Fundamental Food Microbiology, Third Edition - Fuad Fathir

CHARACTERISTICS OF PREDOMINANT MICROORGANISMS IN FOOD 15
In this chapter, a brief discussion is included initially on the methods currently
used in the classification and nomenclature of microorganisms and later on the
important characteristics of microorganisms predominant in food.
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II. CLASSIFICATION OF MICROORGANISMS
Living cellular organisms, on the basis of phylogenetic and evolutionary relationships,
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. 1–3 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. 4 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. 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 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.