Like all living organisms, microorganisms are named according to Latinized binomial nomenclature, meaning they are assigned two names, a genus and a species. By convention, both the genus and species names are itali cized, but only the genus is capitalized.Thus, the name of the common food yeast is written as Saccharomyces cerevisae. For some organisms, a trinomial system is applied to indicate a subspecies epithet, as is the case for the dairy organism Lactococcus lactis subsp. lactis.

Microorganisms are named according to the rules established by the appropriate governing body. For bacteria and fungi, the International Committee on Systematic Bacteriology and the International Association for Plant Taxonomy, respectively, define the nomenclature rules. These rules are then published in the respective "codes," the International Code of Nomenclature of Bacteria and the International Code for Botanical Nomenclature. In addition, there is a "running list," called the List of Bacterial Names with Standing in Nomenclature (www, that provides updated bacterial nomenclature. To be included in these lists and considered as "valid," a name must have been published in the scientific literature, along with a detailed description and relevant supporting data.

In some cases, a validly named organism may be referred to by another name, indicated as a synonym. In other instances, the name of an organism may have been replaced by a new name, in which case the original name is indicated as a basonym. In situations where a name was "unofficially" assigned to an organism and does not appear on the list, that name is considered to be illegitimate and its use should be discontinued. However, even if the name assigned to a particular organism is supported by a valid publication, this does not mean that the name is or must be accepted by the scientific community.

Although names are indeed based on official rules (where each taxon has a valid name), the utility of a given classification scheme, on which a given organism is named, is left up to the scientists who use it. That is, a researcher may propose that a given organism be assigned a "new" name, and have the supporting evidence published in a valid journal, but other microbiologists are entitled to disagree with the taxonomy and reject the proposed classification.

It is relevant to raise these issues, because many of the organisms used in food fermentations have either undergone nomenclature revisions or have been reclassified into new taxa. For example, the official name of the dairy organism mentioned above, L. lactis subsp. lactis was originally Bacterium lactis (the first organism isolated in pure culture and named by Joseph Lister in 1873). It was renamed Streptococcus lactis in 1909, which is how this organism was known for more than 70 years (and which still shows up occasionally in "current" texts), before the new genus, Lactococcus, was adopted. In other cases, a name was proposed, then rescinded (see below). There are also instances of organisms that had been assigned "unofficial" names (see above), and through frequent use, had acquired some level of validity, however undeserved. A good example of the latter situation was for Lactobacillus sporo-genes, an organism that is properly classified as Bacillus subtilis.Yeast nomenclature, although under the authority of the International Code for Botanical Nomenclature, is also subject to taxonomical challenges and changes in classification (see below).

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