Taxonomy, Role, and Significance of Microorganisms in Foods
15
DNA fragments of various sizes result that can be sequenced by the Sanger method. From the DNA
sequences, the template 16S rRNA sequence can be deduced. It was through studies of 16S rRNA
sequences that led Woese and his associates to propose the establishment of three kingdoms of life
forms: Eukaryotes, Archaebacteria, and Prokaryotes. The last include the cyanobacteria and the eubacteria, with the bacteria of importance in foods being eubacteria. Sequence similarities of 16S rRNA
are widely employed, and some of the new foodborne taxa were created primarily by its use along
with other information. It appears that the sequencing of 23S rDNA will become more widely used in
bacterial taxonomy.
Nucleotide catalogs of 16S rRNA have been prepared for a number of organisms, and extensive
libraries exist. By this method, 16S rRNA is subjected to digestion by RNase T1, which cleaves the
molecule at G(uanine) residues. Sequences (-mers) of 6–20 bases are produced and separated, and
similarities S AB (Dice-type coefficient) between organisms can be compared. Although the relationship
between S AB and percentage similarity is not good below S AB value of 0.40, the information derived
is useful at the phylum level. The sequencing of 16S rRNA by reverse transcriptase is preferred to
oligonucleotide cataloging, as longer stretches of rRNA can be sequenced.
Analysis of DNA
The mol% G + C of bacterial DNA has been employed in bacterial taxonomy for several decades,
and its use in combination with 16S and 5S rRNA sequence data makes it even more meaningful. By
16S rRNA analysis, the Gram-positive eubacteria fall into two groups at the phylum level: one group
with mol% G + C >55, and the other <50.
53 The former includes the genera Streptomyces, Propionibacterium, Micrococcus, Bifidobacterium, Corynebacterium, Brevibacterium, and others. The group
with the lower G + C values include the genera Clostridium, Bacillus, Staphylococcus, Lactobacillus,
Pediococcus, Leuconostoc, Listeria, Erysipelothrix, and others. The latter group is referred to as the
Clostridium branch of the eubacterial tree. When two organisms differ in G + C content by more than
10%, they have few base sequences in common.
DNA–DNA or DNA–RNA hybridization has been employed for some time, and this technique
continues to be of great value in bacterial systematics. It has been noted that the ideal reference
system for bacterial taxonomy would be the complete DNA sequence of an organism.
49 It is generally
accepted that bacterial species can be defined in phylogenetic terms by use of DNA–DNA hybridization
results, where 70% or greater relatedness and 5
◦ C or less T m (melting point) defines a species.
50 When
DNA–DNA hybridization is employed, phenotypic characteristics are not allowed to override except
in exceptional cases.
50 Although a genus is more difficult to define phylogenetically, 20% sequence
similarity is considered to be the minimum level of DNA–DNA homology.
50
Even if there is not yet a satisfactory phylogenetic definition of a bacterial genus, the continued
application of nucleic acid techniques, along with some of the other methods listed above, should lead
ultimately to a phylogenetically based system of bacterial systematics. In the meantime, changes in
the extant taxa may be expected to continue to occur.
The Proteobacteria
The Gram-negative bacteria of known importance in foods belong to the class Proteobacteria,
which was established following extensive studies on the rRNA sequences of numerous genera of
15
DNA fragments of various sizes result that can be sequenced by the Sanger method. From the DNA
sequences, the template 16S rRNA sequence can be deduced. It was through studies of 16S rRNA
sequences that led Woese and his associates to propose the establishment of three kingdoms of life
forms: Eukaryotes, Archaebacteria, and Prokaryotes. The last include the cyanobacteria and the eubacteria, with the bacteria of importance in foods being eubacteria. Sequence similarities of 16S rRNA
are widely employed, and some of the new foodborne taxa were created primarily by its use along
with other information. It appears that the sequencing of 23S rDNA will become more widely used in
bacterial taxonomy.
Nucleotide catalogs of 16S rRNA have been prepared for a number of organisms, and extensive
libraries exist. By this method, 16S rRNA is subjected to digestion by RNase T1, which cleaves the
molecule at G(uanine) residues. Sequences (-mers) of 6–20 bases are produced and separated, and
similarities S AB (Dice-type coefficient) between organisms can be compared. Although the relationship
between S AB and percentage similarity is not good below S AB value of 0.40, the information derived
is useful at the phylum level. The sequencing of 16S rRNA by reverse transcriptase is preferred to
oligonucleotide cataloging, as longer stretches of rRNA can be sequenced.
Analysis of DNA
The mol% G + C of bacterial DNA has been employed in bacterial taxonomy for several decades,
and its use in combination with 16S and 5S rRNA sequence data makes it even more meaningful. By
16S rRNA analysis, the Gram-positive eubacteria fall into two groups at the phylum level: one group
with mol% G + C >55, and the other <50.
53 The former includes the genera Streptomyces, Propionibacterium, Micrococcus, Bifidobacterium, Corynebacterium, Brevibacterium, and others. The group
with the lower G + C values include the genera Clostridium, Bacillus, Staphylococcus, Lactobacillus,
Pediococcus, Leuconostoc, Listeria, Erysipelothrix, and others. The latter group is referred to as the
Clostridium branch of the eubacterial tree. When two organisms differ in G + C content by more than
10%, they have few base sequences in common.
DNA–DNA or DNA–RNA hybridization has been employed for some time, and this technique
continues to be of great value in bacterial systematics. It has been noted that the ideal reference
system for bacterial taxonomy would be the complete DNA sequence of an organism.
49 It is generally
accepted that bacterial species can be defined in phylogenetic terms by use of DNA–DNA hybridization
results, where 70% or greater relatedness and 5
◦ C or less T m (melting point) defines a species.
50 When
DNA–DNA hybridization is employed, phenotypic characteristics are not allowed to override except
in exceptional cases.
50 Although a genus is more difficult to define phylogenetically, 20% sequence
similarity is considered to be the minimum level of DNA–DNA homology.
50
Even if there is not yet a satisfactory phylogenetic definition of a bacterial genus, the continued
application of nucleic acid techniques, along with some of the other methods listed above, should lead
ultimately to a phylogenetically based system of bacterial systematics. In the meantime, changes in
the extant taxa may be expected to continue to occur.
The Proteobacteria
The Gram-negative bacteria of known importance in foods belong to the class Proteobacteria,
which was established following extensive studies on the rRNA sequences of numerous genera of