NUCB1 and Alzheimer disease: While prophages from HE demonstrate significantly more diverse gene content, across both data sets of HQ prophage genomes and all prophage sequences (including remnants), we found a stronger association between certain VFs and AD-associated prophages (Fig. 5 and 6), such as clfA, nuc, and several toxins (sea, sec, sell, hlgA, lukD) across both data sets, indicating a selective advantage with the enrichment of these VFs in AD strains.