It seems trimethylamine N-oxide, created by intestinal bacteria, can have a significant impact on atherosclerosis.[1]
MGP (a vitamin K dependent protein) protects from atherosclerosis through several mechanisms.[2]
Atherosclerotic plaques in many cases become infected with bacterial biofilms.[3][4]
[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342477/
[2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6387246/