Table 2.

Published CRC 16S rRNA sequencing for gut microbiome studies, 2011–2016.

Publication	Sample Type	No. of CRC patients	Tissue samples	Sample handling	Sample storage	DNA Extraction kit	Hypervariable region	Sequencing Platform	OTU Classification Database	No. of Reads for Downstream/Total Reads	Bioinformatics Pipeline
Thomas et al., 2016	Biopsy Tissue	18	Non-cancer (18)	N/A	N/A	Phenol-Chloroform & Ethanol Precipitation	V4/V5	Ion Torrent PGM	RDP	17, 414 reads/sample	QIIME
Baxter et al., 2016	Stool	120	Adenoma (198) Normal (172)	Prior bowel prep, ship on ice next day	−80°C	MoBio Kit, 50 mg	V4	Illumina MiSeq	RDP	10, 000 reads/sample	MOTHUR
Flemer et al., 2017	Stool, Surgical Tissue, Biopsy Tissue	59	Adenoma (21), Control (56)	RNAlater (4°C, 12H)—Tissue, Ice box—Fecal (prior bowel prep)	−20°C (Tissue), −80°C (Fecal)	QIAGEN AllPrep DNA/RNA kit plus with glass bead homogenization)	V3/V4	Illumina MiSeq	RDP	5, 000 reads/sample	QIIME
Sinha et al., 2016/ Ahn et al., 2013	Stool	42	Normal (89)	Dry ice	−40°C	MoBio PowerSoil DNA Isolation kit	V3/V4	454 Pyro sequencing	Greengenes	5, 000 reads/sample	QIIME
Allali et al., 2015	Surgical Tissue	90	Adjacent-Normal	Snap-frozen in Isopentane	−80°C	QIAGEN Dneasy Blood and Tissue with Lysozyme in ATL buffer	V1/V2	454 Pyro sequencing	Greengenes	719 reads/sample	QIIME
Burns et al., 2015	Surgical Tissue	44	Adjacent-Normal	Flash-frozen Liquid Nitrogen	Not stored	QIAzol, Sonicate Water bath @65°C	V5/V6	Illumina MiSeq	Greengenes	5, 000 reads/sample	QIIME
Gao et al. 2015	Surgical Tissue	30	Adjacent-Normal, Normal (31)	N/A	Not stored	MoBio PowerSoil DNA Isolation kit	V3	454 Pyro sequencing	RDP, Greengenes, ITS Fungus, FGR	17, 018 reads/sample	QIIME
Nakatsu et al., 2015	Biopsy Tissue	52	Adenoma (47), Normal (61)	Flash-frozen Liquid Nitrogen	−80°C	QIAGEN QIAamp Mini kit with beads beating & lysozyme	V1-V4	454 Pyro sequencing	Greengenes	1, 000 reads/sample	MOTHUR
Zeller et al., 2014	Stool & Surgical tissue	89	Adjacent-normal (48), Normal (75)	Flash-frozen liquid nitrogen	−80°C	GNOME® DNA Isolation Kit	V4	Illumina MiSeq	SILVA	10, 000 reads/sample	MOTHUR
Dejea et al., 2014	Surgical & Biopsy tissue	23	Adenoma (2), Normal (22)	RNAlater	−80°C	QIAGEN QIAamp Stool DNA kit	V3-V5	454 Pyro sequencing	RDP	N/A	QIIME
Mira-Pascual et al., 2015	Stool & Biopsy tissue	7	Adenoma (11), Normal (10)	N/A	−80°C	Machery-Nagel DNA kit with glass beads	V1/V2	454 Pyro sequencing	RDP	Biopsy/stool−6, 000 reads/sample, Biopsy-3groups−18, 000 reads/sample	MOTHUR
Zackular et al., 2014	Stool	30	Adenoma (30), Normal (30)	On ice (next day)	−80°C	MoBio PowerSoil DNA Isolation kit	V4	Illumina MiSeq	RDP	25, 993 reads/sample	MOTHUR
Geng et al., 2013	Biopsy Tissue	8	Adjacent-normal	Flash-frozen Liquid Nitrogen	−80°C	QIAGEN QIAamp DNA Mini kit with Silica beads	V1/V2	454 Pyro sequencing	BLAST	1, 400 reads/sample	QIIME
Weir et al., 2013	Stool	10	Normal (11)	Transport <24 h	N/A	MoBio PowerSoil DNA Isolation kit	V4	454 Pyro sequencing	Greengenes	125 sequence/sample	MOTHUR
Wu et al., 2013	Stool	20	Normal (20)	Frozen	−80°C	QIAGEN QIAamp Stool DNA kit	V3	454 Pyro sequencing	RDP	N/A	MOTHUR
Chen et al., 2012	Surgical Tissue, Stool & Swab	47	Normal (9)	N/A	−80°C	QIAamp DNA Mini/Stool kit with lysozyme	V1-V3	454 Pyro sequencing	N/A	N/A	MOTHUR
Kostic et al., 2012	Surgical tissue	95	Adjacent-Normal	Flash-frozen Liquid Nitrogen	−80°C	N/A	V3-V5	454 Pyro sequencing	RDP	N/A	MOTHUR
Wang et al., 2012	Stool	46	Normal (56)	Frozen	−80°C	Bead-beating + Phenol-Chloroform Purification	V3	454 Pyro sequencing	RDP	N/A	DOTUR
Marchesi et al., 2011	Surgical tissue	6	Adjacent-Normal	N/A	−80°C	QIAGEN AllPrep DNA/RNA kit	V1-V3	454 Pyro sequencing	RDP	N/A	MOTHUR
Sobhani et al., 2011	Stool	6	Normal (6)	N/A	N/A	GNOME® DNA Isolation kit with Silica beads	V3/V4	454 Pyro sequencing	BLAST	N/A	R Package: VEGAN

N/A, Data/method was not described/stated.