Interestingly enough, there is still a raging debate on what was the causative organism of this plague. The consensus has always been on Y. pestis; however, there have always been intrepid contrarians arguing that descriptions of the symptoms aren’t accurate enough to really identify the disease as bubonic plague. Some putting forth anthrax, others some yet unknown filovirus.
A paper appearing in PLOS Pathogens by a German group have confirmed Y pestis in DNA extracted from the teeth of bodies found in a 6th century cemetery in Bavaria. The extra steps taken to use independent labs and prevent modern DNA contamination have pretty much put paid to the notion of an alternate cause to the Plague of Justinian. I never really had any doubt. I’m glad this controversy is finally over.