTTA CAAGGAGTTTGTTTCCTAATTTTTGTTGACACTCTA- 3’ |
This manuscript | allBtetA-f |
| 5’- ACGGGCATTGCAGGGCCAGATTACTGCTGATGTTTA AGGATAAATTGACCATCAAAGGGAAAACTGTCCATA T-3’ |
This manuscript | allBsacB-r |
| 5’-CTTTATGGAACCGTTATCACG-3’ | This manuscript | allBseq-f |
| 5’-CAGAAAGTAGCGTAGGAGG-3’ | This manuscript | allBseq-r |
| 5’- AGTCACAGTGAAATAAACCACTTTGCCTGTCATTCC ACTACCGGGACTTTTCCTAATTTTTGTTGACACTCTA −3’ |
This manuscript | ygeWtetA-f |
| 5’- AGTGGCTTAAATGAAAATGGCCGGATGGTATTACCC ATCCGGCCTTTAAAATCAAAGGGAAAACTGTCCATA T-3’ |
This manuscript | arcCsacB-r |
| 5’-ACAAACAACCGGAAGCTGG-3’ | This manuscript | ygeWseq-f |
| 5’-GATATCGATCCTCGTGGTG-3’ | This manuscript | arcCseq-r |
| 5’- ACTTTTAAGTAAGTCTGGAAGGTAAAGCTATGGAGC TTGCGACTACGCAGTCCTAATTTTTGTTGACACTCTA −3’ |
This manuscript | ygeVtetA-f |
| 5’- CGGATTCTCAGAGGTTATGTGTTTAACAACTCATATT TCTTAATCTTGCGATCAAAGGGAAAACTGTCCATAT- 3’ |
This manuscript | ygeVsacB-r |
| 5’-GCAGGGTATCTCTCTTCAG-3’ | This manuscript | ygeV-seqF |
| 5’-GCGATGCTGGCAAAACCAC-3’ | This manuscript | ygeV-seqR |
| Recombinant DNA | ||
| Plasmid pSIM5 | Thomason et al. 88 | |
| Software and algorithms | ||
| R v3.6.3 or v4.0.3 | The R foundation | https://www.rproject.org/ |
| Python v3.7.4 | Python Software Foundation | https://www.python.org/ |
| FASTX | Cold Spring Harbor Laboratory | http://hannonlab.cshl.edu/fastx_toolkit/ |
| Bowtie2 | Langmead et al. 100 | https://bowtiebio.sourceforge.net/bowtie2/ |
| BLAST | NCBI | https://blast.ncbi.nlm.nih.gov/ |
| RSEM | Li et al. 101 | https://github.com/deweylab/RSEM/ |
| Kraken2 | Wood et al. 104 | https://ccb.jhu.edu/software/kraken2/ |
| Xgboost | Chen et al. 105 | N/A |
| PLS-DA | Pang et al. 107 | https://www.metaboanalyst.ca/ |
| Prism | Graphpad | https://www.graphpad.com/ |
| COPRO-Seq pipeline | McNulty et al. 99 | https://github.com/nmcnulty/COPROSeq |
| caret | R package 106 | https://cran.rproject.org/web/packages/caret/ |
| ImageJ | National Institute of Health | Imagej.net |
| Syngo Calcium Scoring Software | Siemens | N/A |
| Other | ||
| Western diet | Research Diets | Cat#D10042101 |
| LabDiet 5021 (Autoclavable mouse breeder diet) | LabDiet | Cat#5021 |
| Standard chow supplemented with 0.2% cholesterol | Envigo | TD.07798 |
| Vistro DT60 II Analyzer | University of Massachusetts Medical School MMPC |
N/A |
| Shimadzu HPLC system (CBM-40 controller, LC-40D pumps, SIL-40C autosampler, CTO-40C column oven, SPD-M40 diode array detector) | Shimadzu Scientific Instruments, Columbia, MD |
N/A |
| Luna Omega 5 μm Polar C18 LC column (250 × 4.6 mm) | Phenomenex | Cat# 00G-4754-E0 |
| Dionex UltiMate 3000 uHPLC | Thermo Scientific | N/A |
| Q Exactive Orbitrap Mass Spectrometers | Thermo Scientific | N/A |
| Bio-Bond C4 3 μm column (150 × 2.1 mm) | Dikma | Cat#84413 |
| Agilent 7890B GC with 5977A MSD | University of Wisconsin Mass Spectrometry Facility |
N/A |
| Agilent DB-1 1 ms 0.25 mm x 60 m column | University of Wisconsin Mass Spectrometry Facility |
N/A |
| SH-Stabilwax column (30 m, 0.25 mm ID, 0.10 μm df) | Shimadzu Scientific Instruments, Columbia, MD |
Cat#227-36246-01 |
| Bacterial RNA sequencing | Microbial Genome Sequencing Center (MiGS) |
N/A |
| Untargeted UPLC Mass Spectrometry | Metabolon, Inc. Morrisville, NC | N/A |
| Targeted purine and pyrimidine Mass Spectrometry | TMIC, The Metabolomics Innovation Centre, UVic Genome BC Proteomics Centre, Victoria, Canada |
N/A |
| MiSeq | University of Wisconsin Biotechnology Center DNA Sequencing Facility |
N/A |
| HiSeq 2500 | University of Wisconsin Biotechnology Center DNA Sequencing Facility |
N/A |
| Roche Cobas analyzer | Sahlgrenska University University Hospital |
N/A |
| Dual-source CT scanner with a Stellar Detector (Siemens) | Sahlgrenska University University Hospital |
N/A |
| Nikon Eclipse TE300 Inverted Microscope | University of Wisconsin-Madison Experimental Animal Pathology Laboratory |
N/A |
| Mini-Bead Beater 96 | BioSpec Products, Barlesville, OK | Cat#1001 |
| 20 ml headspace vials | Restek, Bellefonte, PA | Cat#21163 |
| Amicon Ultra-0.5 3kDa ultrafiltration device | MilliporeSigma | Cat#UFC500324 |