At present, most metagenomic surveys rely on high-output platforms such as Illumina. However, the short reads generated by these platforms limit specificity of taxonomic assignment and result in highly fragmented assemblies. Single molecule sequencing platforms are able to sequence much longer molecules and the output of these platforms, particular the PromethION from Oxford Nanopore now supports the study of complex microbial communities using shotgun metagenomics. We assessed a variety of commercially available and manual extraction methods using both a ten-species mock community and clinical samples seeking to find a method capable of generating ultra-long reads (100 kb) from these samples. The results presented here demonstrate the importance of having lysis methods capable of extracting high-molecular weight DNA from recalcitrant organisms such as Gram-positive bacteria and fungi. Development of these methods is critical to support the growing field of clinical microbiome research including the ability to perform strain tracking and produce high-quality metagenome assembled genomes (MAGs) from metagenomic samples. Articles from Journal of Biomolecular Techniques : JBT are provided here courtesy of The Association of Biomolecular Resource Facilities.
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