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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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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