Henderson_DNA_comparison_archaea

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Different methods were used to extract DNA from cow and sheep rumen samples. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in apparent microbial community composition were observed among extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Results obtained using some methods can be cautiously compared to those obtained using certain other methods, but generally care must be exercised when comparing data from studies in which different DNA extraction methods were employed.