Comparison of soil and stool DNA extraction kits for yield and quality of DNA in sheep faecal microbiome analysis
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Reliable extraction of high-quality DNA from ruminant faecal samples is essential for microbiome profiling, pathogen surveillance, and nutritional studies relevant to pastoral livestock systems. Faecal material from grazing sheep presents particular challenges due to high plant fibre content and the presence of PCR inhibitors. This study compares the performance of commercial soil and stool-specific DNA extraction kits for sheep faecal samples. Faecal samples were collected from eight adult Romney ewes grazing research pastures in New Zealand and processed in parallel using a stool and a soil-specific kit. DNA concentration and purity were assessed by NanoDrop spectrophotometry. The soil DNA kit yielded significantly higher DNA concentrations than the stool DNA kit (mean ± SD: 140.2 ± 65.1 ng µL−1 vs. 74.5 ± 36.4 ng µL−1; Wilcoxon signed-rank test, p = 0.0006), while purity ratios (A260/280 and A260/230) did not differ significantly between kits and met recommended thresholds for downstream sequencing. These results demonstrate that soil DNA extraction kits can provide superior DNA yields from sheep faecal samples without compromising purity, supporting their use in high-throughput ovine microbiome studies. These findings provide practical guidance for microbiome laboratories working with fibre-rich faecal matrices and support broader application of soil-oriented extraction protocols in ruminant microbiome research.
