Y. Pestis was finally identified with the culprit of the Black Death (1346/47-53) that ravaged across Western Eurasia by genome analysis from the skeleton of victims in 2011. Until then, some scholars had challenged this general assumption of Y. pestis as a sole agent of the outbreak that robbed roughly a third to half of the total population in the 14th century Europe.

Now the Black Death is also called as a second pandemic of Y. Pestis (1st was the plague of Justinian in 541/2-544, and the 3rd one was in the late 19th century).

As for more detailed of the historiographical and epidemiological background of the debate, please check also the answers in: Is Y. pestis firmly accepted as the cause of the Black Death?

References:

• Aberth, John (ed.). The Black Death: The Great Mortality of 1348-1350: A Brief History with Documents. 2nd ed. Boston: Macmillan, 2017.
• Bos, K., Schuenemann, V., Golding, G. et al. A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506–510 (2011). https://doi.org/10.1038/nature10549
• Spyrou, M.A., Keller, M., Tukhbatova, R.I. et al. Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes. Nat Commun 10, 4470 (2019). https://doi.org/10.1038/s41467-019-12154-0