That's the thing: We sequence a lot of microbials already. Some, it's actually hard NOT to sequence.
Say, for instance, that you are sequencing an insect. To do that, you need at least a part of the insect. When you sequence it, you won't just find that insect's DNA in there, but DNA from viruses and bacteria that live in that insect. The same thing will happen if you are sequencing from a plant, or a human.
Contamination from other sources is so common that after getting a bunch of reads from a large organism, it's pretty much mandatory to do comparisons with something with the same species and with a DNA database of microbials to remove the reads that hit a contaminant, so that the assembly that we produce represents the organism correctly.
Other times, we just look for said microbials specifically. Imagine I want to know the bacteria that grow in the roots of a wheat plant. I could try to culture them all in a lab, and if something doens't grow, I lose it. Or I could sequence the root, take out everything that actually looks like wheat, and try to assemble bacteria out of the rest of the DNA.
Say, for instance, that you are sequencing an insect. To do that, you need at least a part of the insect. When you sequence it, you won't just find that insect's DNA in there, but DNA from viruses and bacteria that live in that insect. The same thing will happen if you are sequencing from a plant, or a human.
Contamination from other sources is so common that after getting a bunch of reads from a large organism, it's pretty much mandatory to do comparisons with something with the same species and with a DNA database of microbials to remove the reads that hit a contaminant, so that the assembly that we produce represents the organism correctly.
Other times, we just look for said microbials specifically. Imagine I want to know the bacteria that grow in the roots of a wheat plant. I could try to culture them all in a lab, and if something doens't grow, I lose it. Or I could sequence the root, take out everything that actually looks like wheat, and try to assemble bacteria out of the rest of the DNA.