5 Microbial Taxonomy Flashcards by Belle Unknown

 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

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A group or “level” within the classification system

 Taxon:

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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:

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Groups are based on convenient, observable
characteristics.

Phenetic Classification System:

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This approach includes phenotypic,
phylogenetic, and genotypic features.

Polyphasic taxonomy

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 seeks to compare the genetic similarity between organisms.
Individual genes or whole genomes can be compared

Genotypic Classification

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(IJSEM)

International Journal of Systematic and Evolutionary Microbiology

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Taxonomy is consists of 3 parts or components

Classification

Nomenclature

Identification

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is the orderly arrangement of
organisms into groups, preferably in a format
that shows evolutionary relationships.

Classification

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is the process of assigning
names to the various taxonomic rankings of each
microbial species.

Nomenclature

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is the process of discovering
and recording the traits of organisms so that they
may be placed in an overall taxonomic scheme.

Identification

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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

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*Classification Systems

Two Kingdom System

 Plantae/Animalia
- bacteria, fungi, and algae were classified as animals

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*Classification Systems

Three Kingdom System (Haeckel, 1866)

animals

plants

protist

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*Classification Systems

Five Kingdom System (Whittaker, 1969)

Animalia

Plantae

Fungi

Protista

Prokaryotae/Monera

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– who propposed the 3-kingdom system: animals, plants and protist

Ernst Haeckel (1866)

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what are the Five Kingdom System of Robert H. Whittaker (1969)

Kingdom Prokaryotae/Monera
Kingdom Protista
Kingdom Fungi
Kingdom Plantae
Kingdom Animalia

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(Binary fission; Energy source: organic chemicals, inorganic
chemicals, or photosynthesis)

Eubacteria (true bacteria)

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Unusual metabolism Extreme living conditions
No peptidoglycan in cell walls
Examples: Methanogens; Halophiles; thermoacidophiles

Archaebacteria/archaea

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*what kingdom

* Primarily unicellular eukaryotes
* Protozoa, algae, slime molds, water molds

Kingdom Protista

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* Unicellular yeasts
* Multicellular molds
* Mushrooms
* Saprophytes with hyphae

Kingdom Fungi

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what kingdom
 Some alga, mosses, ferns, conifers, flowering plants
* Multicellular
* Photosynthetic (autotrophs)

Kingdom Plantae

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*what kingdom

* Sponges, worms, insects, chordates
* Heterotrophic
* multicellular

Kingdom Animalia

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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

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* 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)