title: Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing.
abstract: The gastrointestinal tract contains a vast community of microbes that to this day remain largely unculturable, making studies in this area challenging. With the newly affordable advanced sequencing technology, important breakthroughs in this exciting field are now possible. However, standardized methods of sample collection, handling, and DNA extraction have yet to be determined. To help address this, we investigated the use of 5 common DNA extraction methods on fecal samples from 5 different species. Our data show that the method of DNA extraction impacts DNA concentration and purity, successful NGS amplification, and influences microbial communities seen in NGS output dependent on the species of fecal sample and the DNA extraction method used. These data highlight the importance of careful consideration of DNA extraction method used when designing and interpreting data from cross species studies.
authors.affiliation: Comparative Medicine Program, Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Marcia L
authors.initials: ML
authors.lastname: Hart
authors.affiliation: College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Meyer
authors.affiliation: Department of Veterinary Medicine and Surgery, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Johnson
authors.affiliation: Comparative Medicine Program, Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America.|University of Missouri Metagenomics Center, University of Missouri, Columbia, Missouri, United States of America.|Mutant Mouse Resource and Research Center, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Aaron C
authors.initials: AC
authors.lastname: Ericsson
mesh_terms: D000818:Animals; D044822:Biodiversity; D002415:Cats; D005591:Chemical Fractionation / Q000379:methods*; D004247:DNA / Q000302:isolation & purification*; D004285:Dogs; D005243:Feces / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006736:Horses; D054892:Metagenome; D051379:Mice; D064307:Microbiota; D012372:ROC Curve; D015027:Zebrafish
chemical_list: D004247:DNA