Commercial DNA Extraction Kits for Composted Animal Manures: A Systematic Review of Performance, Limitations, and Research Gaps

Culture-independent methods have emerged as powerful tools for studying the diversity and functional potential of microbial communities in composted animal manure (CAM), a valuable agricultural resource. The foundational step in these studies is metagenomic DNA extraction, but humic acids in manure often interfere with yield and purity. While numerous commercial kits are available, there is no clear guidance on which performs best for CAM. This systematic review bridges that gap by consolidating and evaluating existing evidence and providing practical guidance for kit selection. We included original research that evaluated commercial kits on CAM and reported evaluation of DNA quality. Fifty-five studies met our criteria and were analyzed. Seventeen distinct commercial DNA extraction kits were reported, with the FastDNA Spin kit for soil and the PowerSoil DNA Isolation Kit being the most frequently cited. Methods varied widely, with sample sizes of 100 mg-30 g and storage conditions from 4°C to −80°C. Sample sources included livestock manure types such as swine, dairy, chicken, pig, cattle, etc. Our review shows soil-based kits are most appropriate for CAM compared to fecal based kits due to their suitability for diverse inhibitor-rich sample types. By comparing kits, it brings together scattered findings and gives kits recommendations. It highlights key gaps in the literature, including the lack of comparisons between commercial kits, inconsistent reporting of DNA quality metrics, and the absence of assessments benchmarking commercial kits against academic or national laboratory protocols. Addressing these gaps will improve standardization, reproducibility, and data driven decision making in CAM microbiome research.