Living cellular organisms, on the basis of phylogenetic and evolutionary relation- ships, were grouped originally in ﬁve kingdoms, in which bacteria belonged to procaryotes (before nucleus) and the eucaryotic (with nucleus) molds and yeasts were grouped under fungi. In the 1970s, the procaryotic domain was changed to Eubacteria (with murine on cell wall) and Archaebacteria (without murine on cell wall). In the 1990s, this was changed to Bacteria and Archaea, respectively. Archaea include most extremophiles and are not important to food microbiology. Viruses are not considered as living cells and are not included in this classiﬁcation system.
For the classiﬁcation of yeasts, molds, and bacteria, several ranks are used after the kingdom: divisions, classes, orders, families, genera (singular genus), and species. The basic taxonomic group is the species. Several species with similar characteristics form a genus. Among eucaryotes, species in the same genus can interbreed. This is not considered among procaryotes, although conjugal transfer of genetic materials exists among many bacteria. Several genera make a family, and the same procedure is followed in the hierarchy. In food microbiology, ranks above species, genus, and family are seldom used. Among bacteria, a species is regarded as a collection of strains having many common features. A strain is the descendent of a single colony (single cell). Among the strains in a species, one is assigned as the type strain, and is used as a reference strain while comparing the characteristics of an unknown isolate. However, by knowing the complete genome sequence, this system will change in the future.
Several methods are used to determine relatedness among bacteria, yeasts, and molds for taxonomic classiﬁcation. In yeasts and molds, morphology, reproduction, biochemical nature of macromolecules, and metabolic patterns are used along with other criteria. For bacterial morphology, Gram-stain characteristics, protein proﬁles, amino acid sequences of some speciﬁc proteins, base composition (mol % G + C), nucleic acid (DNA and RNA) hybridization, nucleotide base sequence, and computer-assisted numerical taxonomy are used. Protein proﬁle, amino acid sequence, base composition, DNA and RNA hybridization, and nucleotide base sequence are directly or indirectly related to genetic makeup of the organisms and thus provide a better chance in comparing two organisms at the genetic level. In mol % G + C ratio, if two strains differ by 10% or more, they are most likely not related. Similarly, in a hybridization study, two strains are considered the same if their DNAs have
90% or more homology. For the nucleotide base sequence, the sequences in 16S rRNA among strains are compared. A sequence of about 1500 nucleotide bases over a stretch of 16S rRNA is most conserved, so related strains should have high homology. In numerical taxonomy, many characteristics are compared, such as morphological, physiological, and biochemical. Each characteristic is given the same weightage. Two strains in the same species should score 90% or more.
Evolutionary relationships among viruses, if any, are not known. Their classiﬁ- cation system is rather arbitrary and based on the types of disease they cause (such as the hepatitis virus, causing inﬂammation of the liver), nucleic acid content (RNA or DNA, single stranded or double stranded), and morphological structures. In food, two groups of viruses are important: the bacterial viruses (bacteriophages) of starter culture bacteria and some foodborne pathogenic bacteria, and the human pathogenic viruses associated with foodborne diseases.