Dear colleagues,
How do I extract DNA from rodent fecal sample for whole genome/shotgun sequencing? The objective of the research is to characterize the total microbial diversity in the fecal sample, function and also identify zoonotic pathogens.
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Probably best to enrich your microbes/pathogens using a density gradient centrifugation step (https://www.nature.com/articles/srep16807).
For total DNA extraction, you can pulverise and digest the pellets using any lysis buffer and Proteinase K and follow the normal fecal DNA protocol.
After DNA extraction you can try doing MBD enrichment which enriches the host DNA and separates microbial/prokaryotic DNA.
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Or you can directly use the DNA extract for shotgun sequencing, as only 1-5% of fecal DNA extract will be of host species. Rest is from the gut microbiota, intestinal and environmental parasites and other microbes, etc.
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