REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical commercial assays
Fast DNA Stool Mini Kit	Qiagen	Cat# 51604
Hybrid-R Total RNA Isolation Kit	GeneAll Biotechnology	Cat# 305-101
Polypropylene pestles	SP Scienceware	Cat# F19923-0001
Deposited data
Microbiome data	This study	PRJNA703470
Transcriptome data	This study	PRJNA703469
Source code	This study	https://doi.org/10.5281/zenodo.6056333
Software and algorithms
QIIME2 version 2020.11	Bolyen et al., 2019	https://docs.qiime2.org/2021.8/install/
Phyloseq version 1.34.0	McMurdie and Holmes, 2013	http://www.bioconductor.org/packages/release/bioc/html/phyloseq.html
FastQC version 0.11.9	Andrews, 2010	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Trimmomatic version 0.39	Bolger et al., 2014	http://www.usadellab.org/cms/?page=trimmomatic
SortMeRNA version 4.2.0	Kopylova et al., 2012	https://github.com/biocore/sortmerna/releases
STAR version 2.5.4b	Dobin et al., 2013	https://github.com/alexdobin/STAR/releases
DESeq2 version 1.28.1	Love et al., 2014	http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
gage version 2.40.1	Luo et al., 2009	http://www.bioconductor.org/packages/release/bioc/html/gage.html
PMA version 1.2.1	Witten et al., 2009	https://github.com/bnaras/PMA
xCell version 1.1.0	Aran et al., 2017	https://github.com/dviraran/xCell
CIBERSORT version 1.05	Newman et al., 2015	https://cibersort.stanford.edu/
R version 4.0.4	https://cran.r-project.org/doc/manuals/fullrefman.pdf	https://www.r-project.org