It was in vogue a few years back to deny Y. Pestis as the cause of The Plague, but DNA research has taken a chain saw to that silly notion. But yeah, there are always different causes of death, and most of them have come and gone a few times, due to non-human reservoirs. Smallpox emerged perhaps no more than 3K years ago, and has no known non-human host -- the eradication program worldwide has worked -- the CDC says no cases since 1980. The Egyptian 18th Dynasty pharaohs' mummified remains have survived for the most part, and the non-invasive study (CAT scans and whatev') have shown the lesions on at least two of them.
The lecturer said that the experience of England with the Black Death suggests anthrax was going on at the same time, described in contemporaneous sources as “a cattle murrain.”