Living cellular organisms, on the basis of phylogenetic and evolutionary relationships, were grouped originally in five kingdoms, in which bacteria belonged to prokaryotes (before nucleus), and the eukaryotic (with nucleus) molds and yeasts were grouped under fungi.1 In the 1970s, the
prokaryotic domain was changed to Eubacteria (with murein or peptidoglycan on cell wall) and Archaebacteria (without murein on cell wall). In the 1990s, this was changed to Bacteria and Archaea, respectively.2,3 Figure 2.1 depicts a phylogenetic tree representing three major divisions:
Bacteria, Archaea, and Eukarya. The Archaea include most extremophiles and are not important to food microbiology. Fungi and parasites are included under Eukarya and are responsible for foodborne disease and/or spoilage. Viruses 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 eukaryotes, spe- cies in the same genus can interbreed. This is not considered among prokaryotes although the 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
Archaea Bacteria Eukarya · Microsporidia · Myxogastria · Entamoebidae · Blastocystis · Cryptophyta · Metazoa · Fungi · Actinobacteri a · Bacilli · Clost ridia · Chlam ydiae · Cyanobacteri a · Proteob acteria · Bacteroidetes · M ethano bacter iaceae · Meth anothe rmace ae · Methanopyraceae · Meth anococ caceae · Halo bacter iaceae · Sulfol obacea e · Thermo coccac eae
Figure 2.1 Phylogenetic tree for microorganisms representing three major divisions (phyla): Bacteria, Archaea, and eukarya. (Redrawn based on eckburg, P.B. et al., Infect. Immun., 71, 591–596, 2003.) Representative classes of microorganisms are listed for each division (phylum).
Characteristics of Predominant Microorganisms in Food ◾ 13
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 taxo- nomic classification. In yeasts and molds, morphology, reproduction, the biochemical nature of macromolecules, and metabolic patterns are used along with other criteria. For bacteria, Gram- stain characteristics, protein profiles, amino acid sequences of some specific proteins, base com- position (mol% G+C), nucleic acid (DNA and RNA) hybridization, nucleotide base sequence, and computer-assisted numerical taxonomy are used.1–3 Protein profile, amino acid sequence, base
composition, DNA and RNA hybridization, and nucleotide base sequence are directly or indi- rectly 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 approximately 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 morphology, physiology, and biochemistry. Each characteristic is given the same weight. Two strains in the same species should score 90% or more. Whole genome sequencing is now used for pathogen identification and clas- sification, and it is anticipated this will be a routine microbial identification tool in the near future. Evolutionary relationships among viruses, if any, are not known. Their classification system is rather arbitrary and based on the types of disease they cause (such as the hepatitis virus, caus- ing inflammation of the liver cells), 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 enteric pathogenic viruses associated with foodborne diseases. Bacteriophages are also used as biocontrol to kill foodborne pathogens in meat animals during preharvest production and in food products during postharvest processing (see Chapter 38). Bacteriophages are also used as an elegant detection tool for pathogens because of their strong interaction with host pathogens (see Chapter 42).
nomenclature
The basic taxonomic group in bacteria, yeasts, and molds is the species, and each species is given a name. The name has two parts (binomial name): The first part is the genus name, and the second part is the specific epithet (adjective). Both parts are Latinized; when written, they are italicized (or underlined) with the first letter of the genus written with a capital letter (e.g., Saccharomyces
cerevisiae, Penicillium roquefortii, Listeria monocytogenes, and Lactobacillus acidophilus). A bacte-
rial species can be divided into several subspecies (subsp. or ssp.) if the members show minor but consistent differences in characteristics. Under such conditions, a trinomial epithet (subspe- cific epithet) is used (e.g., Lactococcus lactis ssp. lactis or Lactococcus lactis ssp. cremoris). In some instances, ranks below subspecies are used to differentiate strains recognized by specific characters (e.g., serovar, antigenic variation; biovar, producing a specific metabolite; and phagovar, sensitive to a specific phage types). Such ranks have no taxonomic importance but can be practically use- ful (e.g., Lactococcus lactis ssp. lactis biovar diacetilactis is a Lactococcus lactis ssp. lactis strain that produces diacetyl, an important flavor compound in some fermented dairy products). Each strain of a species should be identified with a specific strain number, which can be alphabetic or numeric
14 ◾ Fundamental Food Microbiology
or a mixture of both (e.g., Pediococcus acidilactici LB923; Listeria monocytogenes ATCC 19116). At the family level, bacterial names are used as plural adjectives in feminine gender and agree with the suffix “aceae” (e.g., Enterobacteriaceae). The species and strains in a genus can be represented collectively, either using “spp.” after genus (e.g., Lactobacillus spp.) or plural forms of the genus (e.g., lactobacilli for Lactobacillus; lactococci for Lactococcus; leuconostocs for Leuconostoc, or sal- monellae for Salmonella).
The scientific names of bacteria are given according to the specifications of the International Code of Nomenclature of Bacteria. The International Committee on Systematic Bacteriology of the International Union of Microbiological Association examines the validity of each name and then pub- lishes the approved lists of bacterial names from time to time. A new name (species or genus) must be published in the International Journal of Systematic Bacteriology before it is judged for inclusion in the approved list. Any change in name (genus or species) has to be approved by this committee.
When writing the name of the same species more than once in an article, it is customary to use both genus and specific epithet the first time and abbreviate the genus name subsequently. In the
Bergey’s Manual of Systematic Bacteriology, only the first letter is used (e.g., Listeria monocytogenes
and then L. monocytogenes). The same system is used in most publications in the United States. However, it creates confusion when one article has several species with the same first letter in the genus (e.g., Lactobacillus lactis, Leuconostoc lactis, and Lactococcus lactis as L. lactis). In some European journals, more than one letter is used, but there is no definite system (e.g., Lact. lactis,
Lc. lactis, Leu. lactis, Lb. lactis, List. monocytogenes). In this book, to reduce confusion among read-
ers, many of whom might not be familiar with the current rapid changes in bacterial nomencla- ture, a three-letter system is used (e.g., Lis. monocytogenes, Leu. lactis; Shi. dysenterie for Shigella;
Sta. aureus for Staphylococcus). In rare cases, a slight modification is used (e.g., Lactococcus lactis
and Lactobacillus lactis are written as Lac. lactis and Lab. lactis, respectively, for the two genera). The nomenclature system for Salmonella has been modified (Chapter 26).
The viruses, as indicated previously, have not been given specific taxonomic names as given for bacteria. They are often identified with alphabetic or numeric designations or a combination of both (e.g., T4 or T1 bacteriophages), the type of disease they produce (e.g., hepatitis A, caus- ing liver disease), or by other methods, for example, Norwalk-like viruses (now called norovirus), causing a type of foodborne gastroenteritis in humans, originally isolated from the town called Norwalk in Ohio (United States).