The original observation of the positive role played by certain bacteria was first introduced by Russian scientist and Nobel laureate Eli Metchnikoff, who in the beginning of the 20th century suggested that it would be possible to modify the gut flora and to replace harmful microbes by useful microbes.
''Bifidobacteria'' were first isolated from a breast-fed infant by Henry Tissier who also worked at the Pasteur Institute. The isolated bacterium named Bacillus bifidus communis was later renamed to the genus ''Bifidobacterium''. Tissier found that bifidobacteria are dominant in the gut flora of breast-fed babies and he observed clinical benefits from treating diarrhea in infants with bifidobacteria. The claimed effect was bifidobacterial displacement of proteolytic bacteria causing the disease.
During an outbreak of shigellosis in 1917, German professor Alfred Nissle isolated a strain of ''Escherichia coli'' from the feces of a soldier who was not affected by the disease. Methods of treating infectious diseases were needed at that time when antibiotics were not yet available, and Nissle used the ''Escherichia coli'' Nissle 1917 strain in acute gastrointestinal infectious salmonellosis and shigellosis.
In 1920, Rettger demonstrated that Metchnikoff's "Bulgarian Bacillus", later called ''Lactobacillus delbrueckii subsp. bulgaricus'', could not live in the human intestine, and the fermented food phenomena petered out. Metchnikoff's theory was disputable (at this stage), and people doubted his theory of longevity.
After Metchnikoff’s death in 1916, the centre of activity moved to the United States. It was reasoned that bacteria originating from the gut were more likely to produce the desired effect in the gut, and in 1935 certain strains of ''Lactobacillus acidophilus'' were found to be very active when implanted in the human digestive tract. Trials were carried out using this organism, and encouraging results were obtained especially in the relief of chronic constipation.
The term "probiotics" was first introduced in 1953 by Kollath. Contrasting antibiotics, probiotics were defined as microbially derived factors that stimulate the growth of other microorganisms. In 1989 Roy Fuller suggested a definition of probiotics which has been widely used: "''A live microbial feed supplement which beneficially affects the host animal by improving its intestinal microbial balance''". Fuller's definition emphasizes the requirement of viability for probiotics and introduces the aspect of a beneficial effect on the host.
In the following decades intestinal lactic acid bacterial species with alleged health beneficial properties have been introduced as probiotics, including ''Lactobacillus rhamnosus'', ''Lactobacillus casei'', and ''Lactobacillus johnsonii''.
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