5 Microbial Taxonomy Flashcards
Science of classification and naming of organisms
* (Greek taxis, arrangement or order, and nomos, law, or nemein, to distribute or govern)
– Aids in categorizing organisms not yet studied in detail
– Aids in identifying already classified organisms
– Provides common frame of reference when organisms are discussed
Taxonomy
A group or “level” within the classification system
Taxon:
- Groups reflect genetic similarity and evolutionary relatedness
- phylogeny (Greek phylon, tribe or race, and genesis, generation or origin) refers to the evolutionary development of a species.
- evolutionary history of an organism
Phylogenetic/Phyletic Classification System:
- Groups are based on convenient, observable
characteristics.
Phenetic Classification System:
This approach includes phenotypic,
phylogenetic, and genotypic features.
Polyphasic taxonomy
seeks to compare the genetic similarity between organisms.
Individual genes or whole genomes can be compared
Genotypic Classification
(IJSEM)
International Journal of Systematic and Evolutionary Microbiology
Taxonomy is consists of 3 parts or components
Classification
Nomenclature
Identification
is the orderly arrangement of
organisms into groups, preferably in a format
that shows evolutionary relationships.
Classification
is the process of assigning
names to the various taxonomic rankings of each
microbial species.
Nomenclature
is the process of discovering
and recording the traits of organisms so that they
may be placed in an overall taxonomic scheme.
Identification
infers a more general scientific study of organisms with the ultimate objective of arranging them in an orderly manner
Encompasses a broader scope, including taxonomy as well as the study of the evolutionary relationships between organisms
Thus this encompasses disciplines such as morphology, ecology, epidemiology, biochemistry, genetics, molecular biology, and physiology.
Systematics
*Classification Systems
Two Kingdom System
Plantae/Animalia
- bacteria, fungi, and algae were classified as animals
*Classification Systems
Three Kingdom System (Haeckel, 1866)
animals
plants
protist
*Classification Systems
Five Kingdom System (Whittaker, 1969)
Animalia
Plantae
Fungi
Protista
Prokaryotae/Monera
– who propposed the 3-kingdom system: animals, plants and protist
Ernst Haeckel (1866)
what are the Five Kingdom System of Robert H. Whittaker (1969)
Kingdom Prokaryotae/Monera
Kingdom Protista
Kingdom Fungi
Kingdom Plantae
Kingdom Animalia
(Binary fission; Energy source: organic chemicals, inorganic
chemicals, or photosynthesis)
Eubacteria (true bacteria)
- Unusual metabolism Extreme living conditions
- No peptidoglycan in cell walls
- Examples: Methanogens; Halophiles; thermoacidophiles
Archaebacteria/archaea
*what kingdom
* Primarily unicellular eukaryotes
* Protozoa, algae, slime molds, water molds
Kingdom Protista
* Unicellular yeasts
* Multicellular molds
* Mushrooms
* Saprophytes with hyphae
Kingdom Fungi
what kingdom
Some alga, mosses, ferns, conifers, flowering plants
* Multicellular
* Photosynthetic (autotrophs)
Kingdom Plantae
*what kingdom
* Sponges, worms, insects, chordates
* Heterotrophic
* multicellular
Kingdom Animalia
Based on the research of Carl 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 & ____ may share a more recent common ancestor with each other than with ____
Eucarya
Bacteria
*Kingdoms in three domain system
*Which domain
Unicellular prokaryotes with cell wall containing peptidoglycan
Domain Bacteria
*Kingdoms in three domain system
*Which domain
prokaryotes
Domain Archaea
*Kingdoms in three domain system
*Which domain
all eukaryotes
* Kingdom Animalia
* Kingdom Plantae
* Kingdom Fungi
* Kingdom Protista
Domain Eukarya
*Prokaryotic
*Lack peptidoglycan
*Often live in extreme environments
*Not known to cause disease in humans or
animals
*Had been considered bacteria until examination of their unique rRNA sequences.
-Includes
–Methanogens
–Extreme halophiles
–Extreme thermophiles
Domain: Archaea
Taxonomical groups
- Linnaeus defined the biological classification system
- what are the Levels in the hierarchy (8)
–Domain
–Kingdom
– Phylum
–Class
–Order
– Family
–Genus
– Species
Domain Bacteria
Kingdom:
Phylum:
Class:
Order:
Family:
Genus:
Species:
Subspecies:
Domain Bacteria
Kingdom: Bacteria
Phylum: Firmicutes
Class: Bacilli
Order: Lactobacillales
Family: Lactobacillaceae
Genus: Lactobacillus
Species: L. delbrueckii
Subspecies: L. d. bulgaricus
a taxonomic category that groups together species that share common characteristics and are closely related.
