Chapter 19
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Chapter 19 Microbial Taxonomy 2 PowerPoint PPT Presentation

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Chapter 19 Microbial Taxonomy 2

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Chapter 19

Chapter 19

Microbial Taxonomy


General introduction and overview

General Introduction and Overview

  • Taxonomy

    • science of biological classification

    • consists of three separate but interrelated parts

      • classification – arrangement of organisms into groups (taxa; s.,taxon)

      • nomenclature – assignment of names to taxa

      • identification – determination of taxon to which an isolate belongs


Importance of taxonomy

Importance of taxonomy

  • allows scientists to organize huge amounts of knowledge about organisms

  • allows scientists to make predictions and frame hypotheses about organisms

  • places organisms into meaningful, useful groups, with precise names, thus facilitating scientific communication

  • essential for accurate identification of organisms


Systematics

Systematics

  • Study of organisms with the ultimate object of characterizing and arranging them in an orderly manner


Phylogenetic tree

Phylogenetic Tree


Taxonomic ranks

Taxonomic Ranks

  • microbiologists often use informal names

    • e.g., purple bacteria, spirochetes, methane-oxidizing bacteria


Chapter 19 microbial taxonomy 2

genus – well defined group of one or

more species that is clearly separate

from other genera


Hierarchical arrangement in taxonomy

Hierarchical arrangement in Taxonomy

  • Species

  • Genus

  • Family

  • Order

  • Class

  • Phylum

  • Domain

    Species is the basic taxonomic group in microbial taxonomy


Defining procaryotic species

Defining procaryotic species

  • two definitions suggested

    • collection of strains that share many stable properties and differ significantly from other groups of strains

    • collection of strains with similar G + C composition and  70% sequence similarity


Strains

Strains

  • Strain within a species is a population of organisms that is distinguishable from others within a taxon

  • descended from a single organism or pure culture isolate

  • vary from each other in many ways

    – differ biochemically and physiologically - Biovars

    – differ morphologically - Morphovars

    – differ in antigenic properties – Serovars


Binomial system of nomenclature

Binomial System of Nomenclature

  • devised by Carl von Linné (Carolus Linnaeus)

  • each organism has two names

    • genus name – italicized and capitalized (e.g., Escherichia)

    • species epithet – italicized but not capitalized (e.g., coli)

  • can be abbreviated after first use (e.g., E. coli)


Major characteristics used in taxonomy

Major Characteristics Used in Taxonomy

  • two major types

    • Classical characteristics

    • molecular characteristics


Classical characteristics

Classical Characteristics

  • Morphological

  • Physiological and metabolic

  • Ecological

    • life-cycle patterns

    • symbiotic relationships

    • ability to cause disease

    • habitat preferences

    • growth requirements

  • Genetic analysis

    • study of chromosomal gene exchange by transformation and conjugation


Molecular characteristics

Molecular Characteristics

  • Comparison of proteins

    • determination of amino acid sequence

    • comparison of electrophoretic mobility

  • Nucleic acid base composition

    • G + C content

      • Mol% G + C =

        (G + C/G + C + A + T)100

      • variation within a genus usually < 10%

  • Nucleic acid hybridization


Nucleic acid hybridization

Nucleic acid hybridization

  • measure of sequence homology

  • common procedure

    • bind nonradioactive DNA to nitrocellulose filter

    • incubate filter with radioactive single-stranded DNA

    • measure amount of radioactive DNA attached to filter


The major divisions of life

The Major Divisions of Life

  • Based on rRNA analysis

  • Proposed by Carl Woese in 1978

  • currently held that there are three domains of life

    • Bacteria

    • Archaea

    • Eucarya


Bergey s manual of systematic bacteriology

Bergey’s Manual of Systematic Bacteriology

  • Published in 1923 by Bergey

  • detailed work containing descriptions of all procaryotic species currently identified


