Table 2.

Methodology of studies using 16S rRNA gene sequencing or shotgun metagenomics to analyse the microbiome in patients with BTC.

Author	Sample storage	DNA extraction	Selected region of 16 S gene	Sequencing platform
Lenz et al. [55]	Not stated	Not stated	V3–V4	Illumina
Tsuchiya et al. [48]	Stored at −80 °C	NucleoSpin Soil	V3–V4	Illumina Miseq
Jia et al. [50]	Stored at −80 °C	PowerSoil DNA Isolation kit	V4	Illumina Miseq
Lee et al. [57]	Stored in a freezer	PowerSoil DNA Isolation kit	V3–V4	Illumina Miseq
Chen et al. [52]	Stored at −80 °C	OMEGA DNA kit	V3–V4	Illumina Miseq
Chng et al. [51]	Thawed on ice and transferred into lysing tubes	EZ1 DNA Tissue kit	V3–V6	Illumina Hiseq 2000
Poudel et al. [49]	Not stated	PowerViral DNA Isolation kit	Not stated	Illumina
Avilés-Jiménez et al. [42]	Stored at −80 °C	QIAamp DNA easy kit	V4	Illumina Miseq
Dangtakot et al. [53]	Stored at −80 °C	QIAamp DNA easy kit	V3–V4	Illumina Hiseq 2500
Katsuyuki et al. [56]	Not stated	Not stated	V3–V5	Illumina Miseq
Zhang et al. [54]	Placed on ice and transferred to laboratory	QIAamp DNA mini kit	V3–V4	Illumina Hiseq
Song et al. [58]	Stored at −80 °C	QIAamp DNA mini kit	N/A (metagenomic study)	Illumina Hiseq ×10
Saab et al. [38]	Stored at −80 °C	QIAsymphony kit	V3-4	Illumina Miseq