Microbial Taxonomy

 Classification Systems
 Levels of Classification
 Definition of “Species”
 Nomenclature
 Useful Properties in Microbial Classification
 Microbial Phylogeny
 Classification Systems
 Taxonomy:
• Classification of living organisms into groups
 Phylogenetic Classification System:
• Groups reflect genetic similarity and evolutionary
relatedness
 Phenetic Classification System:
• Groups do not necessarily reflect genetic
similarity or evolutionary relatedness. Instead,
groups are based on convenient, observable
characteristics.
 Levels of Classification
 Taxon:
• A group or “level” of classification
• Hierarchical; broad divisions are divided up into
smaller divisions:
– Kingdom (Not used by most bacteriologists)
– Phylum (Called “Division” by botanists)
– Class
– Order
– Family
– Genus (plural: Genera)
– Species (Both singular & plural)
 Definition of “Species”
 The “basic unit” of taxonomy, representing a
specific, recognized type of organism
 For sexually reproducing organisms, a
fundamental definition of “species” has been
reproductive compatibility
 This definition fails for many microbial
species (including bacteria), because they do
not reproduce sexually
 Definition of “Species”
 Definition of “species” in microbiology:
• Classic definition: A collection of microbial
strains that share many properties and differ
significantly from other groups of strains
• Species are identified by comparison with known
“type strains”: well-characterized pure cultures;
references for the identification of unknowns
• There are several collections of type strains,
including the American Type Culture Collection
(ATCC)
 Definition of “Species”
 Definition of “species” in microbiology
(cont.):
• Strain:
– A population of microbes descended from a single
individual or pure culture
– Different strains represent genetic variability within a
species
– Biovars: Strains that differ in biochemical or
physiological differences
– Morphovars: Strains that vary in morphology
– Serovars: Stains that vary in their antigenic properties
 Nomenclature
 Scientific
name (Systematic Name)
Binomial System of Nomenclature
• Genus name + species name
– Italicized or underlined
– Genus name is capitalized and may be abbreviated
– Species name is never abbreviated
– A genus name may be used alone to indicate a genus
group; a species name is never used alone
– eg: Bacillus subtilis
      B. subtilis
 Nomenclature
 Common or descriptive names
(trivial names)
• Names for organisms that may be in common
usage, but are not taxonomic names
– eg: tubercle bacillus
        (Mycobacterium tuberculosis)
– meningococcus
(Neiserria meningitidis)
– Group A streptococcus
(Streptococcus pyogenes)
 Useful Properties in Classification
 Colony morphology
 Cell shape & arrangement
 Cell wall structure (Gram staining)
 Special cellular structures
 Biochemical characteristics
 Useful Properties in Classification
 Serological Tests
• Use group specific antiserum isolated from the
plasma of animals that have been sensitized to the
organism
– The antiserum contains antibody proteins that react
with antigens on the unknown organism.
– The reaction can be detected by examining
agglutination or by using sera labeled with
colorimetric or fluorescent labels
 Useful Properties in Classification
 Serological Tests (cont.)
• Advantages:
– Highly specific
– Does not usually require the organism to be isolated
into pure culture
– Can be used to identify organisms that can’t be grown
on medium
 Useful Properties in Classification
G + C content
GC
Mol% (G  C)  100%
GCAT

