(1)Classification of Bacteria
Definitions
Classification, nomenclature, and identification are the three separate but interrelated areas of
taxonomy. Classification can be defined as the arrangement of organisms into taxonomic groups
(taxa) on the basis of similarities or relationships. Classification of prokaryotic organisms such as
bacteria requires a knowledge obtained by experimental as well as observational techniques,
because biochemical, physiologic, genetic, and morphologic properties are often necessary for an
adequate description of a taxon. Nomenclature is naming an organism by international rules
according to its characteristics. Identification refers to the practical use of a classification scheme:
(1) to isolate and distinguish desirable organisms from undesirable ones; (2) to verify the
authenticity or special properties of a culture; or, in a clinical setting, (3) to isolate and identify the
causative agent of a disease. The latter may permit the selection of pharmacologic treatment
specifically directed toward their eradication. Identification schemes are not classification
schemes, though there may be a superficial similarity. An identification scheme for a group of
organisms can be devised only after that group has first been classified, ie, recognized as being
different from other organisms.
Criteria for Classification of Bacteria
Suitable criteria for purposes of bacterial classification include many of the properties that were
described in the preceding chapter. Valuable information can be obtained microscopically by
observing cell shape and the presence or absence of specialized structures such as spores or
flagella. Staining procedures such as the Gram stain can provide reliable assessment of the nature
of cell surfaces. Some bacteria produce characteristic pigments, and others can be differentiated on
the basis of their complement of extracellular enzymes; the activity of these proteins often can be
detected as zones of clearing surrounding colonies grown in the presence of insoluble substrates
(eg, zones of hemolysis in agar medium containing red blood cells). The use of specific antibodies
can give a rapid indication of similar surface structures carried by independently isolated bacteria.
Tests such as the oxidase test, which uses an artificial electron acceptor, can be used to distinguish
organisms on the basis of the presence of a respiratory enzyme, cytochrome c. Simple biochemical
tests can ascertain the presence of characteristic metabolic functions. Criteria leading to successful
grouping of some related organisms include measurement of their sensitivity to antibiotics.
The value of a taxonomic criterion depends upon the biologic group being compared. Traits shared
by all or none of the members of a group cannot be used to distinguish its members, but they may
define a group (eg, all staphylococci produce the enzyme catalase). In addition, genetic instability
can cause some traits to be highly variable within a biologic group or even within a single cell line.
For example, antibiotic resistance genes or genes encoding enzymes (lactose utilization, etc) may
be carried on plasmids, extrachromosomal genetic elements that may be transferred among
unrelated bacteria or that may be lost from a subset of bacterial strains identical in all other
respects.
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Identification & Classification Systems
Keys
Keys organize bacterial traits in a manner that permits efficient identification of organisms. The
ideal system should contain the minimum number of features required for a correct identification.
Groups are split into smaller subgroups on the basis of the presence (+) or absence (–) of a
diagnostic character. Continuation of the process with different characters guides the investigator
to the smallest defined subgroup containing the analyzed organism. In the early stages of this
process, organisms may be assigned to subgroups on the basis of characteristics that do not reflect
genetic relatedness. It would be perfectly reasonable, for example, for a key to bacteria to include a
group such as "bacteria forming red pigments" even though this would include such unrelated
forms as Serratia marcescens and purple photosynthetic bacteria. These two bacterial
assemblages occupy distinct niches and depend upon entirely different forms of energy
metabolism. Nevertheless, preliminary grouping of the assemblages would be useful because it
would immediately make it possible for an investigator having to identify a red-pigmented culture
to narrow the range of possibilities to relatively few types.
Numerical Taxonomy
Numerical taxonomy (also called computer taxonomy, phenetics, or taxometrics) became widely
used in the 1960s. Numerical classification schemes use a large number (frequently 100 or more)
of unweighted taxonomically useful characteristics. The computer clusters different strains at
selected levels of overall similarity (usually > 80% at the species level) on the basis of the
frequency with which they share traits. In addition, numerical classification provides percentage
frequencies of positive character states for all strains within each cluster. Such data provide a basis
for the construction of a frequency matrix for identification of unknown strains against the defined
taxa. Computerized databases have been used to develop diagnostic tests that identify clinically
relevant isolates through numerical codes or probabilistic systems.
Phylogenetic Classifications: Toward an Understanding of Evolutionary Relationships among
Bacteria
Phylogenetic classifications are measures of the genetic divergence of different phyla (biologic
divisions). Close phylogenetic relatedness of two organisms implies that they share a recent
ancestor, and the fossil record has made such inferences relatively easy to draw for most
representatives of plants and animals. No such record exists for bacteria, and in the absence of
molecular evidence, the distinction between convergent and divergentevolution for bacterial
traits can be difficult to establish.
.
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Table of Taxonomic Ranks.
Formal Rank Example
Kingdom
Prokaryotae
Division
Gracilicutes
Class
Scotobacteria
Order
Eubacteriales
Family
Enterobacteriaceae
Genus
Escherichia
Species
coli
Bergey's Manual of Systematic Bacteriology
The possibility that one might draw inferences about phylogenetic relationships among bacteria is
reflected in the organization of the latest edition of Bergey's Manual of Systematic Bacteriology.
First published in 1923, the Manual is an effort to classify known bacteria and to make this
information accessible in the form of a key. A companion volume, Bergey's Manual of
Determinative Bacteriology, serves as an aid in the identification of those bacteria that have been
described and cultured.
In 1980, the International Committee on Systematic Bacteriology published an approved list of
bacterial names. This list of about 2500 species replaces a former list that had grown to over
30,000 names; since January 1, 1980, only the new list of names has been considered valid.
