Table 1.

Methodological variance reported by the participating laboratories.

16Ss (26 laboratories)		SMs (23 laboratories)
	N		N
1. DNA extraction kit manufacture		1. DNA extraction kit manufacture
Qiagen	9	Qiagen	7
Tiangen	3	Tiangen	3
Zymo Research	3	Zymo Research	2
Omega	3	Omega	3
Other/Custom	8	Other/Custom	8
2. bead-beating included in cell wall disruption?		2. Bead-beating included in cell wall disruption?
Yes	19	Yes	14
No	7	No	9
3. Amplified region of 16S rRNA gene		3. DNA fragmentation method
V3-4	13	Enzymatic	13
V4	6	Physical (ultrasound)	10
V1-9	3	4. Sequencing Platform
V4-5	1	Illumina NovaSeq	9
V1-2	1	Illumina Hiseq	4
V2, V3, V4, V6-7, V8, V9	2	MGISEQ-2000	3
4. Sequencing Platform		Illumina MiSeq	2
Illumina NovaSeq	3	DA8600	2
Illumina MiSeq	14	NextSeq CN500	2
Illumina Hiseq	5	MGISEQ-200RS	1
Ion Torrent PGM	3	5. Sequencing Mode
PacBio Sequel	1	Paired-end	18
5. Sequencing Mode		Single-end	5
Paired-end	22	6. Sequencing read length
Single-end	4	100	4
6. Sequencing read length		150	15
150	5	200	2
250	10	300	2
300	7	7. Taxonomic classifier
400	1	MetaPhlAn2	12
600	2	Kraken 2	5
68,866a	1	SOAPaligner/soap2	3
7. Data Analysis Pipeline		Diamond 0.9.27	2
Qiime	11	Explify V2.1.0 (IDbyDNA Inc.)	1
USEARCH	7	8. Reference Databases
Parallel-META Pipeline	1	Default database in taxonomic classifiers or NCBI nr database	20
Mother	3	MetaHIT database	3
EzBioCloud	1
Ion Reporter™	3
8. Reference Databases
Greengenes	11
SILVA	10
NCBI 16S rRNA database	1
PrecisionGene Database (PRS-DB)	2
EzBioCloud 16S database	1
Custom	1

^aGenerated using a third generation of sequencer (PacBio Sequel) by P24.