Bakterier blev første gang observeret af [[Anton van Leeuwenhoek]] i 1676 igennem et selvlavet [[mikroskop]].<ref>{{cite journal |author=Porter JR |title=Antony van Leeuwenhoek: tercentenary of his discovery of bacteria |journal=Bacteriological Reviews |volume=40 |issue=2 |pages=260–9 |year=1976 |pmid=786250 |pmc=413956}}</ref> Han kaldte dem "animalcules" (latin: små dyr) og offentliggjorde sine observationer i en række breve til [[Royal Society|The Royal Society]].<ref>{{cite journal |doi=10.1098/rstl.1684.0030 |author=van Leeuwenhoek A |title=An abstract of a letter from Mr. Anthony Leevvenhoek at Delft, dated Sep. 17, 1683, Containing Some Microscopical Observations, about Animals in the Scurf of the Teeth, the Substance Call'd Worms in the Nose, the Cuticula Consisting of Scales |url=http://www.journals.royalsoc.ac.uk/content/120136/?k=Sep.+17%2c+1683 |journal=Philosophical Transactions (1683–1775) |volume=14 |pages=568–574 |year=1684 |access-date=2007-08-19 |issue=155–166 |url-status=dead }}</ref><ref>{{cite journal |author=van Leeuwenhoek A |title=Part of a Letter from Mr Antony van Leeuwenhoek, concerning the Worms in Sheeps Livers, Gnats, and Animalcula in the Excrements of Frogs |url=http://www.journals.royalsoc.ac.uk/link.asp?id=4j53731651310230 |journal=Philosophical Transactions (1683–1775) |volume=22 |pages=509–518 |year=1700 |access-date=2007-08-19 |doi=10.1098/rstl.1700.0013 |issue=260–276 |url-status=dead }}</ref><ref>{{cite journal |author=van Leeuwenhoek A |title=Part of a Letter from Mr Antony van Leeuwenhoek, F. R. S. concerning Green Weeds Growing in Water, and Some Animalcula Found about Them |url=http://www.journals.royalsoc.ac.uk/link.asp?id=fl73121jk4150280 |journal=Philosophical Transactions (1683–1775) |volume=23 |pages=1304–11 |year=1702 |access-date=2007-08-19 |doi=10.1098/rstl.1702.0042 |issue=277–288 |url-status=dead }}</ref> Navnet ''bakterie'' blev først indført i 1828 af [[Christian Gottfried Ehrenberg]].<ref>Ehrenberg's Symbolae Physioe. Animalia evertebrata. Decas prima. Berlin, 1828.</ref> I 1835 definerede Ehrenberg ''Bacterium'' som en slægt af ikke-sporedannende stavbakterier,<ref name=status>{{cite journal |author= |year= |title=The Status of the Generic Term Bacterium Ehrenberg 1828 |journal= |publisher= |volume= |issue= |pages= |url= |doi= |pmid=16559906}}</ref> modsat ''Bacillus'', der var en slægt af sporedannende stavbakterier.<ref>EHRENBERG (C.G.): Dritter Beitrag zur Erkenntniss grosser Organisation in der Richtung des kleinsten Raumes. Physikalische Abhandlungen der Koeniglichen Akademie der Wissenschaften zu Berlin aus den Jahren 1833-1835, 1835, pp. 143-336.</ref>
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