KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Bacterial and Virus Strains
See Supplemental Table S5
Biological Samples
Chemicals, Peptides, and Recombinant Proteins
Isotopes: [13C4]-fumaric acid (99%), [13C4, 15N]-L-aspartic acid (99%), [1, 4–13C2]-succinic acid (99%) and [13C4]-L-malic acid (98%)	Cambridge Isotope Laboratories	CLM-1529, CNLM-544-H-0.25, CLM-1084-PK CLM-8065-PK, respectively
Critical Commercial Assays
DuoSet Lipocalin ELISA kit	R&D Systems, Minneapolis, MN, USA	DY1857
AllPrep DNA/RNA Kit	Qiagen	80204
NEXTflex® 16S V4 Amplicon-Seq Kit 2.0	Bio Scientific	NOVA-4203–04
Deposited Data
16S sequencing data of microbiome in mice	this manuscript	http://www.ebi.ac.uk/ena/data/view/PRJEB35643.
Experimental Models: Cell Lines
Experimental Models: Organisms/Strains
Mouse: LCM mice (C57BL/6 genetic background)	(Stecher et al., 2010) (Maier et al., 2013)	N/A
Mouse: 129SvEv	Jackson Laboratories; bred at EPIC mouse facility of ETH Zurich, Switzerland	N/A
Mouse: C57BL/6	Jackson Laboratories; bred at EPIC mouse facility of ETH Zurich, Switzerland	N/A
Oligonucleotides
See Supplemental Table S6
Recombinant DNA
Software and Algorithms
Graphpad Prism Version 6.0 for Windows	GraphPad Software, La Jolla California USA	N/A
eMZed2	(Kiefer et al., 2013) (Hartl et al., 2017)	http://emzed.ethz.ch/
BLASTp of the NCBI BLAST+ (version 2.8.1)	(Camacho et al., 2009)	N/A
Clusters of Orthologous Groups with EggNOG-mapper 2.0.0	(Galperin et al., 2015) (Huerta-Cepas et al., 2017)	N/A
MassHunter Quantitative Analysis Software	(Agilent, version 7.0)	N/A
Other