Table 1.

Published studies comparing 16S rRNA gene amplicon sequencing with Illumina and Nanopore.

Samples	Mock Community Included	Nanopore Sequencing	Illumina Sequencing	Difference in Community Structure	Difference in Diversity	Difference in Replicability	References
2 faecal samples from mice	No	V1-9, SQK-MAP006	V3-4	No difference, except at species level	Not compared	Not assessed	[20]
13 water samples	Yes	V1-9, SQK-RAB204	V4	Focus on the detection of potential pathogens and faecal indicators	Not compared	Not assessed	[21]
1 mock community	Yes	V1-9, SQK-RAB201	V1-3, V3-4, V4, V4-5, V4-6, V6, V8, V8-9	Good results with both at genus level	Not compared	Not assessed	[15]
6 tap water and biofilm samples	Yes	V1-9, SQK-RAB204 or SQK-RAB201	V3-4	Only the 15 most abundant genera were considered	Not compared	Not assessed	[22]
59 human nasal swabs	No	V1-9, SQK-RAB201	V5-6	Similar results	Similar diversity	Not assessed	[23]
12 indoor dust samples	No	V1-9, SQK-LSK108	V3-4	Difference at genus and species level, but not at family level	Not compared	Not assessed	[24]
50 human faecal samples	No	V1-9, SQK-16S024	V3-4	Good correlation at genus level but not at species level	Not compared	Not assessed	[25]
Only a mock community was included in the comparison with Illumina	Yes	V1-9 and 16S-ITS-23S, SQK-PBK004	V3-4	Nanopore performed better at genus level	Not compared	Only assessed for 16S-ITS-23S	[26]
Corneal and conjunctival swabs from 2 patients	No	V1-9, kit not specified	V4	Similar results	Not compared	Not assessed	[27]
6 human faecal samples	Yes	V1-9 and V3-4, SQK-PBK004	V3-4	Only the 15 most abundant genera were considered	Not compared	Not assessed	[28]
8 human endometrial tissue samples	No	V1-9, SQK-RAB204	6 primer pairs pooled to cover V1-9	Similar results	Not compared	Not assessed	[29]
8 mock communities	Yes	V1-9, SQK-LSK108	V1-2, V1-3, V3, V4	Nanopore showed overall higher bias	Not compared	Not assessed	[30]
31 surface swabs from intensive care units	No	V1-9, SQK-16S024	V4	Focused on the detection of potential pathogens	Not compared	Not assessed	[31]
A mixture of DNA from 72 cheek skin swabs	Yes	V1-9 and 16S-ITS-23S, SQK-LSK110	V1-3	Similar results	Not compared	Good correlation between duplicates	[32]
8 soil samples from 2 sites	Yes	V1-9 and V3-4, SQK-LSK109	V3-4	Significant effect, but not as strong as the differences between sites	Difference in richness estimates	Not assessed	[33]