To perform microbiome DNA shotgun sequencing from mouse feces, does one need to worry about non-microbial DNA i.e. mouse/plant? I would use NEB-microbiome enrichment kit if I have too, i.e. if non-microbial DNA reads represent >5% reads. Any comments/help you can provide will be appreciated.
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You can easily filter out mouse in-silico later, without using additional chemistry that might incur bias. But I don't know what proportion of the reads would be non-microbial. -
I don't know about mouse specifically, but other mammals I've seen have host DNA in the 0.1% - 2% range in a fecal sample. The outside is enriched for host material, so if that low level worries you you can scrape a layer off and reduce it. But as Brian says, the reads can be filtered anyway before assembly. Probably preferable compared to feces-scraping!Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.comComment
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