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vegetables, probiotics

Weissella

confusa

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Weissella

halotolerans

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a Bifidobacterium lactis is not a separate species but included in B. animalis. b Micrococcus varians has been renamed Kocuria varians. c Lacttobacillus bavaricus has been included in L. sakei subsp. sakei.

a Bifidobacterium lactis is not a separate species but included in B. animalis. b Micrococcus varians has been renamed Kocuria varians. c Lacttobacillus bavaricus has been included in L. sakei subsp. sakei.

in organizing species into higher orders of relatedness. The traits traditionally used for identification are cell morphology, Gram staining, growth on various carbohydrates, gas formation, acid production, temperature profile for growth, salt tolerance, amino acid requirements, vitamin requirements, oxygen requirement/sensitivity, hemolysis, and hydrolysis of polysaccharides, proteins, and lipids. At the strain level, methods for discrimination are based on serological tests, phage typing, or very specific biochemical tests. All these traditional tests are still used and important in the microbiology laboratory, particularly those relating directly to the metabolisms exploited for the fermentation process. Identification, classification, and taxonomy of microorganisms have, however, undergone dramatic changes during the past two decades due to the introduction of methods from molecular biology (15). These methods have allowed us to base identification and taxonomy on the properties common to all microorganisms instad of the traits that differ. Several of the fundamental processes in a living cell are shared by all organisms, and one of these is protein synthesis. The ubiquitous presence of ribosomes allows taxonomists to use their degree of similarity to deduce evolutionary distances between organisms. For practical reasons the RNA molecules of the ribosome are particularly convenient for this purpose (16, 17). The phylogenetic relationships between the species listed in Table 3 are also presented in Fig. 1. A few G+ pathogens, as well as the Escherichia coli, have been included for reference, whereas a large number of other bacterial species have been omitted for purposes of clarity. It has previously been pointed out that species of lactic acid bacteria do not have a close phylogenetic relationship, but share a common strategy for survival in nutrient-rich environments (15). By inspecting Fig. 1, it is apparent that further changes in the taxonomy of the Lactobacillus-Pediococcus group will be necessary before the taxons can be represented in clades. Fig. 1 also clearly illustrates how small the evolutionary distance can be between beneficial and lethal microorganisms.

Pediococcus Phylogenetic Tree

Figure 1 The phylogenetic relationship between the bacterial species listed in Table 3. The phylogenetic tree was constructed based on the 16S rRNA sequences using the server of the ribosomal database project (http://rdp.cme.msu.edu, 17). The G- species, Escherichia coli, has been included for reference. Also included as references are a few G+ pathogens and spoilage organisms:

Mycobacterium tuberculosis, Clostridium tyrobutyricum, Clostridium botulinum, Streptococcus pneumoniae, Enterococcus faecalis, Staphylococcus aureus, and Bacillus cereus.

Figure 1 The phylogenetic relationship between the bacterial species listed in Table 3. The phylogenetic tree was constructed based on the 16S rRNA sequences using the server of the ribosomal database project (http://rdp.cme.msu.edu, 17). The G- species, Escherichia coli, has been included for reference. Also included as references are a few G+ pathogens and spoilage organisms:

Mycobacterium tuberculosis, Clostridium tyrobutyricum, Clostridium botulinum, Streptococcus pneumoniae, Enterococcus faecalis, Staphylococcus aureus, and Bacillus cereus.

General methods for identification below the species level are now also based on molecular methods. DNA fingerprint methods able to identify individual strains have been developed; one of the most reliable and portable methods uses pulsed field gel electrophoresis of restriction patterns of entire bacterial chromosomes (18).

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