Because it is likely that emerging information concerning phylogenetic relationships will lead to
further modifications in the organization of bacterial groups within Bergey's Manual, its
designations must be regarded as provisional.
Description of the Major Categories & Groups of Bacteria
there are two different groups of prokaryotic organisms: eubacteria and archaebacteria. Eubacteria
contain the more common bacteria, ie, those with which most people are familiar. Archaebacteria
do not produce peptidoglycan, a major difference between them and typical eubacteria. They also
differ from eubacteria in that they live in extreme environments (eg, high temperature, high salt, or
low pH) and carry out unusual metabolic reactions, such as the formation of methane. A key to the
four major categories of bacteria and the groups of bacteria comprising these categories is
presented in Table 3–2. The four major categories are based on the character of the cell wall:
gram-negative eubacteria that have cell walls, gram-positive eubacteria that have cell walls,
eubacteria lacking cell walls, and the archaebacteria.
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Table 3–2. Major Categories and Groups of Bacteria That Cause Disease in Humans Used As an
Identification Scheme in Bergey's Manual of Determinative Bacteriology, 9th Ed.
I. Gram-negative eubacteria that have cell walls
Group 1: The spirochetes
Treponema
Borrelia
Leptospira
Group 2: Aerobic/microaerophilic, motile helical/vibroid gram-negative Campylobacter
bacteria
Helicobacter
Spirillum
Group 3: Nonmotile (or rarely motile) curved bacteria
None
Group 4: Gram-negative aerobic/microaerophilic rods and cocci
Alcaligenes
Bordetella
Brucella
Francisella
Legionella
Moraxella
Neisseria
Pseudomonas
Rochalimaea
Bacteroides (some species)
Group 5: Facultatively anaerobic gram-negative rods
Escherichia
bacteria)
(and
Klebsiella
Proteus
Providencia
Salmonella
Shigella
Yersinia
Vibrio
Haemophilus
Pasteurella
Group 6: Gram-negative, anaerobic, straight, curved, and helical rods
Bacteroides
Fusobacterium
Prevotella
Group 7: Dissimilatory sulfate- or sulfur-reducing bacteria
None
Group 8: Anaerobic gram-negative cocci
None
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related
coliform
Group 9: The rickettsiae and chlamydiae
Rickettsia
Coxiella
Chlamydia
Group 10: Anoxygenic phototrophic bacteria
None
Group 11: Oxygenic phototrophic bacteria
None
Group 12: Aerobic chemolithotrophic bacteria and assorted organisms
None
Group 13: Budding or appendaged bacteria
None
Group 14: Sheathed bacteria
None
Group 15: Nonphotosynthetic, nonfruiting gliding bacteria
Capnocytophaga
Group 16: Fruiting gliding bacteria: the myxobacteria
None
II. Gram-positive bacteria that have cell walls
Group 17: Gram-positive cocci
Enterococcus
Peptostreptococcus
Staphylococcus
Streptococcus
Group 18: Endospore-forming gram-positive rods and cocci
Bacillus
Clostridium
Group 19: Regular, nonsporing gram-positive rods
Erysepelothrix
Listeria
Group 20: Irregular, nonsporing gram-positive rods
Actinomyces
Corynebacterium
Mobiluncus
Group 21: The mycobacteria
Mycobacterium
Groups 22–29: Actinomycetes
Nocardia
Streptomyces
Rhodococcus
III. Cell wall-less eubacteria: The mycoplasmas or mollicutes
Group 30: Mycoplasmas
Mycoplasma
Ureaplasma
IV. Archaebacteria
Group 31: The methanogens
None
Group 32: Archaeal sulfate reducers
None
Group 33: Extremely halophilic archaebacteria
None
Group 34: Cell wall-less archaebacteria
None
Group 35: Extremely thermophilic and hyperthermophilic sulfur None
metabolizers
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Gram-Negative Eubacteria that Have Cell Walls
This is a heterogeneous group of bacteria that have a complex (gram-negative type) cell envelope
consisting of an outer membrane, an inner, thin peptidoglycan layer (which contains muramic acid
and is present in all but a few organisms that have lost this portion of the cell envelope), and a
cytoplasmic membrane. The cell shape may be spherical, oval, straight or curved rods, helical, or
filamentous; some of these forms may be sheathed or encapsulated. Reproduction is by binary
fission, but some groups reproduce by budding. Fruiting bodies and myxospores may be formed by
the myxobacteria. Motility, if present, occurs by means of flagella or by gliding. Members of this
category may be phototrophic or nonphototrophic bacteria and include aerobic, anaerobic,
facultatively anaerobic, and microaerophilic species; some members are obligate intracellular
parasites.
Gram-Positive Eubacteria that Have Cell Walls
These bacteria have a cell wall profile of the gram-positive type; cells generally, but not always,
stain gram-positive. Cells may be spherical, rods, or filaments the rods and filaments may be
nonbranching, or may show true branching. Reproduction is generally by binary fission. Some
bacteria in this category produce spores as resting forms (endospores). These organisms are
generally chemosynthetic heterotrophs and include aerobic, anaerobic, and facultatively
anaerobic species. The groups within this category include simple asporogenous and sporogenous
bacteria as well as the structurally complex actinomycetes and their relatives.
Eubacteria Lacking Cell Walls
These are microorganisms that lack cell walls (commonly called mycoplasmas and comprising the
class Mollicutes) and do not synthesize the precursors of peptidoglycan. They are enclosed by a
unit membrane, the plasma membrane. They resemble the L forms that can be generated from
many species of bacteria (notably gram-positive eubacteria); unlike L forms, however,
mycoplasmas never revert to the walled state, and there are no antigenic relationships between
mycoplasmas and eubacterial L forms.
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