MIC 251: MICROBIAL TAXONOMY

14. Principles and Methods of Microbial Taxonomy

Learning Outcomes

• Understand the basic principles of microbial classification systems

• Be familiar with structural and biological characteristics to classify Microbes

• List the genetic approaches that can be used in identification and classification
of Microbes

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 Introduction
• Microorganisms are tremendously diverse in size, shape, physiology and lifestyle.
• Purpose of taxonomy is to provide useful ways of identifying and comparing organisms
 helpful to assess extent of diversity of different types of organisms.
• Taxonomy
= Science of biological classification consisting of 3 interrelated parts.
1. Classification- arrangement of organisms into taxa (taxon). (groups)
2. Nomenclature- assignments of names to taxa. (rules)
3. Identification- determination of taxon to which an isolate belongs. (data & process)
• Systematics- the study of organisms with the ultimate object of characterizing and
arranging them in an orderly manner.

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 Microbial Evolution and Diversity
• First prokaryotes probably arose at least 3.5 to 3.8 billion years ago (bya)  probably
anaerobic.
• Eukaryotes evolved from prokaryotes probably about 1.4 bya
• Carl Woese et al. (1970’s) suggested that organisms fall into one of three domains
(empires) into which the traditional kingdoms are distributed  based on ribosomal
RNA studies.

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 Microbial Evolution and Diversity
• Eucarya- contains all eukaryotic organisms.
• Bacteria (Eubacteria)- contains prokaryotic organisms with eubacterial rRNA and
membrane lipids that are primarily diacyl glycerol ethers. One RNA polymerase.
• Archaea- contains prokaryotic organisms with archaeobacterial rRNA and membrane
lipids that are primarily isoprenoid glycerol diether or diglycerol tetraether derivatives.
Three RNA polymerases. Cell walls lack peptidoglycan.

Types of Diversity
• Metabolic- differences between metabolic needs of hetero- and autotrophs/ catabolic
styles such as fermentation vs. respiration
• Structural- differences between gram-positives and -negatives/ structural differences
between bacteria and archaea/ presence or absence of cell wall, external appendages,
endospores, etc
• Morphological- cocci, bacilli, spirals, filamentous, pleiomorphic/ size
• Genetic- small ribosomal subunit sequencing has altered perception of this type of
diversity  genomes are currently being sequenced  bulk of life’s diversity is in
the bacteria and archaea

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 Major Divisions
Domains (Empires) based primarily on rRNA analysis

• Currently held that there are three domains of life

• Bacteria- comprise the vast majority of prokaryotes; peptidoglycan contains muramic

acid; membrane lipids contain ester-linked straight-chain fatty acids.

• Archaea- prokaryotes that lack muramic acid and have lipids with ether-linked branched
aliphatic chains, tRNA’s lack thymine, RNA polymerase is distinctive, ribosomes have a
different composition and shape when compared to the eubacteria.

• Eucarya- have a more complex membrane-delimited organelle structure. Cell organelles, such
as the Golgi complex, mitochondria, chloroplasts, lysosomes, the endoplasmic reticula and the nucleus, are
delimited by membranes.

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 Major Divisions
Kingdoms

Five Kingdom system

Animalia – multi-cellular, non-walled eukaryotes with ingestive nutrition.

Plantae – multi-cellular, walled eukaryotes with photoautotrophic nutrition.

Fungi – multi-cellular, and unicellular, walled eukaryotes

with absorptive nutrition.

Protista - unicellular eukaryotes with various nutritional

mechanisms.

Monera (Procaryotae) - all prokaryotic organisms.

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 Major Divisions
• Six Kingdom System - separate Monera into Eubacteria and Archaeobacteria

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 Major Divisions
Two Empire – Eight Kingdom System

• Separates Monera into Eubacteria and Archaeobacteria

• Redefines protists into several better-defined kingdoms

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 Taxonomic Ranks
• Microbiologists often use common/informal group or section names- e.g., purple bacteria,
lactic acid bacteria, methanogens, etc.

• Taxonomic ranks in ascending order are species, genus, family, order, class, phylum,
kingdom, domain.

• Basic taxonomic group is the species.

• Bacterial species are not defined based on sexual reproductive compatibilities like higher
organism but rather on phenotypic and genotypic differences.
• A bacterial species is a collection of strains that share many stable properties and
differ significantly from other groups of strains.
• A Strain is a population of organisms that descends from a single organism or pure
culture isolate.
1. Biovars - strains that differ biochemically or physiologically.
2. Morphovars - strains that differ morphologically.
3. Serovars/type - strains that differ in antigenic properties (ELISA tests - proteins).
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 Taxonomic Ranks
• The type strain is usually the first studied (or most fully characterized) strain of a species;
it does not have to be the most representative member. ATCC = American Type Culture Collection
• A genus is a well defined group of one or more species that is clearly separate from other
genera (plural).
• The binomial system of nomenclature devised by Carl von Linne (Carolus Linnaeus) is
used in which the genus name is capitalized while the specific epithet is not; both terms
are italicized (e.g. Escherichia coli)
• A category in any rank unites groups in the level below - based on shared properties

https://www.americanpharmaceuticalreview.com/133579-The-Benefits-of-Depositing-Materials-with-
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 Classification Systems
Natural classification
• Arranges organisms into groups whose members share many characteristics.
• Most desirable system because reflects biological nature of organisms.

Two methods for construction

• Phenetically  grouped together based on overall similarity.

• Phylogenetically  grouped based on probable evolutionary relationships.

Phenetic System

• Groups organisms together based on mutual similarity of phenotypes.

• May or may not reveal evolutionary relationships e.g., groups motile organisms into one
group and non-motile into another.

