This set of notes goes with the Bacterial unit.
Intro. To Taxonomy & The Classification of the
Bacteria
Organisms
are classified into any particular group because they have certain common characteristics. Classification of organisms 1.) establishes the criteria for identifying
organisms; 2.) it arranges related organisms into groups based on shared characteristics;
and 3.) it provides important information on how organisms evolved.
A
classification system based on collecting individuals into groups and groups into
progressively more inclusive and broader groups is called a hierarchical scheme of
classification. A basic principle of
taxonomy is that members of higher-level groups share fewer characteristics than those in
lower-level groups. For example, humans have
backbones like all other vertebrates, but they share fewer characteristics with fish and
birds than with other mammals. Likewise,
nearly all bacteria have a cell wall, but in some the wall is G(+) and in others it is G
(-).
Taxonomy is the science of classifying organisms.
A
Swedish biologist names Carolus Linnaeus
devised a taxonomic scheme that was both practical and adaptable to expanding information. The Linnaean
scheme remains the basis for biological classification today in 2 regards: 1.) we
continue to group organisms hierarchically, & 2.)
we use his nomenclature (see below).
Species
defined: groups of actually or potentially interbreeding
natural populations which are reproductively isolated from other such groups. Bacteria, with their variety of forms of genetic
exchange, do not fit this definition neatly. Microbiologists
use the term “species,” more as a category of convenience (bacteria are grouped
based on similarities), existing more in the human mind than in the natural world.
The
Linnaean scheme uses the following hierarchical classification scheme:
Kingdom
Phylum
(division)
Class
Order
Family
Genus
Specific
epithet
Example: Humans
Example: Treponema pallidum
(causes syphilis)
Kingdom – Animalia
Kingdom Monera (Prokaryotae)
Phylum – Chordata
Phylum Gracilicutes
[Subphylum - Vertebrata]
Class – Mammalia
Class Scotobacteria
Order – Primates
Order Spirochaetales
Family – Hominidae
Family Spriochaetaceae
Genus – Homo
Genus Treponema
Species - Homo sapiens
Species – Treponema pallidum
Linnaeus
introduced a binomial nomenclature (each organism is designated by 2 names). The
first name is the organism’s genus designation & the second is its specific
epithet. Together, the 2 constitute the species name.
The species name is always latinized and underlined or italicized. The genus designation is capitalized, but the
specific epithet is not. Thus, the proper
designation for humans is Homo sapiens (or
Homo sapiens ).
By convention, the genus designation can be replaced with an initial if the
complete genus name has been used recently enough to avoid possible confusion. For example, the bacterium Staphylococcus aureus becomes S.
aureus . All eukaryotes & prokaryotes
are named this way. Viruses are not!
1. Artificial
- the Linnaean scheme; he grouped organisms on the basis of visible similarities, but does
not indicate how closely organisms are related.
2. Natural
- based on evolutionary (phylogenetic) relatedness.
Biologists
often use a taxonomic key to id. organisms according to their characteristics. The most common kind of key is a dichotomous key,
which has paired statements describing characteristics or organisms. Paired statements present an “either
–or” choice, such that only one statement is true. Each statement is followed by directions to go to
another pair of statements until the name of the organism finally appears. See example given in class.
Kingdom
Protista
– eukaryotes; most are unicellular (some are organized
into
colonies); cell wall present in some, absent in others; reproduction mostly asexual,
sometimes sexual; some are photosynthetic; acquire nutrients from environment by
absorption and ingestion; this group includes the algae (resemble plants), the protozoa
(resemble animals), and the euglenoids (resemble both plants and animals).
Kingdom
Fungi
– eukaryotic; unicellular or multicellular; cell wall present;
sexual
and asexual reproduction; acquire nutrients by absorption of organic matter from dead
organisms.
Kingdom
Plantae
– eukaryotic; multicellular; cell wall present; sexual and
asexual
reproduction; photosynthetic; acquire nutrients
from environment by absorption.
Kingdom
Animalia
- eukaryotic; multicellular; no cell wall; primarily sexual
reproduction;
acquire nutrients from environment by ingestion (some parasites by absorption).
