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 taxonomic classification. In yeasts and molds, morphology, reproduction, the biochemical nature of
macromolecules, and metabolic patterns are used along with other criteria. For bacteria, Gramstain 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. 1–3 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 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 classification, 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, causing 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 bacterial 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 (subspecific 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 useful (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
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, the biochemical nature of
macromolecules, and metabolic patterns are used along with other criteria. For bacteria, Gramstain 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. 1–3 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 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 classification, 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, causing 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 bacterial 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 (subspecific 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 useful (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