TABLE 1.

Overview of QIIME2 processing for 15 microbiome datasets. Samples were collected from the listed ENA accession, with only samples corresponding to individuals in North America retained. SR refers to single read and PE to paired-end sequencing runs for the corresponding length in bp. Trim length was used as input for the trunc_len parameter, forward trim as the trim_left input for single end read and trim_left_f for paired-end reads, and reverse trim as the trim_left_r input for paired-end reads in the python API for QIIME2’s Dada2 plugin.

Study ID	ENA Accession	Hypervariable Region	Trim Length	Forward Trim	Reverse Trim	Mean Reads	SD
American Gut	ERP012803	V4	124	0	0	30864.7	30259.6
CVDF	PRJNA308319	V3-V4	290	40	40	402901.1	77178.6
GEVERSC	PRJEB13680	V4	174	0	0	76323.2	62701
GEVERSM	PRJEB13679	V4	174	0	—	40903.8	41606.2
GLS	PRJEB23009	V4	99	0	—	75901.4	59442.8
HMP	ibdmdb.org	V4	249	0	0	44154.7	15479
MUC	PRJNA317429	V4	174	19	21	84848	36257.9
PRJNA418765	PRJNA418765	V4	245	0	3	24329.9	14107.2
PRJNA436359	PRJNA436359	V4	170	0	3	80925.9	90657.2
QIITA10184	PRJEB13895	V4	120	0	—	93773.8	31830.3
QIITA10342	PRJEB13619	V4	100	0	—	78873.1	68866.2
QIITA10567	PRJEB14674	V4	99	0	—	17547.5	7,522.5
QIITA1448	PRJEB13051	V4	99	0	—	159739	57806.5
QIITA2202	PRJEB6518	V4	99	0	—	243402.8	190268.4
QIITA550	PRJEB19825	V4	149	0	—	37658.8	7,065.2