The first edition of bergey s manual of systematic bacteriology

The First Edition of Bergey’s Manual of Systematic Bacteriology

  • primarily phenetic

  • cell wall characteristics play important role

  • Emphasis on

    • Shape and morphology

    • Gram staining properties

    • Oxygen relationships

    • Motility

    • Presence of endospores

    • Mode of energy production


First edition

First Edition

  • Procaryotes are divided into

    • Gram-negative

    • Gram-positive

    • Gram-negative with distinctive properties such as cyanobacteria and archaea

    • Actinomycetes = gram-positive filamentous bacteria


The second edition of bergey s manual of systematic bacteriology

The Second Edition of Bergey’s Manual of Systematic Bacteriology

  • largely phylogenetic rather than phenetic

  • Contains 5 volumes


The second edition of bergey s manual of systematic bacteriology1

The Second Edition of Bergey’s Manual of Systematic Bacteriology

  • Volume 1 – Archeae and branching phototrophic bacteria

  • Volume 2 – Proteobacteria Gram-negative

  • Volume 3 – low G+C Gram-positive

  • Volume 4 – high G+C Gram-positive

  • Volume 5 – Spirochetes, Planctomycetes, Fusobacteria, Fibrobacteres, Bacteroidetes


Volume 1

Volume 1

  • Two domains

    • Archaea

      • Phylum Crenarchaeota

      • Phylum Eucaryochaeota

    • Bacteria


Domain archaea

Domain Archaea


Domain bacteria

Domain Bacteria


Phylum crenarchaeta

Phylum Crenarchaeta


Phylum crenarchaeta1

Phylum Crenarchaeta

  • Most are extremely thermophilic

  • Many are acidophiles

  • Many are sulfur-dependent

  • Almost all are strict anaerobes

  • Contains 69 genera

    • two best studied are Sulfolobus and Thermoproteus


Phylum crenarchaeta2

Phylum Crenarchaeta

  • grow in geothermally heated water or soils that contain elemental sulfur


Phylum encaryochaeta

Phylum Encaryochaeta

  • Consists of many classes, orders, and families

  • Often divided informally into five major groups

    • methanogens

    • halobacteria

    • extremely thermophilic S0-metabolizers

    • sulfate-reducers


Phylum encaryochaeta1

Phylum Encaryochaeta

  • Methanogens

    • important in wastewater treatment

    • can produce significant amounts of methane

  • Extreme halophiles or Halobacteria

    • Dependence on high concentration of NaCl

    • Grow in high salinity habitats such as in dead sea and great lake in Uttah

    • Have red to yellow pigmentation

  • Extremely thermophilic S metabolizers

    • 2 genera Thermococcus and Pyrococcus


Volume 2 phylum proteobacteria

Volume 2 – Phylum Proteobacteria

  • Contains Gram-negative Proteobacteria or purple bacteria

  • Important genera

    • Escherichia

    • Neisseria

    • Pseudomonas

    • Ricketssia

    • Salmonella

    • Vibrio


Volume 3

Volume 3

  • Gram-positive with low G+C content in their DNA placed in phylum Firmicutes

  • Some are rods, cocci while Mycoplasma are pleomorphic

  • Endospores may be present

  • Phylum Firmicutes is divided into 3 classes

    • Class Mollicutes (Mycoplasma) – no cell wall

    • Class Clostridia

    • Class Bacilli


Class mollicutes the mycoplasmas

Class Mollicutes (The Mycoplasmas)

