Key Resources Table
| Chemicals, Peptides, and Recombinant Proteins | ||
| DEUTERIUM OXIDE (D, 99.9%) | Cambridge Isotope Laboratories | Cat# DLM-4-PK |
| D-GLUCOSE (U-13C6, 99%) | Cambridge Isotope Laboratories | Cat# CLM-1396-PK |
| SODIUM L-LACTATE (13C3, 98%) 20% W/W in H2O | Cambridge Isotope Laboratories | Cat# CLM-1579-PK |
| L-GLUTAMINE (13C5, 99%) | Cambridge Isotope Laboratories | Cat# CLM-1822-H-PK |
| L-GLUTAMINE (ALPHA-15N, 98%) | Cambridge Isotope Laboratories | Cat# NLM-1016-PK |
| L-GLUTAMINE (AMIDE-15N, 98%+) | Cambridge Isotope Laboratories | Cat# NLM-557-PK |
| SODIUM D-3-HYDROXYBUTYRATE (13C4, 99%) 97% CHEMICAL PURITY | Cambridge Isotope Laboratories | Cat# CLM-3853-PK |
| LINOLEIC ACID, POTASSIUM SALT (U-13C18, 98%) | Cambridge Isotope Laboratories | Cat# CLM-8835-PK |
| OLEIC ACID, SODIUM SALT (U-13C18, 98%) | Cambridge Isotope Laboratories | Cat# CLM-8763-PK |
| SODIUM PALMITATE (U-13C16, 98%+) | Cambridge Isotope Laboratories | Cat# CLM-6059-PK |
| SODIUM ACETATE (1,2–13C2, 99%) | Cambridge Isotope Laboratories | Cat# CLM-440-PK |
| CITRIC ACID (13C6, 99%) | Cambridge Isotope Laboratories | Cat# CLM-9021-PK |
| SUCCINIC ACID (13C4, 99%) | Cambridge Isotope Laboratories | Cat# CLM-1571-PK |
| L-MALIC ACID (13C4, 99%) | Cambridge Isotope Laboratories | Cat# CLM-8065-PK |
| ALPHA-KETOGLUTARIC ACID, DISODIUM SALT (1,2,3,4–13C4, 99%) | Cambridge Isotope Laboratories | Cat# CLM-4442-PK |
| L-ALANINE (13C3, 99%) | Cambridge Isotope Laboratories | Cat# CLM-2184-H-PK |
| L-ALANINE (15N, 98%) | Cambridge Isotope Laboratories | Cat# NLM-454-PK |
| L-VALINE (13C5, 99%) | Cambridge Isotope Laboratories | Cat# CLM-2249-H-PK |
| L-VALINE (15N, 98%) | Cambridge Isotope Laboratories | Cat# NLM-316-PK |
| L-LEUCINE (13C6, 99%) | Cambridge Isotope Laboratories | Cat# CLM-2262-H-PK |
| L-LEUCINE (15N, 98%) | Cambridge Isotope Laboratories | Cat# NLM-142-PK |
| L-ISOLEUCINE (13C6, 99%) | Cambridge Isotope Laboratories | Cat# CLM-2248-H-PK |
| L-ISOLEUCINE (15N, 98%) | Cambridge Isotope Laboratories | Cat# NLM-292-PK |
| L-SERINE (13C3, 99%; 15N, 99%) | Cambridge Isotope Laboratories | Cat# CNLM-474-H-PK |
| GLYCINE (13C2, 97–99%) | Cambridge Isotope Laboratories | Cat# CLM-1017-PK |
| GLYCINE (13C2, 99%; 15N, 99%) | Cambridge Isotope Laboratories | Cat# CNLM-1673-H-PK |
| L-TYROSINE (13C9, 99%) | Cambridge Isotope Laboratories | Cat# CLM-2263-H-PK |
| UREA (15N2, 98%+) | Cambridge Isotope Laboratories | Cat# NLM-233-PK |
| AMMONIUM CHLORIDE (15N, 99%) | Cambridge Isotope Laboratories | Cat# NLM-467-PK |
| L-LYSINE:2HCL (ALPHA-15N, 98%) | Cambridge Isotope Laboratories | Cat# NLM-143-PK |
| L-ARGININE:HCL (ALPHA-15N, 98%+) | Cambridge Isotope Laboratories | Cat# NLM-1267-PK |
| ALGAL STARCH (U-13C, 98%+) | Cambridge Isotope Laboratories | Cat# CLM-1699-PK |
| INULIN (FROM CHICORY) (U-13C, 97%+) 97% CHEMICAL PURITY | Cambridge Isotope Laboratories | Cat# CLM-9181-PK |
| Algal crude protein extract-13C | Sigma-Aldrich | Cat# 642878 |
| Algal crude protein extract-15N | Sigma-Aldrich | Cat# 586773 |
| Algal crude protein extract-13C,15N | Sigma-Aldrich | Cat# 608254 |
| Algal amino acid mixture-13C | Sigma-Aldrich | Cat# 426199 |
| Algal fatty acid mixture-13C | Sigma-Aldrich | Cat# 487937 |
| AZD 3965 | AstraZeneca | Cat# AZD3965 |
| Ampicillin | Sigma-Aldrich | Cat# A0166 |
| Neomycin trisulfate salt hydrate | Sigma-Aldrich | Cat# N6386 |
| Metronidazole | Sigma-Aldrich | Cat# M1547 |
| Vancomycin hydrochloride from Streptomyces orientalis | Sigma-Aldrich | Cat# V1130 |
| Trypsin | Promega | Cat# V5113 |
| Lysyl endopeptidase R | Wako Chemicals USA | Cat# 12902541 |
| Aspartame | Sigma-Aldrich | Cat# 47135 |
| GAM Broth Modified | HyServe | Cat# 5433 |
| LB Broth (Miller, Luria Broth) | Sigma | Cat# L3522 |
| MRS Broth | Sigma | Cat# 69966 |
| TSB (Tryptic Soy Broth) | Bacto | Cat# 211825 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6 | Charles River Laboratories | Cat #027 |
| Strain: Bacteroides dorei (CL02T00C15) | BEI | #HM-717 |
| Strain: Clostridium sporogenes (ATCC 15579) | ATCC | 15579 |
| Strain: Escherichia coli (ATCC 25922) | ATCC | 25922 |
| Strain: Lactobacillus reuteri (CF-48–34A) | BEI | #HM-102 |
| Strain: Staphylococcus aureus subsp. Aureus Rosenbach | ATCC | 29213 |
| Software and Algorithms | ||
| El-MAVEN software | Elucidata | https://resources.elucidata.io/elmaven |
| AccuCor | GitHub | https://github.com/XiaoyangSu/AccuCor |
| PepMID | GitHub | https://github.com/xxing9703/pepMID_simul |
| MATLAB R2021b | MathWorks | N/A |
| Others | ||
| PicoLab Rodent Diet 20 | LabDiet | Cat# 5053 |
| 20% Diet premix | Research Diets | Cat# D11112201Npx2i |
| 20% Amino acids diet | Research Diets | Cat# A11112201Bi |