Table 2.

Sample and methodology characteristics of the included studies.

Study	Sample	Sample Transport	DNA Extraction	Microbiota Analysis Technique	Sequencing Target	Sequencing Platform	Data Analysis Platform	Reference Sequences Database
Yeh et al., 2019 [19]	stool	DNA stabilizer, Immediate freezing, Transport on ice	QIAamp DNA Stool Mini Kit	16S rRNA gene sequencing	V3–V4	Ilumnia MiSeq platform	QIIME	Kyoto Encyclopedia of Genes and Genomies database
Shapiro et al., 2019 [20]	stool	Immediate freezing	PowerSoil HTP 96 Kit	16S rRNA gene sequencing	V4	Ilumnia MiSeq platform	QIIME	Greengenes database
Huang et al., 2019 [21]	stool	Transport on ice	PowerSoil HTP 96 Kit	16S rRNA gene sequencing	V4–V5	Ilumnia MiSeq platform	UPARSE	National Center for Biotechnology Information Sequence Read Archive database
Hidalgo-Cantabrana et al., 2019 [22]	stool	Immediate freezing	QIAamp DNA Stool Mini Kit	16S rRNA gene sequencing	V2–V3	Ion Gene Studio S5 sequencer	QIIME	SILVA database
Chen et al., 2018 [23]	stool	Transport on ice	QIAamp DNA Stool Mini Kit	16S rRNA gene sequencing	V3–V4	Ilumnia MiSeq platform	UPARSE	Greengenes database
Codoner et al., 2018 [24]	stool	Immediate freezing	QIAamp DNA Stool Mini Kit	16S rRNA gene sequencing	V3–V4	Ilumnia MiSeq platform	QIIME	National Center for Biotechnology Information
Tan et al., 2018 [25]	stool	Immediate freezing	E.Z.N.A. stool DNA Kit	16S rRNA gene sequencing	V4	Ilumnia MiSeq platform	USEARCH	Ribosomal Database Project (RDP)
Eppinga et al., 2016 [26]	stool	Ambient temperature	NR	real-time quantitative PCR	-	quantitative PCR	-	-
Massallat et al., 2016 [27]	stool	NR	QIAamp DNA Stool Mini Kit	real-time quantitative PCR	-	quantitative PCR	-	-
Scher et al., 2015 [28]	stool	NR	NR	16S rRNA gene pyro-sequencing	V1–V2	454 GS FLX Titanium platform	Mothur	SILVA database

NR—not reported.