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Emil von Behring and Shibasaburo Kitasato working together in Berlin in 1890 announce the discovery of diphtheria antitoxin serum, the first rational approach to therapy of infectious diseases. They inject a sublethal dose of diphtheria filtrate into animals and produce a serum that is specifically capable of neutralizing the toxin. They then inject the antitoxin serum into an uninfected animal to prevent a subsequent infection. Behring was awarded the Nobel Prize in Medicine or Physiology in 1901.
Behring, E. 1890. Untersuchungen ueber das Zustandekommen der Diphtherie-Immunitat bei Thieren. Dt. Med. Wochenschr. 16: 1145-1148. In Milestones in Microbiology: 1556 to 1940, translated and edited by Thomas D. Brock, ASM Press. 1998, p141 [pdf]
Behring, E. and Kitasato, S. 1890. Ueber das Zustandekommen der Diphtherie-Immunitat und der Tetanus-Immunitat bei thieren. Deutsche medizinsche Wochenschrift 16:1113-1114 In Milestones in Microbiology: 1556 to 1940, translated and edited by Thomas D. Brock, ASM Press. 1998, p138 [pdf]
Sergei Winogradsky succeeds in isolating nitrifying bacteria from soil. During the period 1890-1891, Winogradsky performs the definitive work on the organisms responsible for the process of nitrification in nature.
Winogradsky, S. 1890. Recherches sur les Organismes de la Nitrification.
Computer Rendu Vol 110: 1013-1016 In Milestones in Microbiology: 1556 to 1940, translated and edited by Thomas D. Brock, ASM Press. 1998, p231 [pdf]
Paul Ehrlich proposes that antibodies are responsible for immunity. He shows that antibodies form against the plant toxins ricin and abrin. With Metchnikoff, Ehrlich is jointly awarded the Nobel Prize in Medicine or Physiology in 1908.
Dmitri Ivanowski publishes the first evidence of the filterability of a pathogenic agent, the virus of tobacco mosaic disease, launching the field of virology. He passes the agent through candle filters that retain bacteria, but he isn't sure that the agent is a unique organism.
When Did Virology Start, ASM News 62, 1996. p.142 [pdf]
Theobald Smith and F.L. Kilbourne establish that ticks carry Babesia microti, which causes babesiosis in animals and humans. This is the first account of a zoonotic disease and also the foundation of all later work on the animal host and the arthropod vector.
Martinus Beijerinck recognizes "soluble" living microbes, a term he applies to the discovery of tobacco mosaic virus. He demonstrates that juice pressed from tobacco leaves that had been filtered free of bacteria retains the ability to cause disease in plants even after repeated dilutions. He calls the disease agent "contagium vivum fluidium" or contagious living fluid.
Martinus Beijerinck (1851-1931), ASM News 62, 1996. p.539 [pdf]
Beijerinck, M. 1899. Ueber ein Contagium vivum fluidum als Ursache der Fleckenkrankheit der Tabaksblatter. Centralblatt fur bacteriologie und Parasirenkunde, Part II, 5: 27-33. In Milestones in Microbiology: 1556 to 1940, translated and edited by Thomas D. Brock, ASM Press. 1998, p153 [pdf]