KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Human Fecal Samples	This paper	N/A
Chemicals, peptides, and recombinant proteins
AL Buffer	QIAgen	cat. # 19075
pGEM T-Easy vector	Promega	cat. # PR-A1360
TaqMan Universal PCR Master Mix	Applied Biosystems	cat. # 4304437
SYBR Green PCR master mix	Applied biosystems	cat. #4309155
tert-butyl methyl ether	Sigma	cat# 306975
Critical commercial assays
KAPA Hyper Prep kit	Kapa Biosystems	cat. # 07962363001(KK8504)
Gel Extraction kit	QIAgen	cat. # 28706X4
pGEM T-Easy vector	Promega	cat. # PR-A1360
Pure Link Plasmid Extraction Kit	Invitrogen	cat. #K210010
QIAmp DNA Stool Mini Kit	QIAgen	cat. #51504
Deposited data
Raw and analyzed data	This paper	SRA: PRJNA751448
Oligonucleotides
Primer total 16s quantification: TotalbacF 5’-TCCTACGGGAGGCAGCAGT-3’	Nadkarni et al.	N/A
Primer total 16s quantification: TotalbacR 5’-GGACTACCAGGGTATCTAATCCTGTT-3’	Nadkarni et al.	N/A
Probe total 16s quantification: TotalbacProbe 5’-FAM CGTATTACCGCGGCTGCTGG CA-BHQ-3’	Nadkarni et al.	N/A
Primer but gene quantification: BcoATF: 5’-GCIGAICATTTCACITGGAAYWSITGGCAY ATG-3’	Louis and Flint	N/A
Primer but gene quantification: BcoATR:5’-CCTGCCTTTGCAATRTCIACRAANGC-3’	Louis and Flint	N/A
Primer Roseburia/Eubacterium 16s quantification: RoseEub16sF1 5’-CGKACTAGAGTGTCGGAGG −3’	Ramirez-Farias et al.	N/A
Primer Roseburia/Eubacterium 16s quantification: RoseEub16sF2 5’-GTCATCTAGAGTGTCGGAGG-3’	Ramirez-Farias et al.	N/A
Primer Roseburia/Eubacterium quantification: RoseEub16sR 5’-AGTTTYATTCTTGCGAACG-3’	Ramirez-Farias et al.	N/A
Primer Faecalibacterium prausnitzii 16s quantification: FPR16sF 5’-GGAGGAAGAAGGTCTTCGG-3’	Ramirez-Farias et al.	N/A
Primer Faecalibacterium prausnitzii 16s quantification: FPF16sR 5’-AATTCCGCCTACCTCTGCACT-3’	Ramirez-Farias et al.	N/A
Software and algorithms
GraphPad Prism 7.0	Graphpad	https://www.graphpad.com/
R Software	R Core Team	https://www.r-project.org/
Cutadapt	Matrin et al.88	https://cutadapt.readthedocs.io/en/stable/
FastQC	Babraham Bioinformatics	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
PrinSEQ	Schmieder et al.89	http://prinseq.sourceforge.net/
Bowtie2	Langmead and Salzberg90	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Kraken2	Lu et al.91	https://ccb.jhu.edu/software/kraken2/
Bracken	Lu et al.92	https://ccb.jhu.edu/software/Bracken
ANCOM-II	Kaul et al.93	https://github.com/FrederickHuangLin/ANCOM-Code-Archive
QIIME2	Bolyen et al.94	https://qiime2.org/
FMAP	Kim et al.95	https://github.com/jiwoongbio/FMAP
NetShift	Kuntal et al.44	https://web.rniapps.net/netshift/
MaAsLin2	Mallick et al.38	https://huttenhower.sph.harvard.edu/maaslin/
GOmixer	Darzi et al.40	https://raeslab.org/software/omixer.html
AGS-and-ACN-tools	Pereira-Flores et al.39	https://github.com/pereiramemo/AGS-and-ACN-tools
FlashWeave	Tackmann et al.43	https://github.com/meringlab/FlashWeave.jl
Cytoscape v3.9.1	Cytoscape Team	https://cytoscape.org/