REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Stool samples KETO cohort	This paper	PRJEB51723
Stool samples CARBFUNC cohort	This paper	PRJEB51775
Serum samples KETO cohort	Urbain et al.32	N/A
Serum samples CARBFUNC cohort	This paper	N/A
Chemicals, peptides, and recombinant proteins
3-nitrophenylhydrazones	Sigma Aldrich	Cat#N21804; CAS: 636-95-3
RNAlater	Thermo Fisher Scientific	Cat#AM7021M
Lysozyme	Sigma Aldrich	Cat#L6876 ; CAS: 12650-88-3
Mutanolysin	Sigma Aldrich	Cat#SAE0092; CAS: 55466-22-3
Lysostaphin	Sigma Aldrich	Cat#SAE0091; CAS: 9011-93-2
Proteinkinase K	VWR	Cat#97062-238; CAS: 39450-01-6
RNase A	Thermo Fisher Scientific	Cat#EN0531
Lysis buffer	Zymo Reseach	Cat#D7001-1-50
2x Phusion Master Mix	Thermo Fisher Scientific	Cat#F531L
Critical commercial assays
ZR Fecal DNA Miniprep Kit	Zymo Reseach	Cat#D6010
SequalPrep normalization plate kit 96	Illumina	Cat#A1051001
DNA Clean and Concentrator 5 kit	Zymo Reseach	Cat#D4013
TruSeq Nano DNA LT Library Prep kit	Illumina	Cat#20015964
Quick 16S NGS Library Prep Kit	Zymo Reseach	Cat#D6400
MiSeq Reagent Kit v3, 600 cycles	Illumina	Cat#MS-102-3003
Deposited data
16S rRNA amplicon sequencing data of KETO cohort	This paper	PRJEB51723
16S rRNA amplicon sequencing data of CARBFUNC cohort	This paper	PRJEB51775
Serum lipid, glucose and insulin levels of KETO cohort	This paper, see Table S3	N/A
Serum lipid levels, glucose and insulin of CARBFUNC cohort	This paper, see Table S3	N/A
Fecal metabolite levels of KETO cohort	This paper, see Table S3	N/A
Fecal metabolite levels of CARBFUNC cohort	This paper, see Table S3	N/A
Oligonucleotides
Primers for 16S rRNA amplicon sequencing of KETO cohort	This paper, see Table S4	N/A
Primers for 16S rRNA amplicon sequencing of CARBFUNC cohort, V3-V4 of Quick 16S NGS Library Prep Kit	Zymo Research	Cat#D6400
Software and algorithms
cutadapt (v1.10)	Kechin et al.67	https://github.com/marcelm/cutadapt/
DADA2	Callahan et al.72	https://benjjneb.github.io/dada2/
Prodi 6.4 basis nutritional database software	Nutri-Science GmbH	https://www.nutri-science.de/software/
QIIME 1 (v1.9.1)	Caporaso et al.68	http://qiime.org/
QIIME 2 (v2019.7)	Bolyen et al.69	https://qiime2.org/
q2-feature-classifier	Bokulich et al.70	https://github.com/qiime2/q2-feature-classifier
R (v3.6.1)	packages for analytical part: vegan, biomformat, phyloseq, moments, nortest, lmerTest, emmeans, sjPlot and ComplexHeatmap	https://www.r-project.org/
SILVA database v132	Quast et al.71	https://www.arb-silva.de/documentation/release-132/
bowtie2 (v2.2.5)	Langmead and Salzberg60	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
kneaddata (v0.6.1)	Huttenhower lab	https://github.com/biobakery/kneaddata