I. Principles of Biological Classification
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:
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
II. Binomial Nomenclature
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!
III. Artificial & Natural Systems of Classification
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.
IV. Using a Taxonomic Key
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.
V. The Five Kingdom Classification System
No single classification system is completely accepted by all biologists, but one of the most widely accepted is the five-kingdom system.
Kingdom Monera – prokaryotic; unicellular; most have a cell wall; reproduction
usually by binary fission; photosynthetic, some chemosynthetic; acquire nutrients from environment by absorption.
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).
VI. The Three-Domain Classification System
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)
VII. Classification of Bacteria
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
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
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.