Absolutely. No method perfect. But to make overarching statements about what drives viral communities or what viruses drive in general when you’re looking at a random 2-3% of a non perfect sample is just ridiculous.
A. You're alive! 🍻
B. counter-counterargument, viruses in the <0.2 µ fraction were lytic at some point and therefore definitely had an effect on the microbial community.
C. There's no guarantee that viral contigs from bulk DNA are doing anything. They could be lysogens or just junk DNA.