1847, plural of Modern Latin bacterium, from Greek bakterion "small staff," diminutive of baktron "stick, rod, staff, cudgel." So called because the first ones observed were rod-shaped. Introduced as a scientific word 1838 by German naturalist Christian Gottfried Ehrenberg. A classical plural sometimes also erroneously used as a singular.
The Greek word is from a PIE *bak- "staff used for support, peg" (compare Latin baculum "rod, walking stick;" Irish bacc, Welsh bach "hook, crooked staff;" Middle Dutch pegel "peg, pin, bolt"). De Vaan writes, "Since *b was very rare in PIE, and Celtic shows an unexplained geminate, we are probably dealing with a loanword from an unidentified source."