• Estimated by determining the melting

temperature of the DNA
• Higher G + C gives a higher melting
temperature
 Useful Properties in Classification
 Nucleic acid hybridization
• By mixing ssDNA from two different species and
determining the percentage of the DNA that can
form dsDNA hybrids
• The greater the percent hybridization, the closer
the species
 Useful Properties in Classification
 Nucleic acid sequencing
• Genes for specific enzymes
• The nucleic acid sequence for the complete
genome of several species is now available
• 5S and 16S rRNA (ribosomal RNA) sequences;
comparison of these sequences has been
extensively used to determine the phylogenetic
relationships of microbial groups
 Microbial Phylogeny
 Bergey’s Manual of Systematic Bacteriology
• In 1927, David Bergey & colleagues published
Bergey’s Manual of Determinative Bacteriology,
a manual that grouped bacteria into phenetic
groups, used in identification of unknowns. It is
now in its 9th edition.
• In 1984, a more detailed work entitled Bergey’s
Manual of Systematic Bacteriology was
published, still primarily phenetic in its
classification.
 Microbial Phylogeny
 Bergey’s Manual of Systematic Bacteriology
• Publication of the second edition of Bergey’s
Manual of Systematic Bacteriology was begun in
2001.
• The 2nd edition gives the most up-to-date
phylogenic classification of prokaryotic
organisms, including both eubacteria and archaea.
• When it is completed, it will consist of 5 volumes.
• The classification in Bergey’s Manual is accepted
by most microbiologists as the best consensus for
prokaryotic taxonomy.
 Microbial Phylogeny
 Domains
• Based on the research of Woese and others in the
1980s and 1990s, most biologists divide all living
organisms into 3 domains:
– Domain Archaea
– Domain Bacteria
– Domain Eucarya
• rRNA sequence data suggests that Archaea &
Eucarya may share a more recent common
ancestor with each other than with Bacteria
• Diagram
 Microbial Phylogeny
 Domains (cont.)
• Many microbiologists reject the “kingdom”
designation.
• Each domain is divided into phyla, phyla into
classes. etc.
• There is often great metabolic and ecological
diversity among the members of a group, perhaps
reflecting parallel evolution of such things as
fermentation pathways, photosynthetic pathways,
etc.
 Microbial Phylogeny
 Phylogeny of domain Archaea
• Based primarily on rRNA sequence data, domain
Archaea is divided into two phyla:
– Phylum Crenarchaeota
 Originally containing thermophylic and hyperthermophilic
sulfur-metabolizing archaea
 Recently discovered Crenarchaeota are inhibited by sulfur
& grow at lower temperatures
– Phylum Euryarchaeota
 Contains primarily methanogenic archaea, halophilic
archaea, and thermophilic, sulfur-reducing archaea
 Microbial Phylogeny
 Phylogeny of domain Bacteria
• The 2nd edition of Bergey’s Manual of Systematic
Bacteriology divides domain Bacteria into 23
phyla. Nine of the more notable phyla are
described here.
– Phylum Aquiflexa
 The earliest “deepest” branch of the Bacteria
 Contains genera Aquiflex and Hydrogenobacter that can
obtain energy from hydrogen via chemolithotrophic
pathways
 Microbial Phylogeny
 Phylogeny of domain Bacteria (cont.)
– Phylum Cyanobacteria
 Oxygenic photosynthetic bacteria
– Phylum Chlorobi
 The “green sulfur bacteria”
 Anoxygenic photosynthesis
 Includes genus Chlorobium
 Microbial Phylogeny
 Phylogeny of domain Bacteria (cont.)
– Phylum Proteobacteria
 The largest group of gram-negative bacteria
 Extremely complex group, with over 400 genera and 1300
named species
 All major nutritional types are represented: phototrophy,
heterotrophy, and several types of chemolithotrophy
 Sometimes called the “purple bacteria,” although very few
are purple; the term refers to a hypothetical purple
photosynthetic bacterium from which the group is believed
to have evolved
 Microbial Phylogeny
 Phylogeny of domain Bacteria (cont.)
– Phylum Proteobacteria (cont.)
 Divided into 5 classes: Alphaproteobacteria,
Betaproteobacteria, Gammaproteobacteria,
Deltaproteobacteria, Epsilonproteobacteria
 Microbial Phylogeny
 Phylogeny of domain Bacteria (cont.)
– Phylum Proteobacteria (cont.)
 Significant groups and genera include:
» Photosynthetic genera such as Rhodospirillum (a purple
non-sulfur bacterium) and Chromatium (a purple sulfur
bacterium)
» Sulfur chemolithotrophs, genera Thiobacillus and
Beggiatoa
» Nitrogen chemolithotrophs (nitrifying bacteria), genera
Nitrobacter and Nitrosomonas
» Other chemolithotrophs, genera Alcaligenes,
Methylobacilllus, Burkholderia
 Microbial Phylogeny
 Phylogeny of domain Bacteria (cont.)
– Phylum Proteobacteria (cont.)
 Significant groups and genera include:
» The family Enterobacteriaceae, the “gram-negative
enteric bacteria,” which includes genera Escherichia,
Proteus, Enterobacter, Klebsiella, Salmonella, Shigella,
Serratia, and others
» The family Pseudomonadaceae, which includes genus
Pseudomonas and related genera
» Other medically important Proteobacteria include
genera Haemophilus, Vibrio, Camphylobacter,
Helicobacter, Rickessia, Brucella
 Microbial Phylogeny
 Phylogeny of domain Bacteria (cont.)
– Phylum Firmicutes
 “Low G + C gram-positive” bacteria
 Divided into 3 classes
» Class I – Clostridia; includes genera Clostridium and
Desulfotomaculatum, and others
» Class II – Mollicutes; bacteria in this class cannot make
peptidoglycan and lack cell walls; includes genera
Mycoplasma, Ureaplasma, and others
» Class III – Bacilli; includes genera Bacillus,
Lactobacillus, Streptococcus, Lactococcus,
Geobacillus, Enterococcus, Listeria, Staphylococcus,
and others
 Microbial Phylogeny
 Phylogeny of domain Bacteria (cont.)
– Phylum Actinobacteria
 “High G + C gram-positive” bacteria
 Includes genera Actinomyces, Streptomyces,
Corynebacterium, Micrococcus, Mycobacterium,
Propionibacterium
– Phylum Chlamidiae
 Small phylum containing the genus Chlamydia
 Microbial Phylogeny
 Phylogeny of domain Bacteria (cont.)
– Phylum Spirochaetes
 The spirochaetes
 Characterized by flexible, helical cells with a modified
outer membrane (the outer sheath) and modified flagella
(axial filaments) located within the outer sheath
 Important pathogenic genera include Treponema, Borrelia,
and Leptospira
– Phylum Bacteroidetes
 Includes genera Bacteroides, Flavobacterium, Flexibacter,
and Cytophyga; Flexibacter and Cytophyga are motile by
means of “gliding motility”
 Microbial Phylogeny
 Phylogeny of domain Eucarya
• The domain Eucarya is divided into four
kingdoms by most biologists:
– Kingdom Protista, including the protozoa and algae
– Kingdom Fungi, the fungi (molds, yeast, and fleshy
fungi)
– Kingdom Animalia, the multicellular animals
– Kingdom Plantae, the multicellular plants