  • Lack cell wall

  • Penicillin-resistant

  • Pleomorphic, most are nonmotile

  • Most are facultative anaerobes, few are obligate anaerobes

  • Colonies with fried egg appearance


Class clostridia

Class Clostridia

  • Obligate anaerobes, Gram-positive

  • Form endospores

  • Important species of Clostridium

    • C. botulinum – food spoilage (especially canned foods); botulism

    • C. tetani – tetanus

    • C. perfringens – gas gangrene

    • C. acetobutylicum – manufacture of butanol


Class bacilli

Class Bacilli


Class bacilli1

Class Bacilli

  • Genus Bacillus

  • Genus Staphylococcus

  • Genus Listeria

  • Genera Lactobacillus, Streptococcus, Enterococcus, Lactococcus


Genus bacillus

Genus Bacillus

  • Contains Gram-positive, endospore forming bacteria

  • Rods, motile and peritrichously flagellated

  • Aerobic and catalase positive

  • various species produce antibiotics

  • Important species of Bacillus

    • B. subtilis

    • B. cereus

    • B. anthracis

    • B. Thuringiensis


Important species of bacillus

Important species of Bacillus

  • B. subtilis – important experimental organism

    • genome recently sequenced

  • B. cereus – food poisoning

  • B. anthracis – anthrax

  • B. thuringiensis and B. sphaericus – used as insecticide


Genus staphylococcus

Genus Staphylococcus

  • Facultative anaerobes, nonmotile, Gram-positive cocci

  • Ferment glucose and have techoic acid in their cell wall

  • Associated with skin and mucous membranes

  • Important species

    • S. aureus

    • S. epidermidis


Genus listeria

Genus Listeria

  • Short rods

    • motile by peritrichous flagella

  • Aerobic or facultative

  • Catalase positive

  • Important species is Listeria monocytogenes – listeriosis

    • food-borne disease


Genus lactobacillus

Genus Lactobacillus

  • Nonsporing rods, facultative or microaerophilic

  • Produces lactic acid as their fermentation product

  • Grow under acidic conditions

  • widely distributed in nature

    • on plant surfaces

    • in dairy products, meat, water, sewage, beer, fruits, and other materials

    • normal flora of mouth, intestinal tract, and vagina

      • usually not pathogenic


Genus streptococcus

Genus Streptococcus

  • Facultative anaerobes

  • do not form endospore, and nonmotile

  • Homolactic fermentation – ferment sugars but no gas production

  • Important species

    • Streptococcus pyogenes – streptococcal sore throat, acute glomerulonephritis, and rheumatic fever

    • Streptococcus pneumoniae – pneumonia and otitis media

    • Streptococcus mutans – dental caries


Genus enterococcus

Genus Enterococcus

  • Enterococcus faecalis

    • Normal residents of intestinal tracts of humans and other animals

    • Opportunistic pathogen that can cause urinary tract infections and endocarditis

    • Grow in 6.5% NaCl unlike streptococci


Genus lactococcus

Genus Lactococcus

  • Lactococcus lactis

    • Ferment sugars to lactic acid

    • Grow at 10oC

    • Used in production of buttermilk and cheese


Volume 4

Volume 4

  • High G+C Gram-positive bacteria

  • Are the Actinomycetes

  • Are aerobic, nonmotile and soil inhabitants

  • Most are free living, a few are pathogens of humans, other animals and some plants

  • Contain important genera

    • Micrococcus

    • Corynebacterium

    • Mycobacterium

    • Propionibacterium

    • streptomyces


Actinomyctes

Actinomyctes


Important genera

Important Genera


Practical importance

Practical importance

  • widely distributed in soil

    • degrade wide variety of organic compounds

    • important in mineralization process

  • produce most of medically important natural antibiotics

  • some are pathogenic in humans, animals, and plants


Genus corynebacterium

Genus Corynebacterium

  • many are animal and human pathogens

  • some are harmless soil and water microorganisms

  • e.g., C. diphtheriae - diphtheria


Genus mycobacterium

Genus Mycobacterium

  • Mycobacterial cell walls

    • contain waxes with 60 to 90 carbon mycolic acids

    • acid-fast

      • basic fuchsin dye cannot be removed from cell by acid alcohol treatment

  • Important species

    • M. bovis – tuberculosis in cattle and other ruminants

    • M. tuberculosis – tuberculosis in humans

    • M. leprae - leprosy


Genus propionibacterium

Genus Propionibacterium

  • found on skin and in digestive tract of animals

    • used in dairy products such as cheese

    • used in production of Swiss cheese

  • e.g., P. acne – involved in development of body odor and acne vulgaris


Volume 5

Volume 5

  • Phylum planctomycetes

    • Grow in aquatic habitats

  • Phylum Chlamydiae

    • Obligate intracellular parasites

  • Phylum Spirochetes

    • Helical, motile, Gram-negative

    • Can be free-living, symbiotic or parasitic

  • Phylum Bacteroidetes


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