Application of Sequence-Dependent Electrophoresis Fingerprinting in Exploring Biodiversity and Population Dynamics of Human Intestinal Microbiota: What Can Be Revealed?

Table 1

DNA extraction procedures used in SDE-based profiling of human intestinal microbial communities.

Description or reference	Sample type	Cell lysis (reagents or principle)	DNA extraction	Application(s)	Selected reference(s)
FastDNA kit (Bio101 Carlsbad, Calif, USA)^a FastDNA SPIN kit (Qbiogene, Carlsbad, Calif, USA)^a	Feces; mucosa biopsies	Chemical (guanidium salts and detergents) and mechanical (bead beating using garnet mix)	Silica-based binding matrix (and spin filters)^a	DGGE; SSCP; real-time PCR; cloning; sequencing	[43, 63, 68–76]
QIAampDNA Stool Mini Kit (Qiagen, Valencia, Calif, USA)	Feces; mucosa biopsies	Chemical (guanidium salts and detergents)	Silica-gel membrane spin columns	DGGE; TGGE; real-time PCR; cloning; sequencing	[63, 77–86]
Modified protocol of [87]	Feces	Enzymatic (lysozyme and mutanolysin) and chemical-enzymatic (SDS and proteinase K)	Phenol-chloroform-isoamylalcohol and chloroform	DGGE; sequencing	[88]
Modified protocol of [89]	Feces	Enzymatic (lysozyme and mutanolysin) and chemical (guanidiumthiocyanate-EDTA-sarkosyl)	Chloroform-isoamylalcohol	DGGE; real-time PCR	[64, 90]
[24]	Feces; mucosa biopsies	Mechanical (bead beating)	TTGE	[91–94]
[95]	Feces; cecal fluids; mucosa biopsies	Mechanical (bead beating in acid phenol)	Phenol-chloroform and chloroform	DGGE; TGGE; cloning; sequencing	[6, 65, 66, 96–102]
[32]	Feces	Mechanical-chemical (bead beating in buffer-saturated phenol and SDS)	Phenol-chloroform	Group-specific PCR; real-time PCR	[33]
[103]	Feces	Chemical (guanidiumthiocyanate and sarkosyl) and mechanical (bead beating)	Polyvinyl-polypyrrolidone	TTGE; cloning; sequencing	[21, 104–109]^b

^aFastDNA kit (Bio101) and FastDNA SPIN Kit (Qbiogene) only differ in the use of spin filters during the silica-DNA purification.^bThe authors of [106–108] reported a modified protocol of [103] in which also phenol and chloroform-isoamylalcohol were applied in the extraction procedure.