Taxonomy

Biology 5.3

Aristotle's Classification (5)

• Classified living things as plants or animals.

• Animals further classified into:

  • land dwellers

  • water dwellers

  • air dwellers

Micro-organism Naming Sources (4)

• Descriptive names

• Scientist's names

• Geographic places

• Organizations

Bacterial Taxonomy (3)

• Classification, naming, and identification of bacteria

• Provides a standardized process for identifying and categorizing bacteria

• Organizes bacterial species into hierarchical categories

  • Genetic

  • Phenotypic

  • Ecological characteristics

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Domain definition and types (4)

The highest taxonomic rank

• Bacteria

• Eukaryota

• Archea

Bacteria Classification (7)

• Phylum

  • Broad structural or genetic similarities

  • Fx.: Eubacteria

• Class

  • A group of related orders

  • Fx.: Gammaproteobacteria

• Order

  • A group of related families

  • Fx.: Enterobacterales

• Family

  • A group of related genera

  • Fx.: Enterobacteraceae

• Genus

  • A group of species, closely related and share common characteristics

  • Fx.: Escherichia

• Species

  • The most specific level

  • Individual organisms that can interbreed and share common traits

  • Fx.: coli

• Sub-species

  • A species that is too closely related to be regarded as different species, but too distantly related to be regarded as the same species

Common Bacterial Phyla (3)

• Proteobacteria

  • Gram-negative bacteria

  • Fx.: Escherichia coli, Pseudomonas aeruginosa

• Firmicutes

  • Mostly Gram-positive bacteria

  • Fx.: Bacillus anthracis, Clostridium perfringens, Staphylococcus aureus

• Actinobacteria

  • Gram-positive bacteria with high G+C content

  • Fx.: Mycobacterium tuberculosis, Corynebacterium diphtheriae

Methods of Classification

• Genotypic Classification

  • 16S rRNA Gene Sequencing

    • Highly preserved across bacterial species with enough variability to differentiate species

  • Whole Genome Sequencing

    • Provides comprehensive genetic information for more accurate identification and relationship determination

• Phenotypic Classification

  • Morphology

  • Staining reaction (Gram’s stain)

    • Gram-positive or Gram-negative

  • Metabolism

    • Oxygen requirement, fermentation patterns, nutrient requirements

  • Biochemical test reactions

    • Enzymatic activity (catalase, coagulase)

  • Antibiotic sensitivity

    • Natural resistance

Role of Taxonomy in Diagnostic Microbiology (9!!)

• Establishes and maintains records of key characteristics of clinically relevant microorganisms

• Facilitates communication among the scientific and medical communities by assigning universally useful names to clinically relevant microorganisms

• Establishing an association between an organism and a disease or syndrome

• Accumulating knowledge regarding management and outcome of a disease

• Understanding the mechanisms and patterns of antimicrobial resistance and detecting new resistance mechanisms

• Recognizing new and emerging pathogenic microorganisms

• Recognizing changes in types of infections or diseases

• Developing new methods for the detection and identification of infectious agents

• Developing new anti-infective therapies

Anatomy of Bacterial Nomenclature + example (4)

• Descriptive

  • Staphylococcus aureus (Grape-like cluster of spheres, golden in color)

• Scientist’s Names

  • Escherichia spp. (Theodor Escherich)

  • Listeria spp. (Joseph Lister)

• Geographic Places

  • Legionella longbeachiae (Long Beach, California)

  • Salmonella gozo (Gozitan bovines)

  • Salmonella enterica subsp. enterica ser. Gozo

• Organizations

  • Legionella spp. (American Legion)

Introduction to Micro-organism Nomenclature people (3)

• Carl Linnaeus (1707 - 1778)

• Joseph Lister (1827 - 1912)

• Theodor Escherich (1857 - 1911)

Rules of Nomenclature use of (9)

• Binary Names

  • Genus name first then species name

  • fx.: Escherichia coli

• Capitalization

  • The Genus name is always capitalized

  • The species name is never capitalized

• Italicize/ italics

  • Names of taxa are printed in italics

  • Underlined if handwritten

  • Strain designations and numbers are NOT italicized

• Taxa

  • Kingdom, phyla, classes, orders, families, genus

  • Streptococcus bovis serotype II

    • Genus: Streptococcus

    • Species: bovis

    • Serotype II: This refers to a specific variant or strain

• Initials

  • Written in full the first time

  • After the generic name is abbreviated to the initial capital letter

    • Proteus mirabilis → P. mirabilis

  • Not be confusable

• Common Names

  • Vernacular names should be in lowercase, non-italicized

    • streptococci, brucella

• Sub-species

  • Salmonella enterica → S. enterica

  • Salmonella enterica subsp. arizonae → S. enterica subsp. arizonae

• Serovars

  • Identify different strains of bacteria that belong to the same species but have distinct immunological properties

    • Salmonella enterica serovar Typhimurium

    • Salmonella enterica serovar Typhi

• Abbreviation for Species

  • Use sp. for a particular species

  • Use spp. for several species

  • Do not italicize

    • Brucella species, Providencia sp., Acinetobacter spp.

Alternative Terminology (photo)

Bacterial Classification (photo)

Gram-Positive Bacteria (photo)

Gram-Negative Bacteria (photo)

Other Bacterial Groups (photo)

Principles of Bacterial Cultivation (3)

• Grow and isolate bacteria from clinical specimens

• Identify bacteria most likely causing an infection versus contaminants or colonizers

• Obtain sufficient bacterial growth for identification and characterization

Types of Culture Media (photo)