• Best systems compare as many attributes / characteristics as possible.

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 Numerical Taxonomy
• To create phenetic classification systems:

• Uses a variety of characteristics: e.g., gram stain, cell shape, motility, size,
aerobic/anaerobic capacity, nutritional capabilities, cell wall chemistry, immunological
characteristics, etc.
• Relies on similarity coefficients.
• It uses  50 characteristics, then match organisms.
• Example: A and B share 40 characters out of 50:
• similarity coefficient Sab is 40/50 = 0.8
• Can use many such values to establish similarity matrix.
• Dendrograms help display this information clearly.
• Organisms with great similarity are grouped together
• called phenons
•  80% similarity (80% phenon line) - 2sp. +1 sp + 2 sp + 4 sp = 4 genera
• = bacterial species

• Clusters of similar groups are termed phenons and phenons may be assigned rank according to the level on the
phenogram at which they branch off. Thus in the diagram the four clusters above the 80% phenon line could be assigned
the rank of genus while the two clusters at the 55% similarity level might be assigned the rank of subfamily. 12
 Phylogenetic (phyletic) System
Phylogeny
• Evolutionary development of a species groups organisms based on shared evolutionary
heritage.

• E.g., Mycoplasma (no cell wall) and Bacillus (cell wall, gram negative) are not grouped
together phenetically  however evolutionary similar.

• Phylogenetic trees look similar to dendrograms but are very different, since it seeks to
display how and when organisms diverged from a common ancestor over time.

• Usually based on direct comparison of genetic material (DNA and RNA sequencing) and
gene products (proteins).

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 Major Characteristics used in Taxonomy
• Classical characteristics

1. Morphological- are easy to analyze, genetically stable and do not vary greatly with
environmental changes; often are good indications of phylogenetic relatedness.

2. Physiological and metabolic- directly related to enzymes and transport proteins

(gene products) and therefore provide an indirect comparison of microbial genomes.

3. Ecological- include life-cycle patterns, symbiotic relationships, ability to cause

disease, habitat preferences and growth requirements.

4. Genetic- includes the study of chromosomal gene exchange through transformation

and conjugation; these processes only rarely cross genera; one must take care to
avoid errors that result from plasmid-borne traits (toxin & hormone production).

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 Major Characteristics used in Taxonomy
• Molecular characteristics

1. Comparison of proteins- is useful because it reflects the genetic information of the

organism; analysis by e.g., determination of the amino acid sequence of the
protein

2. Nucleic acid base comparison (G+C content) - determined by melting

temperature of DNA which is related to the temperature at which the two
strands of a DNA molecule separate.

3. Nucleic acid hybridization- measures sequence homology.

4. Nucleic acid sequencing- rRNA gene sequences are most ideal for comparisons
because they contain both evolutionarily stable and evolutionarily variable
sequences

• Currently sequencing complete bacterial genomes; direct comparisons of complete

genome sequences will undoubtedly become important in bacterial taxonomy
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 The DNA sequence of an organism's genome is often
referred to as its genetic blueprint. Analysis of microbial
genome data available thus far has already yielded
surprising discoveries. In each microbial genome that
has been sequenced, 40 to 50% of the putative genes
encode proteins of unknown function, and 20 to 30%
encode unknown proteins apparently unique to that
species. Genomic analysis also suggests that less than
1% of the microbes on earth have been cultured and
studied in the laboratory.
http://microbialgenomics.energy.gov/primer/primer_why
.shtml

Ordered restriction map (colored circle) and optical of a

single circular 415,000-base (415-kb) DNA molecule
snipped apart using a special DNA-cutting protein, the
restriction enzyme Nhe I. Circular DNA elements are
difficult to identify using nonoptical approaches, since
these molecules break and become linear elements.
Optical mapping generates a picture of the entire
genome's architecture, revealing the number of
chromosomes and the existence of extrachromosomal
elements. This technique was critical to the discovery
that Deinococcus radiodurans has four chromosomal
elements rather than just one.
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ugs.shtml#superbug 18
 Bergey’s Manual of Systematic Bacteriology
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The Bergey’s Manual of Systematic Bacteriology is the main resource for determining the
identity of bacteria species, utilizing every characterizing aspect.

The manual was published subsequent to the Bergey's Manual of Determinative

Bacteriology, though the latter is still published as a guide for identifying unknown bacteria.
First published in 1923 by David Hendricks Bergey, it is used to classify bacteria based on
their structural and functional attributes by arranging them into specific familial orders.
However, this process has become more empirical in recent years.
The change in volume set to "Systematic Bacteriology" came in a new contract in 1980, whereupon the new style
included "relationships between organisms" and had "expanded scope" overall. This new style was picked up for a four
volume set that first began publishing in 1984. The information in the volumes were separated as follows:
Volume 1 included information on all types of Gram-negative bacteria that were considered to have "medical and
industrial importance." Volume 2 included information on all types of Gram-positive bacteria. Volume 3 deals with all of
the remaining, slightly different Gram-negative bacteria, along with the archaea. Volume 4 has information on
filamentous actinomycetes and other, similar bacteria.

The current volumes differ drastically from previous volumes in that many higher taxa are not defined in terms of
phenotype, but solely on 16S phylogeny, as is the case of the classes within Proteobacteria.
The current grouping is as follows:
Volume 1 (2001): The Archaea and the deeply branching and phototrophic Bacteria
Volume 2 (2005): The Proteobacteria — divided into three books:
2A: Introductory essays
2B: The Gammaproteobacteria
2C: Other classes of Proteobacteria
Volume 3 (2009): The Firmicutes
Volume 4 (2011): The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres,
Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and
Planctomycetes
Volume 5 (in two parts) (2012): The Actinobacteria