REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical commercial assays
DNeasy PowerSoil Pro Kit	QIAGEN	47014
Oligonucleotides
16S rRNA forward primer	CCTACGGGNGGCWGCAG	341F
16S rRNA reverse primer	GACTACHVGGGTATCTAATCC	805R
Deposited data
16S amplicon data (Korea)	This study	BioProject: PRJNA917086
16S amplicon data (Brazil)	Cortez et al.27	BioProject: PRJNA610934
16S amplicon data (Canada)	Alipour et al.24	BioProject: PRJNA298762
16S amplicon data (China)	Wang et al.22	CRA005251
16S amplicon data (Czech)	Hurych et al.31	BioProject: PRJNA958468
16S amplicon data (Israel)	Turner et al.53	BioProject: PRJNA532645
16S amplicon data (UK)	Ijaz et al.52	BioProject: PRJEB18780
16S amplicon data (UK)	Douglas et al.21	BioProject: PRJEB21933
16S amplicon data (USA)	Gevers et al.28	BioProject: PRJNA237362 BioProject: PRJNA205152
16S amplicon data (USA)	Nusbaum et al.16	BioProject: PRJNA438164
16S amplicon data (USA)	Zuo et al.23	BioProject: PRJNA759642
16S amplicon data (USA/Canada)	Schirmer et al.25	BioProject: PRJNA436359
Software and algorithms
fastp	https://github.com/OpenGene/fastp	0.21.0
Usearch	http://www.drive5.com/usearch/	11.0.667
Vsearch	https://github.com/torognes/vsearch	2.21.1
MMseqs2	https://github.com/soedinglab/MMseqs2	15-6f452
Phyloseq	https://joey711.github.io/phyloseq/	1.22.3
MMUPHin	https://github.com/biobakery/MMUPHin	1.19.1
Scikit-learn	https://scikit-learn.org/	1.2.0
Keras	https://keras.io/	2.11.0
Python	https://www.python.org/	3.10.4
scikeras	https://github.com/adriangb/scikeras	0.10.0
SHAP	https://github.com/shap/shap	0.41.0
Vegan	https://github.com/vegandevs/vegan	2.6.6
metafor	https://wviechtb.github.io/metafor/	4.6–0
ALDEx2	https://github.com/ggloor/ALDEx_bioc	1.38.0
ANCOM-BC	https://github.com/FrederickHuangLin/ANCOMBC	2.8.0