Scaffold-level validation is needed for phage-host inference from metagenome-assembled genomes.

CRISPR-associated regions in MAGs can diverge compositionally from host genomes, and TNF separation between experimentally validated phage-host pairs challenges MAG-level compositional binning assumptions.

• Why it matters: Phage-host prediction from MAGs is widely used for ecological interpretation and experimental targeting, but scaffold-level errors can be missed when only completeness and contamination are used.
• What they did: TNF analyses compared CRISPR-associated regions and experimentally validated phage-host genome pairs, and controlled simulations tested whether adding substantial TNF-matched non-host phage sequences to high-quality MAGs changes completeness and contamination estimates.
• The result: Standard completeness and contamination metrics may not substantially detect these misbinning errors, motivating a scaffold-level validation framework using structural linkage and taxonomic consistency to improve phage-host inference reliability from MAGs.

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