After
the discovery of the archaeobacteria in the 1970’s, scientists suggested that these
organisms represented a third cell type and they proposed another scheme for the evolution
of living things from a universal common ancestor. This
common ancestor gave rise to the archaeobacteria, the urkaryotes, and the eubacteria (true
bacteria). They hypothesized a group of
urkaryotes that gave rise to the eukaryotes directly rather than by way of the
prokaryotes. See figure 9.11 on p. 232. In 1990 Woese
suggested a new taxonomic category, the domain,
to be erected above the level of kingdom. The
three domains Woese proposes are shown in Figure 9.13 on p. 234. The domain Eukarya
contains all those kingdoms of eukaryotic organism (animals, plants, fungi, and protists). The traditional kingdom Monera has been
divided into 2 domains: the domain Bacteria
(true bacteria ) and the domain Arachaea. The Archaea exhibit many differences from the
Bacteria:
¨ Different
cell membrane structure
¨ Cell
wall present, but not composed of peptidoglycan
¨ First
amino acid in proteins not methionine like in other bacteria and eukaryotes
¨ DNA
Contains histone-like proteins similar to eukaryotes (true bacteria have no histone
proteins)
¨ Live
in only extreme environments (groups include extreme halophiles, extreme
thermoacidophiles, and methanogens)
The
artificial scheme of classification in Bergey's
Manual of Systematic Bacteriology is widely used.
Bergey’s Manual disregards
evolutionary relationships because they often group bacteria into assemblages that cannot
be easily identified by standard laboratory procedures.
Instead, the manual takes a strictly practical approach so that it can be used as a
comprehensive & quick reference when accuracy & speed are important, as is often
the case in diagnostic labs. Bergey’s Manual divides bacteria into 4
divisions on the basis of their cell wall [G(+) or G(-)], their lack of a cell wall
(mycoplasmas), & walls lacking peptidoglycan (archaeobacteria). Bacteria species in each division are assigned to
one or two sections; sections have no taxonomic standing; they are simply groups of
bacteria, which share certain easily identifiable properties.
How
do we identify bacteria?
1.) We
begin with morphological characteristics (shape, arrangement, etc.),
2.) Rely
primarily on physiological characteristics (ability to grow on a selective medium,
metabolic end products, etc.).
3.) Knowing
the source of the bacterium is also important.
4.) Can
also use DNA probes.
THE
FOLLOWING IS A LIST OF THE MEDICALLY IMPORTANT MEMBERS OF SELECTED SECTIONS DEFINED IN BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY.
I.
GRAM-NEGATIVE
BACTERIA (eubacteria) - have an outer membrane, a
periplasmic space, & a thin peptidoglycan cell wall.
A. Section
1 - Spirochetes
- Distinguished by their corkscrew shape; possess axial filaments (bundled flagella
contained within the periplasm) that enable them to move through viscous environments
(mud, mucous). Some live harmlessly in our
mouths. Ex. of pathogenic species:
Treponema
pallidum
– syphilis, Borrelia burgdorferi - lyme
disease (carried by
ticks)
Leptospira - leptospirosis
B. Section
2 - Aerobic/Microaerophilic, Motile, Helical/Vibrioid Bacteria - Helical
members are corkscrew shaped, but flagella are ordinary; vibrioid members are
comma-shaped. Ex. of species:
Campylobacter
jejuni
- major cause of diarrhea [hint: the jejunum is part
of
the small intestine]
Helicobacter pylori - cause gastric
ulcers in humans
C. Section
4 - Aerobic Rods & Cocci - large & diverse group. Ex. of species:
Bordetella pertussis - pertussis (whooping cough)
Neisseria meningitidis - meningococcal
meningitis (infection of meninges or
coverings
of the brain/spinal cord)
Neisseria gonorrhoeae - gonorrhea
Pseudomonas aeruginosa -
important opportunistic pathogen; common cause of
infection
in weakened hosts, such as burn victims; another species has been used to clean up oil
spills.
Brucella – brucellosis
Legionella - pneumonia and other respiratory infections.
Francisella - tularemia
D. Section
5 - Facultatively Anaerobic Rods
- Grouped into 3 Families; many can be distinguished by their characteristic fermentation
reactions; includes the enterics; Examples:
Salmonella typhi - typhoid fever; other
species cause food poisoning
Shigella
spp. - shigellosis, a form of dysentery
Yersenia pestis - bubonic plague
Vibrio cholerae - cholera
Escherichia coli - some species cause
diarrhea & dysentery; uti’s
Enterobacter cloacae – opportunistic
infections
Proteus vulgaris – uti’s
Vibrio cholerae - cholera
Haemophilus
influenzae -
upper respiratory infections (epiglottitis, sinusitis,
ear
infections), pneumonia, & meningitis.
Zymomonas - alcoholic fermentation; used
to make tequilla
Klebsiella pneumoniae - pneumonia; uti’s
E. Section 6 - Anaerobic Straight, Curved, & Helical
Rods - most abundant microbes in mouth & intestinal tract; Example: Bacteroides gingivalis - causes gingvivitis &
peridontal disease. Other species cause
digestive & respiratory infections, uti’s, infections of wounds.
