Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis

• Published in: Journal of microbiological methods Vol. 81; no. 2; pp. 127 - 134
• Main Authors: Salonen, Anne, Nikkilä, Janne, Jalanka-Tuovinen, Jonna, Immonen, Outi, Rajilić-Stojanović, Mirjana, Kekkonen, Riina A., Palva, Airi, de Vos, Willem M.
• Format: Journal Article
• Language: English
• Published: Amsterdam Elsevier B.V 01.05.2010; Elsevier
• Subjects: 16s ribosomal-rna; 16S rRNA; Adult; Archaea; Bacteriological methods and techniques used in bacteriology; Bacteriology; Biodiversity; Biological and medical sciences; community composition; DNA extraction; DNA, Archaeal - genetics; DNA, Archaeal - isolation & purification; DNA, Bacterial - genetics; DNA, Bacterial - isolation & purification; Feces - microbiology; Fundamental and applied biological sciences. Psychology; gastrointestinal-tract microbiota; gradient gel-electrophoresis; healthy-subjects; human gut microbiota; human intestinal-tract; Humans; Intestinal microbiota; metagenomic analysis; Metagenomics - methods; methanobrevibacter-smithii; Microarray; Microarray Analysis - methods; Microbiology; real-time pcr; Young Adult; 16S rRNA; DNA extraction; Microarray; Intestinal microbiota; Digestive system; Archaeobacteria; Gut; DNA chip; Microflora; Method; Phylogeny; Ribosomal RNA; 16S-RNA; Bacteria; Feces

Several different protocols are used for fecal DNA extraction, which is an integral step in all phylogenetic and metagenomic approaches to characterize the highly diverse intestinal ecosystem. We compared four widely used methods, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal...