Shallow shotgun metagenomic analysis of up to four fecal samples (furry family members also ok), including mapping to reference genomes and comparing profiles of genetic similarities and differences among different family members. Shallow shotgun metagenomics means instead of using the 16S rRNA as a marker gene, we fragment all the DNA in the sample, grind it up, sequence it in small pieces, and try to figure out what it is afterwards. The bad news is that much of this information is still mysterious because we don’t know the complete genomes of most of the microbes in there, but the good news is that you can get an insight into the gene functions, not just which microbes are there.
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