Genus
most basic unit of biological classification; single unique organism group
a collection of strains that share many stable properties and differ significantly from other groups of strain
species
–A population of microbes descended from a single individual or pure culture
–Different __ represent genetic variability within a species
Strain:
Strains that differ in biochemical or
physiological differences
–Biovars:
Strains that vary in morphology
–Morphovars:
Strains that vary in their antigenic properties
Serovars:
-division of archaea
Originally containing thermophilic and hyperthermophilic sulfur-metabolizing archaea Recently discovered Crenarchaeota are inhibited by sulfur & grow at lower temperatures
Phylum Thermoproteota (formerly known as Crenarchaeota)
-division of archaea
Contains primarily methanogenic archaea, halophilic
archaea, and thermophilic, sulfur-reducing archaea
Phylum Euryarchaeota
-other division of archaea
A relatively small phylum that are often found in hot
springs and geothermal areas
Phylum Korarchaeota
-other division of archaea
This phylum is characterized by its extremely small size and parasitic lifestyle. The only known member of this phylum is Nanoarchaeum equitans
Phylum Nanoarchaeota
-other division of archaea
This phylum includes organisms that are important for nitrogen cycling in the environment. They are often found in soil and aquatic environments
Phylum Thaumarchaeota
-phylogeny of domain bacteria
The earliest “deepest” branch of the Bacteria
can obtain energy from hydrogen via chemolithotrophic pathways
Phylum Aquiflexa/Aquifex
-phylogeny of domain bacteria
Oxygenic photosynthetic bacteria
Also known as blue-green algae
Phylum Cyanobacteria
-phylogeny of domain bacteria
The “green sulfur bacteria”
Anoxygenic photosynthesis
Includes genus Chlorobium
Phylum Chlorobi
-phylogeny of domain bacteria
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
Phylum Proteobacteria
Phylum Proteobacteria (cont.)
Divided into 5 classes:
Alphaproteobacteria – e.g., Rickettsia, Brucella, Rhizobium
Betaproteobacteria – e.g., Nitrosomonas, Neisseria, Burkholderia
Gammaproteobacteria – e.g., Escherichia coli and Salmonella, Pseudomonas.
Deltaproteobacteria – e.g., Campylobacter.
Epsilonproteobacteria – e.g., Helicobacter pylori
*what class of the Phylum Firmicutes (-phylogeny of domain bacteria)
Clostridia; includes genera Clostridium and Desulfotomaculatum, and others
»Class I
*what class of the Phylum Firmicutes (-phylogeny of domain bacteria)
Mollicutes; bacteria in this class cannot make peptidoglycan and lack cell walls; includes genera Mycoplasma, Ureaplasma, and others
»Class II
*what class of the Phylum Firmicutes (-phylogeny of domain bacteria)
Bacilli; includes genera Bacillus, Lactobacillus, Streptococcus, Lactococcus, Geobacillus, Enterococcus, Listeria, Staphylococcus, and others
»Class III
-phylogeny of domain bacteria
“High G + C gram-positive” bacteria
Includes genera Actinomyces, Streptomyces, Corynebacterium, Micrococcus, Mycobacterium, Propionibacterium
Phylum Actinobacteria
-phylogeny of domain bacteria
Small phylum containing the genus Chlamydia
Phylum Chlamydiae
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 Spirochaetes
Includes genera Bacteroides, Flavobacterium, Flexibacter, and Cytophaga; Flexibacter and Cytophaga are motile by means of “gliding motility”
Phylum Bacteroidetes
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
Greek philosopher, attempted to classify all living things as either Plant or Animal
He grouped animals into Land Dwellers, Water Dwellers, and Air Dwellers
Subsequent scientists later tried to classify living creatures
by means of locomotion
grouping butterflies and bats (flying)
barnacles and barley (both rooted in place) This system of classification was obviously flawed as well.
Aristotle
a Swedish botanist
He developed his naming system in the middle 1700’s, which essentially the same one we use today
He attempted to name all known plants, animals, and minerals using Latin and Greek names
Systema Naturae, meaning “The Natural Classification”, was published in 1735
Carl Linnaeus
Known as the “Father of Modern Taxonomy”
was the first to consistently name plants and animals using the binomial system of Latin names for genus and species.
Carl Linnaeus
(grape-like cluster of
spheres, golden in color)
Staphylococcus aureus
(chains of spheres,
green in colony color)
Streptococcus viridans
*Microorganism names originate from four different sources:
____ (first and common)
____ (spiral shaped rod at the entrance to the duodenum)
Proteus vulgaris
Helicobacter pylori
Rules of Nomenclature (9)
1. Use Binary Names
2. When to Capitalize
3. When to Italicize
4. When to use Initials
5. Common Names
6. Subspecies and Serovars
7. Abbreviations for Species
8. Plural Forms
9. Listing References
Useful Properties in Classification
Colony morphology
Cell shape & arrangement
Cell wall structure (Gram staining)
Special cellular structures
Biochemical characteristics
*Which identification method
-size, shape, cellular characteristics (capsule, flagella, endospores, etc.)
Useful for identifying eukaryotes
Morphological characteristics
Which identification method
e.g., Gram stain, Acid
fast stain
Differential staining
*Which identification method
-probe for specific enzyme activities:
-carbohydrate fermentation
-nitrogen fixation
-sulfur oxidation
-gas production
- Acid production
- Nitrate reduction
Determines presence of bacterial enzymes
Biochemical 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
Serological Tests
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
- Genes for specific enzymes
- 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
Nucleic acid sequencing
Determining a strains suceptability to certain phage or bacterial viruses
Phage Typing
Uses differences in electrical conductivity between species
Fluorescence of some species
Cells selectively stained with antibody plus fluorescent dye
Flow Cytometry
Add DNA probe
for S. aureus
FISH (Fluorescent in situ hybridization)
