Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags

J Microbiol Methods. 2013 Dec;95(3):455-62. doi: 10.1016/j.mimet.2013.07.015. Epub 2013 Jul 27.


Low cost and high throughput capacity are major advantages of using next generation sequencing (NGS) techniques to determine metagenomic 16S rRNA tag sequences. These methods have significantly changed our view of microorganisms in the fields of human health and environmental science. However, DNA extraction using commercial kits has shortcomings of high cost and time constraint. In the present study, we evaluated the determination of fecal microbiomes using a direct boiling method compared with 5 different commercial extraction methods, e.g., Qiagen and MO BIO kits. Principal coordinate analysis (PCoA) using UniFrac distances and clustering showed that direct boiling of a wide range of feces concentrations gave a similar pattern of bacterial communities as those obtained from most of the commercial kits, with the exception of the MO BIO method. Fecal concentration by boiling method affected the estimation of α-diversity indices, otherwise results were generally comparable between boiling and commercial methods. The operational taxonomic units (OTUs) determined through direct boiling showed highly consistent frequencies with those determined through most of the commercial methods. Even those for the MO BIO kit were also obtained by the direct boiling method with high confidence. The present study suggested that direct boiling could be used to determine the fecal microbiome and using this method would significantly reduce the cost and improve the efficiency of the sample preparation for studying gut microbiome diversity.

Keywords: DNA extraction; Feces; Illumina; Microbial diversity; Microbiome.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Costs and Cost Analysis
  • DNA / chemistry
  • DNA / genetics
  • DNA / isolation & purification*
  • Feces / microbiology
  • Humans
  • Microbiota*
  • RNA, Ribosomal, 16S / genetics*
  • Sequence Analysis, DNA / economics
  • Sequence Analysis, DNA / methods*
  • Specimen Handling / economics
  • Specimen Handling / methods*
  • Time Factors


  • RNA, Ribosomal, 16S
  • DNA