F. Section
9 - The Rickettsias & Chlamydias - Once
thought to be viruses because of small size. Most
species are obligate intracellular parasites & can't be cultivated outside a
living host cell. In general, rickettsial
pathogens are transmitted by arthropods (ticks, lice, mites, fleas); chlamydiae are spread
directly from one infected human to another. Chlamydiae
alternate between 2 cell types, elementary bodies and vegetative cells. Elementary bodies are tiny, round structures
released when an infected host cell lyses. When
phagocytized, they differentiate into rod-shaped vegetative cells that multiply within the
host cell [This is different from other bacteria which do not invade the host cell!]. They then differentiate into elementary bodies
again before the host cell lyses. Examples:
Rickettsia
spp. - typhus (transmitted by body lice & rat
fleas), Rocky Mt.
Spotted
Fever (transmitted by ticks)
Coxiella – Q fever
Chlamydia
trachomatis - trachoma, sexually transmissible nongonococcal
urethritis
or NGU.
Chlamydia psittaci - ornithosis (parrot
fever) (a respiratory disease)
II.
MYCOPLASMAS
(eubacteria) - Section 10 - All lack a rigid
cell wall. To maintain turgor pressure: 1.) their
cell membrane contain sterols to add strength (sterols are also found in eukaryotic cell
membranes), and 2.) they maintain their
cytoplasm at the same pressure as their external environment by actively pumping sodium
ion out of the cell. All are parasites of
humans, animals, or plants. Almost all are
obligate fermenters (they ferment even in the presence of oxygen). Their colonies have a distinctive fried egg
appearance. They have various shapes, but
when growth conditions are suboptimal, they become distorted, forming long strands that
resemble fungi (thus accounting for the name myco
, which means "fungus"). Their
wall-less structure allows them to squeeze through even the tiny pores in filters used to
sterilize liquids. Mycoplasma pneumoniae - common cold & primary
atypical pneumonia (walking pneumonia)
III.
GRAM-POSITIVE
BACTERIA (eubacteria) - lack an outer membrane & a
periplasmic space; have a thick peptidoglycan cell wall.
A.
Section 12 - Cocci - large group. Some
examples:
Micrococcus spp.
- normal inhabitant of human skin; often contaminants on
agar
plates.
Staphylococcus
spp. - normal inhabitant of human skin; many
species produce
carotenoid
pigments, giving colonies characteristic yellow & orange colors
Staphylococcus
aureus - major human pathogen; can infect almost any
tissue
in
the body; causes impetigo, pneumonia, food poisoning; causes many nosocomial
(hospital-acquired) infections.
Streptococcus
- S.
pyogenes causes strep throat, scarlet
fever, rheumatic
fever,
endocarditis; S. pneumoniae causes life-threatening pneumococcal pneumonia
& meningitis; S. mutans causes dental
plaque.
B. Section
13 - Endospore-Forming Rods & Cocci
- These bacteria are the most heat-resistant living things; they are used as an index of
sterilization; location of endospore can be used to distinguish species. Some examples:
Clostridium
spp. - all strict anaerobes, inhabiting soil &
mud; C. tetani causes
tetanus
(fatal rigid paralysis); C. perfringens causes gas gangrene & food poisoning, C. difficile causes iatrogenic (medically induced) diarrhea
when antibiotics upset the normal balance of intestinal microbes; C. botulinum
causes botulism (food poisoning); some species are harmless.
Bacillus
spp. - aerobes, some facultative anaerobes; B. anthracis - causes
anthrax;
B. cereus causes food poisoning.
C. Section
14 - Nonsporing Rods
- Listeria monocytogenes – food poisoning
(listeriosis); in young, old, & immunocompromised patients it can cause a form of
meningitis.
D. Section
15 - Irregular Nonsporing Rods
- Members have irregular shapes (branched,
club-shaped, etc.); shapes can change with growth phase of culture.
Propionibacterium acnes - causes acne
Corynebacterium diptheriae -
causes diphtheria.
IV.
MYCOBACTERIUM
(Section 16) - have
a waxy outer layer composed of polysaccharides & mycolic acids; protects against
hostile environments & affects staining; identified by the acid-fast stain procedure;
Examples: Mycobacterium tuberculosis - causes tuberculosis;
Mycobacterium leprae - causes leprosy
V.
OTHER SECTIONS
A. Section
27 - Actinomycetes with Multiocular Sporangia
- Bacteria in this group grow as mycelia, masses of branching filamentous cells that
resemble a mycelial fungus. They form spores
within a multiocular sporangium, a many-chambered swelling at the end of a
filament. Dermatophilus
spp. infects animals & sometimes human skin.
B. Section
29 - Streptomyces & Related Genera
- These bacteria are also actinomycetes. Abundant in most soils (important in breakdown of
organic matter). Odor of freshly turned soil
comes from volatile compounds produced by these bacteria.
Colonies have pastel colors, soil-like odor, & are hard & stick into agar. Members of this genus produce most of antibiotics
in current use.